date int64 1,220B 1,719B | question_description stringlengths 28 29.9k | accepted_answer stringlengths 12 26.4k | question_title stringlengths 14 159 |
|---|---|---|---|
1,391,717,026,000 |
I have two files with approximately 12900 and 4400 entries respectively, that I want to join. The files contain location information for all landbased weather observing stations around the globe.
The largest file is updated biweekly, and the smaller once a year or so. The original files can be found here (http://www.wmo.int/pages/prog/www/ois/volume-a/vola-home.htm and
http://weather.rap.ucar.edu/surface/stations.txt). The files I have are already manipulated by me with some mixed awk, sed, and bash script. I use the files to visualize data using the
GEMPAK package, that is freely available from Unidata. The largest file will work with GEMPAK, but only not with its full capability. For this a join is needed.
File 1 contains location information for weather observing stations, where the first 6 digits is the unique station identifier.
The different parameters (station number, station name, country code, latitude longitude, and station elevation) are defined only by its position in the line, i.e. no tabs.
060090 AKRABERG FYR DN 6138 -666 101
060100 VAGA FLOGHAVN DN 6205 -728 88
060110 TORSHAVN DN 6201 -675 55
060120 KIRKJA DN 6231 -631 55
060130 KLAKSVIK HELIPORT DN 6221 -656 75
060160 HORNS REV A DN 5550 786 21
060170 HORNS REV B DN 5558 761 10
060190 SILSTRUP DN 5691 863 0
060210 HANSTHOLM DN 5711 858 0
060220 TYRA OEST DN 5571 480 43
060240 THISTED LUFTHAVN DN 5706 870 8
060290 GROENLANDSHAVNEN DN 5703 1005 0
060300 FLYVESTATION AALBORG DN 5708 985 13
060310 TYLSTRUP DN 5718 995 0
060320 STENHOEJ DN 5736 1033 56
060330 HIRTSHALS DN 5758 995 0
060340 SINDAL FLYVEPLADS DN 5750 1021 28
File 2 contains the unique identifier in File 1 and a second, 4 character identifier (ICAO locator).
060100 EKVG
060220 EKGF
060240 EKTS
060300 EKYT
060340 EKSN
060480 EKHS
060540 EKHO
060600 EKKA
060620 EKSV
060660 EKVJ
060700 EKAH
060780 EKAT
I want to join the two files, so that the resulting file will have the 4 character identifier in the first 4 positions in the line, i.e. the identifier should replace the 4 spaces.
060090 AKRABERG FYR DN 6138 -666 101
EKVG 060100 VAGA FLOGHAVN DN 6205 -728 88
060110 TORSHAVN DN 6201 -675 55
060120 KIRKJA DN 6231 -631 55
060130 KLAKSVIK HELIPORT DN 6221 -656 75
060160 HORNS REV A DN 5550 786 21
060170 HORNS REV B DN 5558 761 10
060190 SILSTRUP DN 5691 863 0
060210 HANSTHOLM DN 5711 858 0
EKGF 060220 TYRA OEST DN 5571 480 43
EKTS 060240 THISTED LUFTHAVN DN 5706 870 8
060290 GROENLANDSHAVNEN DN 5703 1005 0
EKYT 060300 FLYVESTATION AALBORG DN 5708 985 13
060310 TYLSTRUP DN 5718 995 0
060320 STENHOEJ DN 5736 1033 56
060330 HIRTSHALS DN 5758 995 0
EKSN 060340 SINDAL FLYVEPLADS DN 5750 1021 28
Is it possible to accomplish this task with some bash and/or awk script?
|
awk 'BEGIN { while(getline < "file2" ) { codes[$1] = $2 } }
{ printf "%4s%s\n", codes[$1], substr($0, 5) }' file1
| Joining two files with unique identifier |
1,391,717,026,000 |
I have two files having a primary key value as a first field, and a corresponding value(s) as the remaining fields, and some primary key values are missing in one of them but are present in another, and vice versa:
$ cat jointest1.txt jointest2.txt
a 1
b 2
d 4
e 5
a 10
b 11
c 12
d 13
I'd expect an output that merges those files according to a primary key, either substituting the missing values or not, like:
$ joinmerge jointest1.txt jointest2.txt
a 1 10
b 2 11
c - 12
d 4 13
e 5 -
Ability to replace missing values with dashes or something is optional.
I tried join, but it says my files are not properly sorted:
$ join jointest1.txt jointest2.txt
a 1 10
b 2 11
join: file 2 is not in sorted order
d 4 13
What command should I use instead?
|
What implementation of join are you using? With join (GNU coreutils) 5.97, I can use
[0 1021] ~/temp/jointest % join -a1 -a2 jointest1.txt jointest2.txt
a 1 10
b 2 11
c 12
d 4 13
e 5
and the "plain" join works, too (but omits c and e). There is an -e option which supposedly lets you choose the marker for empty fields, but it appears to be broken in my version and only fills case e, not case c.
| Join, filling in missing key values |
1,391,717,026,000 |
I want to write a shell script that get two files A and B, and get a result like this:
File A:
user_a tel_a addr_a
user_b tel_b addr_b
File B:
process_1 user_a
process_2 user_a
process_3 user_b
And the result:
user_a process_1 tel_a addr_a
user_a process_2 tel_a addr_a
user_b process_3 tel_b addr_b
How can i do this? awk or something else?
|
join ...
join -1 2 -2 1 FileB FileA
Output
user_a process_1 tel_a addr_a
user_a process_2 tel_a addr_a
user_b process_3 tel_b addr_b
The input files need to be sorted by the key field ... Your example files are already sorted, so there was no need, but otherwise you could incorporate the sort as follows.
join -1 2 -2 1 <(sort -k2 FileB) <(sort FileA)
| A shell script for joining two files |
1,391,717,026,000 |
I'm trying to match and merge two sets of sorted data, one set per file. Each file contains two columns: the key field and the associated value. The resulting output should contain three columns: the key field, the value (if any) from the first file, and the value (if any) from the second file. I need to include lines of data that are not matched.
First file "john"
apple,green
cherry,red
orange,orange
Second file "jane"
apple,red
banana,yellow
cherry,yellow
kiwi,green
Desired result
apple,green,red
banana,,yellow
cherry,red,yellow
kiwi,,green
orange,orange,
I thought initially that this was a trivial job for join
LC_ALL=C join -j1 -a1 -a2 -t',' john jane
But the result of the -a1 -a2 puts the unmatched value always in the second column:
apple,green,red
banana,yellow
cherry,red,yellow
kiwi,green
orange,orange
I need to be able to see from which source file the unmatched value originates, ideally by having those values in the appropriate second or third column of the result file, but I cannot work out a simple way of achieving this without descending into awk ... getline() type constructs.
Any suggestions, please?
|
You want -o auto:
join -t, -j 1 -a 1 -a 2 -o auto john jane
From man join:
-o FORMAT
obey FORMAT while constructing output line
︙
If FORMAT is the keyword 'auto', then the first line of each file
determines the number of fields output for each line.
Or better explained from GNU Coreutils: join invocation
(follow the link into General options in join):
‘-o auto’
If the keyword ‘auto’ is specified, infer the output format from the first line in each file. This is the same as the default output format but also ensures the same number of fields are output for each line. Missing fields are replaced with the -e option and extra fields are discarded.
% cat john
apple,green
cherry,red
orange,orange
% cat jane
apple,red
banana,yellow
cherry,yellow
kiwi,green
% join -t, -j 1 -a 1 -a 2 -o auto john jane
apple,green,red
banana,,yellow
cherry,red,yellow
kiwi,,green
orange,orange,
| Join two files each with two columns, including non-matching lines |
1,391,717,026,000 |
How can I get two files A and B, and out put a result like this:
File A:
001 Apple, CA
020 Banana, CN
023 Apple, LA
045 Orange, TT
101 Orange, OS
200 Kiwi, AA
File B:
01-Dec-2013 01.664 001 AAA CAC 1083
01-Dec-2013 01.664 020 AAA CAC 0513
01-Dec-2013 01.668 023 AAA CAC 1091
01-Dec-2013 01.668 101 AAA CAC 0183
01-Dec-2013 01.674 200 AAA CAC 0918
01-Dec-2013 01.674 045 AAA CAC 0918
01-Dec-2013 01.664 001 AAA CAC 2573
01-Dec-2013 01.668 101 AAA CAC 1091
01-Dec-2013 01.668 020 AAA CAC 6571
01-Dec-2013 01.668 023 AAA CAC 2148
01-Dec-2013 01.674 200 AAA CAC 0918
01-Dec-2013 01.668 045 AAA CAC 5135
Result:
01-Dec-2013 01.664 001 AAA CAC 1083 Apple, CA
01-Dec-2013 01.664 020 AAA CAC 0513 Banana, CN
01-Dec-2013 01.668 023 AAA CAC 1091 Apple, LA
01-Dec-2013 01.668 101 AAA CAC 0183 Orange, OS
01-Dec-2013 01.674 200 AAA CAC 0918 Kiwi, AA
01-Dec-2013 01.674 045 AAA CAC 0918 Orange, TT
01-Dec-2013 01.664 001 AAA CAC 2573 Apple, CA
01-Dec-2013 01.668 101 AAA CAC 1091 Orange, OS
01-Dec-2013 01.668 020 AAA CAC 6571 Banana, CN
01-Dec-2013 01.668 023 AAA CAC 2148 Apple, LA
01-Dec-2013 01.674 200 AAA CAC 0918 Kiwi, AA
01-Dec-2013 01.668 045 AAA CAC 5135 Orange, TT
(file A: the number should match to middle number from file B)
Is there any possible way to doing this?
|
A simple solution with awk:
awk -v FILE_A="file-A" -v OFS="\t" 'BEGIN { while ( ( getline < FILE_A ) > 0 ) { VAL = $0 ; sub( /^[^ ]+ /, "", VAL ) ; DICT[ $1 ] = VAL } } { print $0, DICT[ $3 ] }' file-B
Here is a commented version:
awk -v FILE_A="file-A" -v OFS="\t" '
BEGIN {
# Loop on the content of file-A
# to put the values in a table
while ( ( getline < FILE_A ) > 0 ){
# Remove the index from the value
VAL = $0
sub( /^[^ ]+ /, "", VAL )
# Fill the table
DICT[ $1 ] = VAL
}
}
{
# Print the line followed by the
# corresponding value
print $0, DICT[ $3 ]
}' file-B
| Join two files, matching on a column, with repetitions |
1,391,717,026,000 |
I have two files
in file A, there are sequence_numbers
in the other file B, there are many columns, and the first column is sequnce numbers,
I want to get a files with all the lines in the B with the sequence numbers which are in the A
how can I achieve this?
thanks
like
file A
1
3
8
9
20
file B
1 kfjk 3243424
2 fkdkf 23543592
3 iefjk 21493402
7 dlafdl 23435231
8 kfkdlkf 309834
|
You want join (1), I guess:
For each pair of input lines with identical join fields, write a
line
to standard output. The default join field is the first, delimited by
whitespace. When FILE1 or FILE2 (not both) is -, read standard input.
[0 1075 12:50:10] ~/temp/sx % join A B
1 kfjk 3243424
3 iefjk 21493402
8 kfkdlkf 309834
join: file 1 is not in sorted order
OK, so apparently you need to combine this with sort (1) to sort by alpha value (not numerical value, so 20 < 3)
join <(sort A) <(sort B) works for me, but that looks weird and might be a zsh extension. There's no harm in doing
sort A > A.tmp; sort B > B.tmp; join A.tmp B.tmp
(As usual, check the man pages for pitfalls.)
| intersection of two files according to the first column |
1,391,717,026,000 |
I have long text files with space-delimited fields:
cat file1.txt
Id leng sal mon
25671 34343 56565 5565
44888 56565 45554 6868
23343 23423 26226 6224
77765 88688 87464 6848
66776 23343 63463 4534
cat file2.txt
Id number
25671 34343
76767 34234
23343 23423
66776 23343
cat output.txt
Id leng sal mon
44888 56565 45554 6868
77765 88688 87464 6848
file1.txt has four columns, file2.txt has two columns. I want to compare 1st column ($1) in both files (file1.txt, file2.txt) and output the file that did not match in file2.txt.
I have tried
join -v1 file1.txt file2.txt >output.txt
But the output has some errors. Any awk/sed command is appreciated.
|
In order to use join, you need to make sure that FILE1 and FILE2 are sorted on the join fields.
The following command should do the trick:
join -v1 <(sort file1.txt) <(sort file2.txt)
| Compare two file columns |
1,391,717,026,000 |
I have this file1.txt
deiauk 9
kespaul 8
luktol 7
titkur 6
and other file2.txt
kespaul b
deiauk a
And I want to merge both files in one by first value, so my result should be
deiauk 9 a
kespaul 8 b
luktol 7
titkur 6
|
sort file2.txt | join -a 1 file1.txt -
join requires sorted input. The '-' specifies that standard input will be used for the second file, which allows the output of sort to be used as input. The '-a 1' specifies that non-matching lines from the first file will be included in the output.
| Merge two files |
1,391,717,026,000 |
I was wondering if anyone would know the complexity of the Unix join command? I had assumed that it might be linear since both files need to be sorted.
Someone insisted to me that it was logarithmic which I doubt. Or perhaps it depends on the files and can be logarithmic (or N*log(N)) when one of the files is small and approach linear when both are large?
|
The BSD join implementation is quite simple to follow and seems to be linear with regards to the number of lines in the files. This has gone mostly unchanged in all BSD systems since at least BSD 4.4 Lite2. The snippet below comes from a current OpenBSD system, for comparison, this is a link to the BSD 4.4 Lite2 code originally committed by Keith Bostic in 1991 (replacing an earlier version of the utility):
/*
* We try to let the files have the same field value, advancing
* whoever falls behind and always advancing the file(s) we output
* from.
*/
while (F1->setcnt && F2->setcnt) {
cval = cmp(F1->set, F1->joinf, F2->set, F2->joinf);
if (cval == 0) {
/* Oh joy, oh rapture, oh beauty divine! */
if (joinout)
joinlines(F1, F2);
slurp(F1);
slurp(F2);
}
else {
if (F1->unpair
&& (cval < 0 || F2->set->cfieldc == F2->setusedc -1)) {
joinlines(F1, NULL);
slurp(F1);
}
else if (cval < 0)
/* File 1 takes the lead... */
slurp(F1);
if (F2->unpair
&& (cval > 0 || F1->set->cfieldc == F1->setusedc -1)) {
joinlines(F2, NULL);
slurp(F2);
}
else if (cval > 0)
/* File 2 takes the lead... */
slurp(F2);
}
}
I looked at the code for join in GNU coreutils, but GNU code has so much going on in it that I really only can guess, based on the comments in the code, that it more or less also implements the same sort of algorithm:
/* Keep reading lines from file1 as long as they continue to
match the current line from file2. */
[...]
/* Keep reading lines from file2 as long as they continue to
match the current line from file1. */
[...]
If you take the sorting into account, and assume an N*log(N) sorting algorithm, then the complete time complexity would be N*(1 + log(N)), or N*log(N) for large N values. That is, the JOIN operation is faster than the sorting.
You can't do better than linear for a JOIN operation, because you can't skip lines (unless you have a precalculated index of some description and don't include the indexing in the time complexity). The best case scenario is that none of the lines join, in which case you need to read all lines from one of the two files and compare these to first line of the other file. The worst case scenario is that all lines join, in which case you need to read both files and do pairwise comparisons between both sets of lines (a linear operation on sorted files). If the user requests to see unpaired lines, then you are forced to read both files completely.
If you manage to do worse than linear for the JOIN alone, then you're doing something wrong.
| Unix join command complexity |
1,391,717,026,000 |
Given the files:
1.txt
1, abc, 123, 456, 789
2, lmn, 123, 456, 789
3, pqr, 123, 456, 789
2.txt
1, abc, 123, 000, 000
3, lmn, 123, 000, 000
9, opq, 123, 000, 000
OUTPUT.txt
ID, NAME, X, 1A, 1B, 2A, 2B
1, abc, 123, 456, 789, 000, 000
2, lmn, 123, 456, 789, MISSING, MISSING
3, pqr, 123, 456, 789, 000, 000
9, opq, 123, MISSING, MISSING, 000, 000
I'ved used this for reference.
I tried using the following:
join -t , -a1 -a2 -1 1 -2 1 -o 0 -o 1.2 -o 1.3 -o 1.4 -o 1.5 -o 2.4 -o 2.5 -e "MISSING" 1.txt 2.txt
Which produces:
1, abc, 123, 456, 789, 000, 000
2, lmn, 123, 456, 789,MISSING,MISSING
3, pqr, 123, 456, 789, 000, 000
9,MISSING,MISSING,MISSING,MISSING, 000, 000
Any help?
|
I don't think you can do it with join alone. You could do:
join -t, -a1 -a2 -o0,1.2,1.3,1.4,1.5,2.2,2.3,2.4,2.5 -e MISSING 1.txt 2.txt |
perl -F, -lape '@F[1..2]=@F[5..6] if $F[1] eq "MISSING";
$_=join",",@F[0..4],@F[7..8]'
-p: use a line by line reading loop like in sed/awk
-a, -F,: like awk, split the lines into fields (into the @F array).
-l: works on the content of lines (works like awk where the input is split on RS ($/) (but RS not included in $0) and ORS ($\) is appended before printing).
-e ...: perl [e]xpression to evaluate for each line.
Then it reads almost like English: fields 1 to 2 are set to fields 5 to 6 if field 1 (the second field as indexes start at 0) is "MISSING". Then set the content of the current record ($_ is like $0 in awk) to the fields 0 to 4 and 7 to 8.
Actually, writing the same in awk is not more complicated:
awk -F, -vOFS=, '$2 == "MISSING"{$2=$6;$3=$7}
{print $1,$2,$3,$4,$5,$8,$9}'
| Join: Two files - but only append last two columns |
1,391,717,026,000 |
I have a file1.txt
USA Joe 123.123.123
Russia Marry 458.786.892
Canada Greg 151.844.165
Latvia Grace 125.895.688
and file2.txt
1 123.123.123
2 151.844.165
3 465.879.515
and I want to create a new file result.txt where I print my only those lines that adresses (xxx.xxx.xxx) are both in file1 and file2 so my result should be
USA Joe 123.123.123
Canada Greg 151.844.165
I need to use awk, but how I need to use it for both files?
|
You can try:
awk 'FNR==NR{a[$2];next};$NF in a' file2.txt file1.txt > result.txt
| Awk: compare two files |
1,391,717,026,000 |
I have 4 tsv (tab separated) files that look like this:
file_1:
abc 1
def 2
ghi 3
file_2:
abc 2
ghi 3
file_3:
def 1
ghi 2
jkl 4
file_4:
ghi 3
jkl 4
I want to join those file to get 1 tsv file like this:
dataset file_1 file_2 file_3 file_4
abc 1 2
def 2 4
ghi 3 3 2 3
jkl 4 4
I have try using awk
$ awk '
BEGIN{OFS=FS="\t"}
FNR==1{f = f "\t" FILENAME}
NR==FNR{a[$1] = $2}
NR!=FNR{a[$1] = a[$1] "\t" $2}
END{printf "dataset%s\n", f; for(i in a) print i, a[i]}
' file_{1..4}
This command is work, but I got shifted value. Let say, if first and second column have empty value and third and fourth column have value 4 and 4, the output that I got from that command is for first and second column have value 4, but for third and fourth column have empty value.
So I try to join my tsv file separately using awk that I mentioned. First only for file_1 and file_2 to get output_1, then join file_3 and file_4 to get output_2. After that I use $ join output_1 output_2 to merge output_1 and output_2 but I only get value that exist in 4 file. I lost data that only exist in one file.
I'll very appreciate if you can give me an advice.
Thank you
|
$ cat tst.awk
BEGIN { FS=OFS="\t" }
{ datasets[$1]; fnames[FILENAME]; vals[$1,FILENAME] = $2 }
END {
printf "%s", "dataset"
for (fname in fnames) {
printf "%s%s", OFS, fname
}
print ""
for (dataset in datasets) {
printf "%s", dataset
for (fname in fnames) {
printf "%s%s", OFS, vals[dataset,fname]
}
print ""
}
}
$ tail -n +1 file?
==> file1 <==
a 1
b 2
c 3
==> file2 <==
a 2
c 3
$ awk -f tst.awk file1 file2
dataset file1 file2
a 1 2
b 2
c 3 3
Add as many files to the list as you like.
| Joining multiple column from different file using awk |
1,391,717,026,000 |
I need to merge below 2 files:
file1:
TABLES REF-IO HEAD-IO DIFF-IO
test 200 500 -300
exam 2 3 -1
final 2 1 1
mail 4 2 2
TOTAL 208 506 -298
file2:
TABLES REF-SELECT HEAD-SELECT DIFF-SELECT
test 5 7 -2
game 3 3 0
exam 0 7 -7
final 12 6 6
TOTAL 20 23 -3
merged file should be as shown below:
TABLES REF-IO HEAD-IO DIFF-IO REF-SELECT HEAD-SELECT DIFF-SELECT
test 200 500 -300 5 7 -2
exam 2 3 -1 0 7 -7
final 2 1 1 12 6 6
mail 4 2 2 0 0 0
TOTAL 208 506 -298 20 23 -3
|
awk '
NR==FNR {vals[$1] = $2 " " $3 " " $4; next}
!($1 in vals) {vals[$1] = "0 0 0"}
{$(NF+1) = vals[$1]; print}
' file2 file1
TABLES REF-IO HEAD-IO DIFF-IO REF-SELECT HEAD-SELECT DIFF-SELECT
test 200 500 -300 5 7 -2
exam 2 3 -1 0 7 -7
final 2 1 1 12 6 6
mail 4 2 2 0 0 0
TOTAL 208 506 -298 20 23 -3
| Merge 2 files based on all values of the first column of the first file |
1,391,717,026,000 |
file1:
abc|123|check
def|456|map
ijk|789|globe
lmn|101112|equator
file2:
abc|123|check
def|456|map
ijk|789|equator
lmn|101112|globe
EXPECTED OUTPUT:
ijk|789|equator
lmn|101112|globe
Current awk script:
awk 'BEGIN{OFS=FS="|"} NR==FNR{a[$3]=$3;next}!($3 in a)' file1 file2
This does comparison based on array content. How to compare line by line and printing only that results.
|
If I understand you correctly, you want to print a line from file2 if the 3rd field is different to the corresponding entry in file1. If so, this should do it:
awk 'BEGIN{FS="|"} NR==FNR{a[$1,$2]=$3;next}(a[$1,$2]!=$3)' file1 file2
Yours wasn't working because you were taking $3 as the key for array a and $3 is not unique (both equator and globe are present in both files).
I agree with @drewbenn that both grep and join are simpler for this particular case, but here's a Perl way of doing the same thing:
perl -laF'\|' -ne '($k{$F[0].",".$F[1]}||=$F[2]) eq $F[2]||print;' file1 file2
| Comparing files line by line in awk with delimiter |
1,391,717,026,000 |
I have two files with tab-separated values that look like this:
file1:
A 1
B 3
C 1
D 4
file2:
E 1
B 3
C 2
A 9
I would like to find rows between files 1 and 2 where the string in column 1 is the same, then get the corresponding values. The desired output is a single file that looks like this:
B 3 3
C 1 2
A 1 9
Can this be done with a Unix one-liner?
|
GNU coreutils includes the command join that does exactly what you want if line sorting in the result is irrelevant:
join <(sort file1) <(sort file2)
A 1 9
B 3 3
C 1 2
If you want the tabs back, do:
join <(sort file1) <(sort file2) | tr ' ' '\t'
A 1 9
B 3 3
C 1 2
Or use the t option to join.
(<() aka process substitution, requires ksh93 (where the feature originated in), bash or zsh)
| Find common elements in a given column from two files and output the column values from each file |
1,391,717,026,000 |
I have a 2 files with the following:
File1.txt
A 1
B 2
C 5
Z 3
File2.txt
A 4
B 7
C 10
D 11
What I would like to do is create something like
A 1 4
B 2 7
C 5 10
D - 11
Z 3 -
Is there a utility that does this? If not how Can this be done? Using a find and awk or something?
|
join -a1 -a2 -o 0,1.2,2.2 -e - file1.txt file2.txt
| Joining two files |
1,391,717,026,000 |
I have 2 files, one having 2 columns, another having 1 column.
The second file is sorted using sort -u.
Now the task is I need to join this column with the first column of the first file, which is not sorted.
So what will be the syntax? Will join -j 1 file2.txt sort -s -n -k 1 file1.txt work?
The output I want is actually the 2nd column of file 2 after joining and the unique entries in it.
File 2
1
2
3
File 1
2 500
1 5000
1 300
3 3000
3 300
4 450
Output
5000
300
500
3000
|
No need to use non-standard process substitution (<(...)) here:
sort file1 | join -o1.2 - file2 | uniq
| How to sort and join at the same time? |
1,391,717,026,000 |
I have two files in these formats:
file1 :
air
smell
hand
dude
road
cat
file 2:
air,4,21,01,13,3,2
smell,21,4,2,5,6
dude,1,31,42,1
road,1,4,2,1,4
cat,1,5,6,3,1
hand,1,4,2,1,6
mouse,1,3,5,6,2
what I want to do is print the entire row of file 2, if the first string in column 1 of file 2 is found in file 1, and I want to keep the order of file 1.
expected output:
air,4,21,01,13,3,2
smell,21,4,2,5,6
hand,1,4,2,1,6
dude,1,31,42,1
road,1,4,2,1,4
cat,1,5,6,3,1
|
This should do it:
awk -F, 'FNR==NR {a[$1]; next}; $1 in a' file1 file2
edit:
Interpreted the wrong file for the ordering. A new attempt (requires gawk if that is acceptable)
gawk -F, '
FNR==NR {a[NR]=$1; next};
{b[$1]=$0}
END{for (i in a) if (a[i] in b) print b[a[i]]}
' file1 file2
edit 2:
With nowmal awk, and swapping the files around:
awk -F, 'FNR==NR {a[$1]=$0; next}; $1 in a {print a[$1]}' file2 file1
| comparing the first column of two files and printing the entire row of the second file if the first columns match |
1,391,717,026,000 |
Objective: Merge the contents of two files using common key present in the files
file1.txt
=========
key1 11
key2 12
key3 13
file2.txt
=========
key2 22
key3 23
key4 24
key5 25
Expected Output :
==================
key1 11
key2 12 22
key3 13 23
key4 24
key5 25
Approaches tried:
join command:
join -a 1 -a 2 file1.txt file2.txt ## full outer join
awk:
awk 'FNR==NR{a[$1]=$2;next;}{ print $0, a[$1]}' 2.txt 1.txt
Approach 2 is resulting in a right outer join and NOT a full outer join:
key1 11
key2 12 22
key3 13 23
What needs to be modified in approach 2 to result in a full outer join?
|
With awk, try:
awk '{a[$1]=($1 in a)?a[$1]" "$2:$2};END{for(i in a)print i,a[i]}' file1 file2
For huge files, you should use join instead of awk approach, since when awk approach will store all files content in memory before printing out.
| Why isn't this awk command doing a full outer join? |
1,391,717,026,000 |
I have multiple .txt files and would like to merge them together base on their first column (numeric), and fill in "NULL" if there's any missing data.
File_1:
1 a
2 b
3 c
File_2:
3 c
4 d
5 e
File_3:
4 d
5 e
6 f
Expected_Output:
1 a NULL NULL
2 b NULL NULL
3 c c NULL
4 NULL d d
5 NULL e e
6 NULL NULL f
join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL -o 0,1.2,2.2 file_1 file_2 | join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL - file_3 > expected_output This command give me correct output of column 1, 2 and 3 ;however, "NULL" is missing in column 4, any idea how to fix it?
Also is there a better way to merge multiple files instead writing a super long pipe command?
|
You are almost there. Using your command, we get:
$ join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL -o 0,1.2,2.2 file_1 file_2 | join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL - file_3
1 a NULL
2 b NULL
3 c c
4 NULL d d
5 NULL e e
6 f
Lines just don't have the same number of columns because we are not setting a format for the right-hand join in the pipeline.
If we add it as -o 0,1.2,1.3,2.2 (the join field + the second and third columns from the first join + the second column of file_3):
$ join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL -o 0,1.2,2.2 file_1 file_2 | join -t $'\t' -a 1 -a 2 -1 1 -2 1 -e NULL -o 0,1.2,1.3,2.2 - file_3
1 a NULL NULL
2 b NULL NULL
3 c c NULL
4 NULL d d
5 NULL e e
6 NULL NULL f
Finally, if we can assume the GNU implementation of join, we can let it do the job of inferring the right format and use -o auto instead of -o 0,1.2,2.2 and -o 0,1.2,1.3,2.2, provided that, for each file, all lines have at most the same number of fields as the first one. Quoting info join:
-o auto
If the keyword auto is specified, infer the output format from the first line in each file. This is the same as the default output format but also ensures the same number of fields are output for each line. Missing fields are replaced with the -e option and extra fields are discarded.
| Join multiple files |
1,391,717,026,000 |
I find join pretty useful. It lets you join file1 against file2 on key fields.
Is it possible to do so dynamically against the results of a command, like:
join -1 1 -2 1 file1 'curl http://example.com?code=$1&fmt=csv'
Maybe using xargs or named pipes?
Ideally it would do one "lookup" per record/line in file1
|
Yes, if your shell supports process substitution (bash and ksh93 does) you may do like this:
$ join file1 <( yourcommand )
This runs the join command with file1 and a file descriptor in /dev/fd connected to the standard output of yourcommand (which would be your curl thingy).
Note that join expects all input to be sorted. It requires sorted input streams to be able to parse them only once. In particular, the input needs to be sorted with sort -b (ignoring leading blanks).
If that's not the case, you may make it so:
$ join <( sort -b file1 ) <( yourcommand | sort -b )
| Can I `join` against a command? |
1,391,717,026,000 |
I have two files. The first file has the following format:
10D0325 2465 0 0 -9 -9
10D0598 2567 0 0 -9 -9
10D0562 2673 0 0 -9 -9
10D0175 2457 0 0 -9 -9
10D0241 2209 0 0 -9 -9
10D0954 2312 0 0 -9 -9
10D0446 2489 0 0 -9 -9
The second file has this format:
10D0325 1
10D0598 1
10D0175 2
10D0954 1
10D0446 2
What I want to do is add the second column of the second file to the first file, based on the ID variable.
As you can see the first column can be used as an identifier variable to match the first dataset with the second. However, the first file contains some lines/ID's that are not present in the second file. Therefore I cannot simply order both files and paste this column into the first file.
There must be a fairly easy way to do this, unfortunately my Linux skills are limited.
P.S. For the sake of clarity, this is what I would like the resulting file to look like (any other symbol may be used to indicate missings instead of blank spaces):
10D0325 2465 0 0 -9 -9 1
10D0598 2567 0 0 -9 -9 1
10D0562 2673 0 0 -9 -9
10D0175 2457 0 0 -9 -9 2
10D0241 2209 0 0 -9 -9
10D0954 2312 0 0 -9 -9 1
10D0446 2489 0 0 -9 -9 2
|
That's pretty easy with awk:
awk 'NR==FNR{a[$1]=$2;next}{print $0,a[$1]}' file2 file1
First (when file2 is being read) we create an array a which stores second column from file2, indexed with first column. And then we print file1 adding value from an array.
| Adding column based on matching of second column |
1,391,717,026,000 |
I have a directory ballgown, in which there are around 1000 subdirectories as sample names. Each subdirectory has a file t_data.ctab. The filename is the same in all subdirectories.
ballgown
|_______TCGA-A2-A0T3-01A
|___________ t_data.ctab
|_______TCGA-A7-A4SA-01A
|___________ t_data.ctab
|_______TCGA-A7-A6VW-01A
|___________ t_data.ctab
Like above ballgown has 1000 subdirectories. The t_data.ctab file in all those 1000 subdirectories looks like below with columns:
t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM
1 1 - 10060 10614 MSTRG.1.1 1 555 MSTRG.1 . 0.000000 0.000000
2 1 + 11140 30023 MSTRG.10.1 12 3981 MSTRG.10 . 2.052715 0.284182
3 1 - 11694 29342 MSTRG.11.1 8 6356 MSTRG.11 . 0.557588 0.077194
4 1 + 11869 14409 ENST00000456328.2 3 1657 MSTRG.10 DDX11L1 0.000000 0.000000
5 1 + 11937 29347 MSTRG.10.3 12 3544 MSTRG.10 . 0.000000 0.000000
6 1 - 11959 30203 MSTRG.11.2 11 4547 MSTRG.11 . 0.369929 0.051214
7 1 + 12010 13670 ENST00000450305.2 6 632 MSTRG.10 DDX11L1 0.000000 0.000000
8 1 + 12108 26994 MSTRG.10.5 10 5569 MSTRG.10 . 0.057091 0.007904
9 1 + 12804 199997 MSTRG.10.6 12 3567 MSTRG.10 . 0.000000 0.000000
10 1 + 13010 31097 MSTRG.10.7 12 4375 MSTRG.10 . 0.000000 0.000000
11 1 - 13068 26832 MSTRG.11.3 9 5457 MSTRG.11 . 0.995280 0.137788
From all the t_data.ctab files I want to extract only t_name and FPKM column and create a new file. In the new file the FPKM column should be the sample name. It should look like below:
t_name TCGA-A2-A0T3-01A TCGA-A7-A4SA-01A TCGA-A7-A6VW-01A
MSTRG.1.1 0 0.028181 0
MSTRG.10.1 0.284182 0.002072 0.046302
MSTRG.11.1 0.077194 0.685535 0.105849
ENST00000456328.2 0 0.307315 0.038961
MSTRG.10.3 0 0.446015 0.009946
MSTRG.11.2 0.051214 0.053577 0.036081
ENST00000450305.2 0 0.110438 0.040319
MSTRG.10.5 0.007904 0 1.430825
MSTRG.10.6 0 0 0.221105
MSTRG.10.7 0 0.199354 0
MSTRG.11.3 0.137788 0.004792 0
If it is two or three files I can use cut -f6,12 on each file and then join them. But I have around 1000 files now.
|
Try this simple way:
first do:
awk 'FNR==1 { print substr(FILENAME,1,16) >substr(FILENAME,1,16)".tmp" }
FNR >1 { print $12 > substr(FILENAME,1,16)".tmp" }
NR==FNR{ print $6 >"first_column.tmp" }' TCGA-A*/t_data.ctab
then paste them together with comma delimited file (remove -d, if you want to have Tab instead):
paste -d, *.tmp
t_name,TCGA-A2-A0T3-01A,TCGA-A7-A4SA-01A,TCGA-A7-A6VW-01A
MSTRG.1.1,0.000000,0.00000,0.0000
MSTRG.10.1,0.284182,0.28418,0.2841
MSTRG.11.1,0.077194,0.07719,0.0771
ENST00000456328.2,0.000000,0.00000,0.0000
MSTRG.10.3,0.000000,0.00000,0.0000
MSTRG.11.2,0.051214,0.05121,0.0512
ENST00000450305.2,0.000000,0.00000,0.0000
MSTRG.10.5,0.007904,0.00790,0.0079
MSTRG.10.6,0.000000,0.00000,0.0000
MSTRG.10.7,0.000000,0.00000,0.0000
MSTRG.11.3,0.137788,0.13778,0.1377
| How to create a new file with required columns from different multiple files in linux? |
1,391,717,026,000 |
I'm using join command under linux, but the results vary between different machines.
I have two simple files:
cat 1.txt
a aaa,0.2
b bbb,0.3
c ccc,0.5
cat 2.txt
a aaa,0.2
b bbb,0.3
c ccc,0.6
I'm running the following command
join -a 1 -1 1 -2 1 -t "," -o 1.1' '1.2' '2.2 <(cat 1.txt| sort -t ",") <(cat 2.txt| sort -t ",")
Result on machine 1:
,0.2a,0.2
,0.3b,0.3
,0.6c,0.5
join --version
join (GNU coreutils) 8.13
locale
LANG=en_US.UTF-8
LANGUAGE=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8
Result on machine 2:
a aaa,0.2,0.2
b bbb,0.3,0.3
c ccc,0.5,0.6
join --version
join (GNU coreutils) 5.97
locale
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=
Clearly, the result on the first machine is wrong. It's been truncated. I've tried to use different locale settings but had no success.
|
Fix your files with dos2unix, or if that's not installed:
sed -i 's/\r$//' {1,2}.txt
| Truncated result returned by JOIN |
1,391,717,026,000 |
I would like to merge a variable from one file to another in linux.
The first variable contains the name I want to merge files on.
I have sorted both files using both -f and -k:
sort -f -k 1,1 SCZ.N.tmp> SCZ.N.tmp.sorted and sort -f -k 1,1 1kg.tmp > 1kG.ref_file.sorted
However, when I join both files with this command: join -1 1 -2 1 SCZ.N.tmp.sorted 1kG.ref_file.sorted> SCZ.freq.joined
I keep getting the error 'join: SCZ.N.tmp.sorted:112855: is not sorted: chr1_100002155_D D I6 0.995112 0.0184 0.7897 87016' Nevertheless, the join continues and the majority is merged. However, I am not sure whether I am losing a small proportion of cases because of mismatch between the files, or because something goes wrong with sorting these files.
Does anybody know what I am doing wrong? And what i can do to not get this error?
Thank you!
I have also tried: LANG=en_EN sort -f -k 1,1 SCZ.N.tmp> SCZ.N.tmp.sorted2 and LANG=en_EN sort -f -k 1,1 1kg.tmp > 1kg.tmp.sorted2, with then joining using: LANG=en_EN join -1 1 -2 1 SCZ.N.tmp.sorted2 1kg.tmp.sorted2> SCZ.freq.joined. But that did not solve it.
|
You are sorting the files with the -f option, as case-independent keys.
However, join expects the keys in normal sorted sequence.
You should add the -i option to the command-line for join, to have it ignore case differences.
Alternatively, omit the -f option from both sorts.
Edit: also found another possibility here. The field separators need to be identical for the sort and the join. It looks like the defaults for sort and join are both whitespace, but it may be the next hurdle.
| Joining two sorted files gives error: join: <file>:112855: is not sorted: |
1,391,717,026,000 |
I am looking to compare two files, printing only records with a matching ID number and without duplicate records.
I have two files:
file1.txt contains:
Simons 0987768798980
West 09809867678
Vickers 768774564650
Simons 76867790987
Peterson 24346576865
Simons 76867790987
Holister 87879655456
Peterson 87686765766
And, file2.txt contains:
768774564650 Harry
76867790987 Steve
0987768798980 Mary
0987768798980 Mary
76856009097 Ali
87879655456 Rick
87686765766 Martin
The desired outcome is:
Harry Vickers 768774564650
Steve Simons 76867790987
Mary Simons 0987768798980
Rick Holister 87879655456
Martin Peterson 87686765766
This is what I have tried:
ARGV[1]==FILENAME{id2lastname[$2]=$1;id2id[$2]=$2}
ARGV[2]==FILENAME{id2firstname[$1]=$2}
$1 in id2id{print id2firstname[$1],id2lastname[$1],id2id[$1],id2firstname[$1]="",id2id[$1]="",id2lastname[$1]=""}
Which produces the following output:
Harry Vickers 768774564650
Steve Simons 76867790987
Mary Simons 0987768798980
Mary
Rick Holister 87879655456
Martin Peterson 87686765766
I would be pleased to know why this removed the last name and ID number of the duplicate record, but left the first name.
Apologies if the technique is odd or unconventional. I have not been learning for long.
If my attempt cannot be fixed or you feel there is a better way, I am happy for you to produce the desired result in a different way, but please:
use GAWK (as I want to progress with it),
try to keep it as simple as possible,
and, explain how it works so I can learn something.
|
The reason the partial line is printed, is that in your code you are not deleting the values you want to remove from the array, but replacing their values with empty strings.
This causes the check $1 in id2id{ ... } to be evaluated to true for the values that are empty strings.
The solution is to replace the code id2id[$1]="" with delete id2id[$1], and then it should work as expected.
Here is a slightly simplified version of the code:
awk 'NR == FNR { a[$2] = $1; next }
$1 in a { print a[$1], $2, $1; delete a[$1] }' file1.txt file2.txt
In a one-liner:
awk 'NR==FNR{a[$2]=$1;next} $1 in a{print a[$1],$2,$1; delete a[$1]}' file1.txt file2.txt
Using awk instead of join has the advantage of being simple and easily customizable.
The disadvantage is that is stores the first file in RAM before merging, so it will not handle huge files effectively.
| Print Arrays Without Duplicates in AWK |
1,391,717,026,000 |
Is there some workaround to join multiple files at once based on the first column? Usually, I would do:
join File1 File2 > File1+File2 and File1+File2 File3 > final_output
Example files:
File1:
1 test1
2 test3
3 test4
4 test5
7 test7
File2:
1 example1
2 example2
3 example3
4 example4
8 example8
File3:
1 foo1
2 foo2
3 foo3
4 foo4
10 foo10
Considering that f.e. fifth line may differs in each file, and there is n number of files.
Edit:
Example output:
1 test1 example1 foo1
2 test2 example2 foo2
3 test3 example3 foo3
4 test4 example4 foo4
On the other hand, I am not sure how lines that don't match in column1 will be processed (fifth line)
Thanks
|
Basically like this for your 3 files example
$ join file2 file3| join file1 -
1 test1 example1 foo1
2 test3 example2 foo2
3 test4 example3 foo3
4 test5 example4 foo4
But important all your input files must be sorted already (sort -k 1b,1, numerical sorted like your example may not work!). So the example above sorted on-the-fly could be written in bash like this:
join <(sort -k 1b,1 file2) <(sort -k 1b,1 file3) | join <(sort -k 1b,1 file1) -\
| sort -k 1n,1
And finally the generic case for n files using a recursive function (tested in bash).:
xjoin() {
local f
local srt="sort -k 1b,1"
if [ "$#" -lt 2 ]; then
echo "xjoin: need at least 2 files" >&2
return 1
elif [ "$#" -lt 3 ]; then
join <($srt "$1") <($srt "$2")
else
f=$1
shift
join <($srt "$f") <(xjoin "$@")
fi
}
xjoin file1 file2 file3 | sort -k 1n,1
If you know what you are doing you may omit the sort pipes. But from my experience join without explicit sort is very often the cause of trouble.
| Merge multiple files with join |
1,391,717,026,000 |
I want to merge two files.
Files A.txt
001;abc;def;ghi;jkl;pqr
002;abc;def;ghi;jkl;pqr
003;abc;def;ghi;jkl;pqr
004;abc;def;ghi;jkl;pqr
005;abc;def;ghi;jkl;pqr
.
Second File B.txt
001;mno
002;mno
003;mno
004;mno
005;mno
to have a text file C.txt
001;abc;def;ghi;jkl;mno;pqr
I am able to merge these two files but I don't know how to insert the output
from file B mno before pqr.
|
join will print each line of sorted input files that have the same first *(by default) field. So, setting the field delimiter (-t) to ; you get:
$ join -t\; A.txt B.txt
001;abc;def;ghi;jkl;pqr;mno
002;abc;def;ghi;jkl;pqr;mno
003;abc;def;ghi;jkl;pqr;mno
004;abc;def;ghi;jkl;pqr;mno
005;abc;def;ghi;jkl;pqr;mno
Combining that with awk to switch the field positions around:
$ join -t\; A.txt B.txt |
awk -F';' -v OFS=';' '{k=$NF; $NF=$(NF-1); $(NF-1)=k; print;}'
001;abc;def;ghi;jkl;mno;pqr
002;abc;def;ghi;jkl;mno;pqr
003;abc;def;ghi;jkl;mno;pqr
004;abc;def;ghi;jkl;mno;pqr
005;abc;def;ghi;jkl;mno;pqr
| Merging Two Files columns in order |
1,560,507,233,000 |
I'm trying to join two csv files, sorted, and with tab delimiter.
I'm new to the join command, so I'm not too sure about how to use it, but it seems to be replacing every tab in the files with spaces (messing up the alignment).
The command I'm using is:
join -1 5 -2 2 -t $'\t' -o $order --header file1.csv file2.csv |
column -t > result.csv
In the first file, the data is sorted according to the 5th column, and the 2nd column in the second file.
The variable $order is a simple string containing the different columns '1.1 1.2 1.3' etc. (28 of them).
The delimiter I'm using comes from SE.
Do you know where this comes from?
|
It is because column -t, with the table mode automatically determines the column width and creates a readable table output and delimits output with spaces and not tabs. To do this explicitly using column, use its output delimiter set flag with -o
join -1 5 -2 2 -t $'\t' -o $order --header file1.csv file2.csv |
column -o '\t' > result.csv
| join replaces tabs by spaces |
1,560,507,233,000 |
I have two files t1 and t2.
root@localhost:~#
root@localhost:~# cat t1
udp UNCONN 0 0 0.0.0.0:68 0.0.0.0:* users:(("dhclient",pid=479,fd=7)) 479
tcp LISTEN 0 128 127.0.0.1:6060 0.0.0.0:* users:(("gggg-ruit",pid=24968,fd=5)) 24968
root@localhost:~#
root@localhost:~# cat t2
root 88 0.0 0.0 0 0 ? I< Jan06 0:00 [scsi_tmf_0]
root 96 0.0 0.0 0 0 ? I< Jan06 0:00 [ipv6_addrconf]
root 24965 0.0 0.2 11592 3004 ? S Jan12 0:00 bash /root/restart_gggg.sh
root 24968 0.7 5.2 112488 53472 ? Sl Jan12 30:52 /usr/local/bin/gggg-ruit -singleInstance :44444
I want to join them on the 8th column of t1 and the 2nd column of t2. I already have them in sorted order. Let's prove it.
root@localhost:~# awk '{print $8}' t1
479
24968
root@localhost:~# awk '{print $2}' t2
88
96
24965
24968
Now when I join them, I got the following error.
root@localhost:~# join -1 8 -2 2 -o 2.1,2.2,1.1,1.2,1.5,1.6,2.11 t1 t2
join: t2:3: is not sorted: root 24965 0.0 0.2 11592 3004 ? S Jan12 0:00 bash /root/restart_gggg.sh
root@localhost:~#
Why it tells me t2 is not sorted on row 3? As you can see, it's been already sorted on the join column.
|
They’re sorted numerically, but join requires them to be sorted lexicographically: 24968, then 479; and 24965, 24968, 88, then 96.
| The "join" utility reports: file is not sorted, but in fact it is sorted |
1,560,507,233,000 |
I have two files which are pipe-delimited and may have column 1+column2 matches in both, or one file may have the entry while the other does not. Assume my match-key I am going off of equals $1"-"$2 using a pipe '|' as the FS.
file1
1111|AAA|foo|50
1111|BBB|foo|30
2222|BBB|foo|10
file2
1111|AAA|bar|10
1111|CCC|bar|20
3333|AAA|bar|40
The desired output would be the following for the first entry (I have this working)
1111|AAA|50|10
For the second entry file1 (If there is no matching column1+column2 in both files, replace the entry which is missing for foo as 0. And the other way around)
1111|BBB|30|0
And for an entry key (column1+column2) in file2, but not in file1 (This is entry 3 of file 2 expected output)
3333|AAA|0|40
So, desired output overall format is listing ALL unique keys which are represented by column1+column2 in BOTH files. With the 3rd column entries being those values from file1 column 4 (or 0 if value doesn't exist in file1) and the 4th column in output as those values in column 4 of file 2 (or 0 if value doesn't exist in file2).
I have done a lot of research and tried many things but I have values not outputting if the column1+column2 pair exists in file2 but not file1 by using the following:
join -t"|" -e0 -a1 -a2 -o 1.2,1.3,1.5,2.5 <(<file1 awk -F"|" '{print $1"-"$2"|"$0}' | sort -k1,1) <(<file2 awk -F"|" '{print $1"-"$2"|"$0}' | sort -k1,1)
The above case gives me expected output if there is a column1+column2 match in file1 but not file2, and appends a 0 for the match not existing... How can I get this to work for ALL scenarios?
Above command will do some process substitution by adding a key in column 1 in both files which is column1+column2, and then join based off of that new key. -e0 will add a 0 if this key exists in file1 but not file2. How can I get it to cover the case of: New key (column1-column2) exists in file 2 but NOT file 1?
|
With your approach you have to use join twice (or change your approach to do it with a single join invocation) :
print the common lines and the unpairable lines from file1 with join -t'|' -e0 -a1 -o 1.2,1.3,1.5,2.5 <(<file1 awk -F'|' '{print $1"-"$2"|"$0}' | sort -t'|' -k1,1) <(<file2 awk -F'|' '{print $1"-"$2"|"$0}' | sort -t'|' -k1,1)
print the unpairable lines from file2 with join -t'|' -e0 -v2 -o 2.2,2.3,1.5,2.5 <(<file1 awk -F'|' '{print $1"-"$2"|"$0}' | sort -t'|' -k1,1) <(<file2 awk -F'|' '{print $1"-"$2"|"$0}' | sort -t'|' -k1,1)
You can do the same with a single awk invocation, storing $4 in two arrays indexed by e.g. $1|$2 and then in the END block iterating over each array indices, comparing them and printing accordingly:
awk -F'|' 'NR==FNR{z[$1"|"$2]=$4;next}{x[$1"|"$2]=$4}
END{for (j in x){if (!(j in z)){print j, "0", x[j]}};
for (i in z){if (i in x){print i, z[i], x[i]} else {print i, z[i], "0"}}
}' OFS="|" file1 file2
| Joining entries based off of column using awk/join |
1,560,507,233,000 |
Is it possible to copy the whole rows of File1 in a new File3 following the instruction given by File2 by using a simple bash script using sed or awk?
File1: /*two or more columns*/
AC 456324
DC 689712
GH 123677
KL 236587
File2: /*one column*/
AC
DC
File3:
AC 456324
DC 689712
I'm actually performing this using Python dictionaries and I wondered if you knew a simple way out.
|
With grep
grep -Ff File2 File1
With awk
awk 'NR==FNR {a[$1]++;next} a[$1]' File2 File1
| Merging files by rows |
1,560,507,233,000 |
My question is similar to this one: Merge multiple columns based on the first column values
I have multiple files (10+) that I want to merge/join into one output file, for example:
file 1
2000 0.0202094
2001 0.0225532
2002 0.02553
2003 0.0261099
2006 0.028843
file 2
2000 0.0343179
2003 0.039579
2004 0.0412106
2006 0.041264
file 3
2001 0.03
2004 0.068689
2006 0.0645474
All files have the same two columns and are of unequal length. Where there is no entry for the columns (missing in one or several files), I would want a 1. If there is no entry in any file (like 2005) I don't want any output.
The desired output would be:
file1 file2 file3
2000 0.0202094 0.0343179 1
2001 0.0225532 1 0.03
2002 0.02553 1 1
2003 0.0261099 0.0395799 1
2004 1 0.0412106 0.0686893
2006 0.028843 0.041264 0.0645474
I have tried to modify the awk code provided by the answer of this other question, but I feel like it could not be possible with that solution.
|
Use join:
join -a1 -a2 -e 1 -o auto <(join -a1 -a2 -e 1 -o auto file1 file2) file3
see in the man join
-a FILENUM
also print unpairable lines from file FILENUM, where FILENUM is 1 or 2, corresponding to FILE1 or FILE2
-e EMPTY
replace missing input fields with EMPTY
-o FORMAT
obey FORMAT while constructing output line
If FORMAT is the keyword 'auto', then the first line of each file
determines the number of
fields output for each line.
Note: join require sorted input, so if those are not sorted (which they are in given samples), sort them first, like:
join -a1 -a2 -e 1 -o auto \
<(join -a1 -a2 -e 1 -o auto <(sort file1) <(sort file2)) \
<(sort file3)
To apply this on multiple files:
join first two files and save output to third file say join.tmp:
join -a1 -a2 -e 1 -o auto file1 file2 >join.tmp
next loop over the rest of the files and update join.tmp file for every run:
for file in rest_files*; do
join -a1 -a2 -e 1 -o auto join.tmp "$file" >join.tmp.1
mv join.tmp.1 join.tmp
done
at the end your join.tmp would be your final joined result.
print with header:
$ hdr() { awk 'FNR==1{ print "\0", FILENAME }1' "$1"; }
$ join -a1 -a2 -e 1 -o auto \
<(join -a1 -a2 -e 1 -o auto <( hdr file1) <(hdr file2)) \
<(hdr file3) |tr -d '\0'
for the multiple files version:
$ hdr() { awk 'FNR==1{ print "\0", FILENAME }1' "$1"; }
$ join -a1 -a2 -e 1 -o auto <(hdr file1) <(hdr file2) >join.tmp
$ for file in rest_files*; do
join -a1 -a2 -e 1 -o auto join.tmp <(hdr "$file") >join.tmp.1
mv join.tmp.1 join.tmp
done
$ tr -d '\0' <join.tmp >final.file
| Merge multiple files by first column |
1,560,507,233,000 |
I have two text files. File 2 has logs over 1,000,000. File 1 has IP addresses line by line. I want to read file 2 lines and search these lines in file 1, I mean:
file 1:
34.123.21.32
45.231.43.21
21.34.67.98
file 2 :
34.123.21.32 0.326 - [30/Oct/2013:06:00:06 +0200]
45.231.43.21 6.334 - [30/Oct/2013:06:00:06 +0200]
45.231.43.21 3.673 - [30/Oct/2013:06:00:06 +0200]
34.123.21.32 4.754 - [30/Oct/2013:06:00:06 +0200]
21.34.67.98 1.765 - [30/Oct/2013:06:00:06 +0200]
...
I want to search for the IP from file 1 line by line in file 2 and print time arguments (example: 0.326) to a new file.
How can I do this?
|
Join + sort
If you're trying to find IP's that are present in both, you can use the join command but you'll need to use sort to pre-sort the files prior to joining them.
$ join -o 2.2 <(sort file1) <(sort file2)
Example
$ join -o 2.2 <(sort file1) <(sort file2)
1.765
0.326
4.754
3.673
6.334
Another example
file 1a:
$ cat file1a
34.123.21.32
45.231.43.21
21.34.67.98
1.2.3.4
5.6.7.8
9.10.11.12
file 2a:
$ cat file2a
34.123.21.32 0.326 - [30/Oct/2013:06:00:06 +0200]
45.231.43.21 6.334 - [30/Oct/2013:06:00:06 +0200]
45.231.43.21 3.673 - [30/Oct/2013:06:00:06 +0200]
34.123.21.32 4.754 - [30/Oct/2013:06:00:06 +0200]
21.34.67.98 1.765 - [30/Oct/2013:06:00:06 +0200]
1.2.3.4 1.234 - [30/Oct/2013:06:00:06 +0200]
4.3.2.1 4.321 - [30/Oct/2013:06:00:06 +0200]
Running the join command:
$ join -o 2.2 <(sort file1) <(sort file2)
1.234
1.765
0.326
4.754
3.673
6.334
NOTE: The original order of file2 is lost with this method, due to the fact that we sorted it first. However this method only needs to scan file2 a single time now, as a result.
grep
You can use grep to search for matches in file2 using lines that are in file1, but this method isn't as efficient as the first method I showed you. It's scanning file2 looking for each line in file1.
$ grep -f file1 file2 | awk '{print $2}'
Example
$ grep -f file1 file2 | awk '{print $2}'
0.326
6.334
3.673
4.754
1.765
1.234
Improving grep's performance
You can speed up the grep's performance by using this form:
$ LC_ALL=C grep -f file1 file2 | awk '{print $2}'
You can also tell grep that the stings in file1 are fixed length (-F) which will also help in getting better performance.
$ LC_ALL=C grep -Ff file1 file2 | awk '{print $2}'
Generally in software, you try to avoid having to do this approach though, since it's basically a loop within a loop type of solution. But there are times when it's the best that can be achieved using a computer + software.
References
Linux tools to treat files as sets and perform set operations on them
| compare files line by line and create new one bash programming |
1,560,507,233,000 |
Because the input to join must be sorted, often the command is called similarly to:
join <(sort file1) <(sort file2)
This is not portable as it uses process substitution, which is not specified by POSIX.
join can also use the standard input by specifying - as one of the file arguments. However, this only allows for sorting one of the files through a pipeline:
sort file1 | join - <(sort file2)
It seems there should be a simple way to accomplish sorting of both files and then joining the results using POSIX-specified features only. Perhaps something using redirection to a third file descriptor, or perhaps it will require created a FIFO. However, I'm having trouble visualizing it.
How can join be used POSIXly on unsorted files?
|
You can do it with two named pipes (or of course you could use one named pipe and stdin):
mkfifo a b
sort file1 > a &
sort file2 > b &
join a b
Process substitution works essentially by setting up those fifos (using /dev/fd/ instead of named pipes where available). For example, in bash:
$ echo join <(sort file1) <(sort file2)
join /dev/fd/63 /dev/fd/62
Note how bash has substituted the process with a file name, in /dev/fd. (Witout /dev/fd/, new enough versions of zsh, bash, and ksh93 will used named pipes.) It's left those open when invoking join, so when join opens those, it'll read from the two sorts. You can see them passed with some lsof-trickery:
$ sh -c 'lsof -a -d 0-999 -p $$; exit' <(sort file1) <(sort file2)
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
sh 1894 anthony 0u CHR 136,5 0t0 8 /dev/pts/5
sh 1894 anthony 1u CHR 136,5 0t0 8 /dev/pts/5
sh 1894 anthony 2u CHR 136,5 0t0 8 /dev/pts/5
sh 1894 anthony 62r FIFO 0,10 0t0 237085 pipe
sh 1894 anthony 63r FIFO 0,10 0t0 237083 pipe
(The exit is to prevent a common optimization where the shell doesn't fork when there is only one command to run).
| Join two unsorted files with POSIX? [duplicate] |
1,560,507,233,000 |
I have N files like so:
file1.txt
Header1,Header2,Header3,Header4,Header5
A,B,RANDOM,1,2
C,D,RANDOM,3,4
fileN.txt
Header1,Header2,Header3,Header4,Header5
A,B,RANDOM,1,2
C,D,RANDOM,3,4
They all have the same headers. I would like to sum all of Header4 and Header5 based on Header1 and Header2. So all items with the A,B fields should sum Header4,Header5.
To print something like
A,B,2,4
C,D,6,8
|
Assuming ordering of output is no requirement...
awk '
BEGIN { FS=OFS=SUBSEP="," }
{ s4[$1,$2]+=$4 ; s5[$1,$2]+=$5 }
END { for (k in s4) print k,s4[k],s5[k] }
' file1 ... fileN
(Edited and restructured for better legibility.)
| Awk sum csv columns based on fields |
1,560,507,233,000 |
I need to match two unequal files using $1 of file 1 and $2 of file 2 and print $1 of file 2 on file 1.
Input file 1
101 2
101 5
101 7
103 2
103 3
103 4
105 3
105 2
Input file 2
24 101
23 103
26 105
Desired output
101 2 24
101 5 24
101 7 24
103 2 23
103 3 23
103 4 23
105 3 26
105 2 26
I have tried the following code but it gave me incorrect output.
awk 'FNR==NR{a[$2]=$0;next};{print a[$2]}' file2 file1
|
A classic job for join:
join -1 1 -2 2 file1 file2
-1 1 specifies the field in the first file.
-2 2 specifies the field in the second file.
| How can I match a field in two different files and append together in output file? |
1,560,507,233,000 |
I have two files. I want to compare the content of one file with the other one. If there is a matching line between both files then print the line and its line number in each file. Example:
File 1:
ABC
PQR
MNO
XYZ
File 2:
qqqq
wewe
ABC
acdd
abcc
nop
MNO
Expected output:
ABC 1 3
MNO 3 7
..
|
With awk you could process the first file, store the lines ($0) and their corresponding line numbers (NR) (as indices/values) in an associative array (l[$0]) then process the second file and if a line is in the the array index print it along with the value of l[$0] and current line number (FNR):
awk 'FNR==NR{l[$0]=NR; next}; $0 in l{print $0, l[$0], FNR}' file1 file2
| Print common lines between two files along with their line numbers in those files |
1,560,507,233,000 |
I have:
File 1 like:
sting_of_printable_characters*sting_of_printable_characters*sting_of_printable_characters*ALPHANUMERIC_PATTERN
File 2 like:
sting_of_printable_characters*ALPHANUMERIC_PATTERN
where * is a field separator and the alphanumeric pattern is always the last field in the line.
I am completely stumped on how to achieve the following and would appreciate some assistance.
I need to essentially "join" (I've tried the join command and it doesn't seem to work with alphanumeric keys) these two files based on "ALPHANUMERIC_PATTERN", and only print where both files contain the same ALPHANUMERIC_PATTERN.
I would prefer to use awk due to it's processing efficiency but anything would be very helpful. (These files are large.)
The catch is that I need to see the output similar to the below:
ALPHANUMERIC_PATTERN*stuff_from_file_1*stuff_from_file_2
|
With join you could try like this:
join -t\* \
<(sed 's/\(.*\)\(\*\)\(.*\)/\3\2\1/' file1 | sort -t\* -k1,1) \
<(sed 's/\(.*\)\(\*\)\(.*\)/\3\2\1/' file2 | sort -t\* -k1,1)
The two seds move the last field to the beginning of line, e.g.
field1*field2*...field(N-1)*field(N)
becomes
field(N)*field1*field2*...*field(N-1)
the results are then then sorted on 1st field and then joined (always on 1st field). This will print lines like:
field(N)*fields(1)to(N-1)*from*file1*fields(1)to(N-1)*from*file2
If you prefer working with temporary files and save join result to e.g. outfile:
sed 's/\(.*\)\(\*\)\(.*\)/\3\2\1/' file1 | sort -t\* -k1,1 > sorted_1
sed 's/\(.*\)\(\*\)\(.*\)/\3\2\1/' file2 | sort -t\* -k1,1 > sorted_2
join -t\* sorted_{1,2} > outfile
rm -f sorted_{1,2}
| Join (large) files on alphanumeric pattern |
1,560,507,233,000 |
bash-3.2$ cat sample.log sample.log.1 sample.log.2
ID COL1 COL2 COL4
1 col1 col2 col4
2 c1 c2 c4
3 co1 co2 co4
ID COL3 COL1
1 col3 col1
2 c3 c1
3 co3 co1
ID COL1 COL2 COL3
1 col1 col2 col3
2 c1 c2 c3
3 co1 co2 co3
I need to write an awk script such that it gives me the values of the columns for a particular id like a select query on multiple tables in db.
give me col1 col2 and col3 fields for id 1 and should not duplicate result.
meaning the result should be like
The result should be
ID COL1 COL2 COL3
1 col1 col2 col3
but not
The result should be
ID COL1 COL2 COL3 COL3
1 col1 col2 col3 col3
Even a suggestion is also good.
awk ' BEGIN { while ( (getline line < "sample.log") > 0 ) {ids[substr(line,1,index(line," ")-1)];} } { // get the column values here based on the stored id's .. } ' sample.log sample.log.1 sample.log.2
I am trying to do something like that mentioned above. I am not sure if it is a good idea.
|
You can use the join command to perform this task:
join -1 1 -2 1 sample.log sample.log.1 -o 1.1,1.2,1.3,2.2
The output will be 'single space' separated, but you can use awk to reformat it to be column aligned.
Note that the join input files must be sorted.
| merging files and getting column values based on id field |
1,560,507,233,000 |
I have file1 (sample):
60108903374
60172485121
60108919381
60174213128
60108919951
60108919970
601112020106
601112020107
601112020108
601112020113
601112020114
60175472940
And file2:
60179970001,A
60172681920,A
60174202041,A
60172514180,A
60174314679,A
60174325306,A
60175472940,A
60174213128,A
60175328984,A
60175349857,A
60172796759,A
60172798922,A
60179195129,A
60172485121,B
60173483126,A
60172683175,A
60174521828,A
60142536314,B
60175347909,B
60175183031,B
I want to merge file1 and file2 with output matching based on the first column as well as shows the second column from file2.
Desired output:
60172485121,B
60174213128,A
file1 has ~80k lines and file2 has 500k lines.
Tried using:
join -1 1 -2 1 -o 1.1,2.2 file1 file2
|
join -t, <(sort file1) <(sort -t, file2)
The above does the job.
| How to merge two files of different lines and column and output matching lines with colums? |
1,560,507,233,000 |
I have a file name "conf1" containing variables like:
name='john'
last=''
custom='1000'
and another file name conf2 like this:
name='john'
last='star'
I want to merge between them to one file but in a way that the merged file contain the variable in the same order I source them.
for example if I source conf1 and then conf2 the variable from conf 2 will override conf1. but I will also have the variable that I don't have in conf2.
I want to merge and create 1 file from both of them with only the variables that are unique and was sources last.
required output:conf3
name='john'
last='star'
custom='1000'
is this possible?
|
You could do:
$ awk -F= '{l[$1]=$0};END{for (i in l) print l[i]}' conf1 conf2
custom='1000'
last='star'
name='john'
Note that the order of the lines in the output is not guaranteed (based on how awk stores the array internally in a hash table), but settings in conf2 will override those in conf1.
where
awk -F= ... conf1 conf2 call awk with = as separator on conf files.
{l[$1]=$0} store definition of each var, newest overriding oldest
END{ ... } in the end, (after all files processed)
for (i in l) loop for all var,
print l[i] and print it.
| source multiple files and output one file |
1,560,507,233,000 |
I want to perform what some data analysis software call an anti-join: remove from one list those lines matching lines in another list. Here is some toy data and the expected output:
$ echo -e "a\nb\nc\nd" > list1
$ echo -e "c\nd\ne\nf" > list2
$ antijoincommand list1 list2
a
b
|
I wouldn't use join for this because join requires input to be sorted, which is an unnecessary complication for such a simple job. You could instead use grep:
$ grep -vxFf list2 list1
a
b
Or awk:
$ awk 'NR==FNR{++a[$0]} !a[$0]' list2 list1
a
b
If the files are already sorted, an alternative to join -v 1 would be comm -23
$ comm -23 list1 list2
a
b
| How to do anti-join or inverse join in bash |
1,560,507,233,000 |
I have a tab separated file that looks like this:
123 some text
123 some different text
334 some other text
341 more text
and I want to do two things. One is to order everything numerically (this is easy to do) and the other is to remove a line if it's number is already present. I.e. the output would look like this:
123 some text
334 some other text
341 more text
I tried getting a file of just the unique numbers, i.e.
123
334
341
and joining it with the original file with:
join -j 1 justNumbers.txt original.txt
but this gave me the original file back. Any ideas?
|
If you want to sort/test for uniqueness the first field specifically, and your system has the GNU coreutils version of sort, then I think you could just use
sort -nu file
viz.
$ sort -nu file
123 some text
334 some other text
341 more text
From info coreutils 'sort invocation'
The commands sort -u and sort | uniq are equivalent, but this
equivalence does not extend to arbitrary sort options. For
example, sort -n -u inspects only the value of the initial numeric
string when checking for uniqueness, whereas sort -n | uniq
inspects the entire line.
| Removing lines with a single common field |
1,560,507,233,000 |
I have two files. file_1.txt looks like this:
R1 C1 C2 C3 C4 C5
R2 C1 C2 C3 C4 C5
R3 C1 C2 C3 C4 C5
R4 C1 C2 C3 C4 C5
R5 C1 C2 C3 C4 C5
R6 C1 C2 C3 C4 C5
R7 C1 C2 C3 C4 C5
R8 C1 C2 C3 C4 C5
R9 C1 C2 C3 C4 C5
R10 C1 C2 C3 C4 C5
file_2.txt looks like this:
R4 C4 C5
R6 C4 C5
R7 C4 C5
R9 C4 C5
I would like to replace the C4 and C5 values in file_1.txt by those that correspond to them from file_2.txt, while keeping the C1, C2, and C3 values in file_1.txt unchanged.
So the resulting file_3.txt should look like this:
R1 C1 C2 C3 C4 C5
R2 C1 C2 C3 C4 C5
R3 C1 C2 C3 C4 C5
R4 C1 C2 C3 C4_new C5_new
R5 C1 C2 C3 C4 C5
R6 C1 C2 C3 C4_new C5_new
R7 C1 C2 C3 C4_new C5_new
R8 C1 C2 C3 C4 C5
R9 C1 C2 C3 C4_new C5_new
R10 C1 C2 C3 C4 C5
All values are numbers. The first columns in file_1.txt and file_2.txt are key fields and are sorted in ascending numerical order.
Is this something that join alone can do?
|
This problem makes for a typical application of awk
awk 'NR == FNR{a1[$1]=$2; a2[$1]=$3; next};
$1 in a1{$5=a1[$1]; $6=a2[$1]};{print}' file_2.txt file_1.txt
You may have to set the output field separator explicitly to tab, in which case
awk -v OFS='\t' 'NR == FNR{a1[$1]=$2; a2[$1]=$3; next};
$1 in a1{$5=a1[$1]; $6=a2[$1]};{print}' file_2.txt file_1.txt
| Join two files with different number of columns and rows |
1,560,507,233,000 |
Table 1 (tab separated):
NC_000001.11 1243 A T 0.14
NC_000005.11 1432 G C 0.0006
NC_000012.12 1284 A T 0.93428
NC_000021.9 9824 T C 0.9
Lookup table (tab separated) - this is in fact huge, around 6G gzipped:
NC_000001.11 1243 rs73647921 A T
NC_000005.11 1432 rs75444 G C
NC_000012.12 1284 rs754723 A T
NC_000021.9 9824 rs865545 T C
I would like the output to match on the first 4 columns of table 1 which correspond to columns 1/2/4/5 of the lookup table; taking table 1 and transforming it into:
MarkerName P-Value
rs73647921 0.14
rs75444 0.0006
rs754723 0.93428
rs865545 0.9
I think I need to use join along the lines of:
join -t, -a 1 -a 2 -o0,1.5,2.3 -e ' -' file1 file2
But this doesn't seem to work. How could I also use a gzipped file?
|
With awk (and bash) you can write
awk '
BEGIN {FS = OFS = "\t"}
NR == FNR {pvalue[$1,$2,$3,$4] = $5; next}
FNR == 1 {print "MarkerName", "P-Value"}
{ key = $1 SUBSEP $2 SUBSEP $4 SUBSEP $5
sub(/\r$/, "", key)
}
key in pvalue {print $3, pvalue[key]}
' table1.tsv <(zcat lookup.tsv.gz)
awk uses the SUBSEP variable to join comma-separated indices for arrays.
That last bit of syntax around the zcat is a bash Process Substitution
For multi-field join conditions, join can be painful to work with. It also complains if the files are not sorted.
| Looking up values in one table and outputting it into another using join/awk |
1,560,507,233,000 |
I have seven (or eight and so on) files with same number of lines.
file1
1.001
1.002
1.003
1.004
file2
2.001
2.002
2.003
2.004
file3
3.001
3.002
3.003
3.004
etc.
Desired output:
1.001;2.001;3.001;4.001;5.001;6.001;7.001
1.002;2.002;3.002;4.002;5.002;6.002;7.002
1.003;2.003;3.003;4.003;5.003;6.003;7.003
1.004;2.004;3.004;4.004;5.004;6.004;7.004
How to do it with short script in awk?
|
As steeldriver said, the reasonable way to do this is with paste:
$ paste -d';' file*
1.001;2.001;3.001;4.001;5.001;6.001;7.001;8.001
1.002;2.002;3.002;4.002;5.002;6.002;7.002;8.002
1.003;2.003;3.003;4.003;5.003;6.003;7.003;8.003
1.004;2.004;3.004;4.004;5.004;6.004;7.004;8.004
But, if you must use awk:
$ awk '{a[FNR]=a[FNR](FNR==NR?"":";")$0} END{for (i=1;i<=FNR;i++) print a[i]}' file*
1.001;2.001;3.001;4.001;5.001;6.001;7.001;8.001
1.002;2.002;3.002;4.002;5.002;6.002;7.002;8.002
1.003;2.003;3.003;4.003;5.003;6.003;7.003;8.003
1.004;2.004;3.004;4.004;5.004;6.004;7.004;8.004
The awk script keeps all the data in memory. If the files are large, this could be a problem. But, for this task, paste is better and simpler anyway.
How it works
In this script a is an array with a[i] being the output for line i. As we read through each of the subsequent files, we append the new information for line i to the end of a[i]. After we have finished reading the files, we print out the values in a. In more detail:
a[FNR]=a[FNR](FNR==NR?"":";")$0
FNR is the line number of the current file we are reading and $0 are the contents of that line. This code adds $0 on to the end of a[FNR]. Except if we are still reading the first file, we put in a semicolon before $0. This is done using the complex looking ternary statement: (FNR==NR?"":";"). This is really just a if-then-else command. If we are reading the first file, that is if FNR==NR, then it returns an empty string "". If not, it returns a semicolon, ;.
END{for (i=1;i<=FNR;i++) print a[i]}
After we have finished reading all the files, this prints out the data that we have accumulated in array a.
| Join seven files with awk line-by-line |
1,560,507,233,000 |
I have two different files and I'd like to do a merge of their information using the first column.
File1.txt
A,info1,info2
234,info3,info4
CD,info5,info6
File2.txt
234,ccc,bb
CD,aaa,dd
Expected output.csv
A,info1,info2,,
234,info3,info4,ccc,bb
CD,info5,info6,aaa,dd
I tried with awk (not my script) join and grep but I didn't obtain the desired result.
awk -F "," 'FNR==NR {h[$1] = $2;next} BEGIN{ OFS = "\t"} {print $0,$2?h[$1]:"0"}' file1.txt prova2.txt
and
join -a 1 <(sort file1.txt) <( sort file2.txt) > output.csv
Could someone help me please?
|
if the number of fields in both files are the same then you can use -o auto to fill-up the number of fields in each line based on the first line of each file (by default it fills the missing fields with the value of -e option which by default it's space character but you can change it to any string you want);
$ join -t, -a1 -o auto <(sort file1) <(sort file2)
234,info3,info4,ccc,bb
A,info1,info2,,
CD,info5,info6,aaa,dd
we also added -t, to specify the field separators for the input &ouptut files.
if you want to add lines which are only exist in file2, add -a2 to the command.
above command is the shortened version of below command which we explicitly saying which fields to output:
join -t, -a1 -o0,1.2,1.3,2.2,2.3 <(sort file1) <(sort file2)
-o #.k prints the kth field from the file number #.
-o 0 here outputs the un-pairable lines.
Or using awk:
awk 'BEGIN{ FS=OFS=","; na="" }
{ key=$1; sub(/[^,]*,/, "") }
NR==FNR { file1[key]=$0; next }
(key in file1){ print key, file1[key], $0; delete file1[key] }
END{ for(key in file1) print key, file1[key], na, na }' file1 file2
In the { key=$1; sub(/[^,]*,/, "") } action, we take a backup from the first column then with sub() we remove that column by striping line upto the first comma character, so the remaining content will be the value for that key for the later uses.
| Merge two files using first column |
1,560,507,233,000 |
I have multiple files which need to be merged based on first column from each file
File1:
foo 12
jhdfeg 25
kjfdgkl 37
File 2:
foo 23
jhdfeg 45
File 3:
foo 35
djhf 37
The output should be like this
file1 file2 file3
foo 12 23 35
jhdfeg 25 45 0
kjfdgkl 37 0 0
djhf 0 0 37
|
perl -F'\s+' -lane '
$. == 1 and @ARGC = ($ARGV, @ARGV); # initialize the @ARGC array
exists $h{$F[0]} or $h[keys %h] = $F[0]; # needed to remember order
$h{$F[0]}->[@ARGC-@ARGV-1] = $F[1]; # populate hash
END {
$, = "\t"; # set the OFS to TAB
print q//, @ARGC; # print the first line with filenames
for my $key (@h) { # print remaninig lines with data
print $key,
map { $h{$key}->[$_] // 0 } 0 .. $#ARGC;
}
}
' file1 file2 file3 # ... you can give as many files here
Output
file1 file2 file3
foo 12 23 35
jhdfeg 25 45 0
kjfdgkl 37 0 0
djhf 0 0 37
| Paste multiple files based on the first column into one single file |
1,560,507,233,000 |
I need to combine two files into a single file with all columns from both files.
I am providing my example files.
File 1
chr loc T1 C1
chr1 100 2 3
chr1 200 3 4
chr2 100 1 4
chr2 400 3 1
File 2
chr loc T2 C2
chr1 100 1 2
chr1 300 4 1
chr2 100 7 5
chr2 500 1 9
and output file should be like this
output file
chr loc T1 C1 T2 C2
chr1 100 2 3 1 2
chr1 200 3 4 0 0
chr1 300 0 0 4 1
chr2 100 1 4 7 5
chr2 400 3 1 0 0
chr2 500 0 0 1 9
|
join -a1 -a2 -e 0 -o 0,1.2,1.3,2.2,2.3 \
<(sed 's/ \+/_/' file1 | sort) \
<(sed 's/ \+/_/' file2 | sort) |
sed 's/_/ /' |
column -t |
sort
chr loc T1 C1 T2 C2
chr1 100 2 3 1 2
chr1 200 3 4 0 0
chr1 300 0 0 4 1
chr2 100 1 4 7 5
chr2 400 3 1 0 0
chr2 500 0 0 1 9
The trickiest part here are the reasons for sed -- join will only join on a single field, and here the join criteria is the first 2 fields. So, we have to combine those fields into a single word: I replace the first sequence of whitespace with an underscore so join will see chr1_100, chr1_200, etc.
join requires its input files to be sorted.
I use process substitution so that join can work with the sed|sort pipelines like files.
Then another sed call to undo the combined field, and then column to make it pretty.
By default, join uses the first field of each file as the key field.
By default, join does an inner join: only keys present in both files are printed. The -a1 and -a2 option enable the full outer join we want. The -e option provides the default value for null fields, and we need the -o option to specify that we want all the fields.
Can also use awk:
awk '
{key = $1 OFS $2}
NR == FNR {f1[key] = $3; f2[key] = $4; next}
!(key in f1) {print $1, $2, 0, 0, $3, $4; next}
{print key, f1[key], f2[key], $3, $4; delete f1[key]}
END {for (key in f1) print key, f1[key], f2[key], 0, 0}
' file1 file2 | sort
chr loc T1 C1 T2 C2
chr1 100 2 3 1 2
chr1 200 3 4 0 0
chr1 300 0 0 4 1
chr2 100 1 4 7 5
chr2 400 3 1 0 0
chr2 500 0 0 1 9
| combine two files to single file with combined columns |
1,560,507,233,000 |
I have four different files: file1, file2, file3, file4. Each file has 2 different columns separated by tab. I want to match first column of file1 (as reference) with the first column of second file, third and fourth file and print first column which is matching and second column of each file which has matching first column.
files look like:
file 1
Bm1_00085|Bm1_22625 0.263974289
Bm1_00087|Bm1_22620 0.663443490
file 2
Bm1_00085|Bm1_22625 0
Bm1_57630|Bm1_52870 0
file 3
Bm1_57630|Bm1_54855 0
Bm1_00085|Bm1_22625 4
file 4
Bm1_57630|Bm1_52870 0
Bm1_00085|Bm1_22625 1
output:
Bm1_00085|Bm1_22625 0.263974289 0 4 1
|
In perl, the tool for this job is a hash. A hash is a set of key-value pairs which makes this sort of cross referencing quite easy.
Note - this will ONLY work if the first field is unique:
#!/usr/bin/env perl
use strict;
use warnings;
my %data;
while (<>) {
my ( $key, $value ) = split;
push( @{ $data{$key} }, $value );
}
foreach my $key ( sort keys %data ) {
if ( @{ $data{$key} } >= @ARGV ) {
print join( "\t", $key, @{ $data{$key} } ), "\n";
}
}
Invoke as myscript.pl file1 file2 file3 file4.
It:
reads a list if files from the command line via <>, and opens them for processing.
Iterates one line at a time, splitting the line into $key and $value.
Stores $value in a hash of arrays.
runs through each key in your hash
if there are a number elements >= number of command line arguments (e.g. number of files) - prints that line.
Output from this is:
Bm1_00085|Bm1_22625 0.263974289 0 4 1
Note:
Assumes unique 'keys' within all the files.
| compare multiple files(more than two) with two different columns |
1,560,507,233,000 |
I have 2 CSV files for each date (csv_2014_4_15 and csv_2014_4_16) , with basic structure and couple of unique columns as below.
id,name,created_at,updated_at,other columns
12, joe, 2013-1-1 18:30, 2014-2-1 12:00
56, bob, datetime, datetime
I want to merge the 2 csv files based on these these conditions. My code so far is as below.
if (csv_date_x.id == csv_date_x+1.id)
{
if(csv_date_x.updated_at < csv_date_x.updated_at)
add csv_date_x+1 row into out.csv
}
else {
if(csv_date_x+1.created_at == TODAY (yyyy-mm-dd)
add csv_date_x+1 row into out.csv
}
|
Try this:
$ awk -F',' -v t="$(date +"%Y-%-m-%-d")" '
FNR == NR {
u[$1] = $4;
next;
}
$4 > u[$1] {
print;
next;
}
t ~ $3
' file_1 file_2
Explanation
We get today date, save it in variable t
While reading file_1 FNR == NR, we save each updated time of each id in associative array u, key is id, value is updated time.
While reading file_2:
If update date of id, $4 greater than correspond id updated time save in array u ($4 > u[$1]), we print the line and skip to next line.
If above condition false, we check if created date of current line is today, t ~ $3, i.e "2014-7-11" ~ "2014-7-11 12:00", if true print the line.
| Merge csv files with conditions |
1,560,507,233,000 |
I have a script equijoin2:
#! /bin/bash
# default args
delim="," # CSV by default
outer=""
outerfile=""
# Parse flagged arguments:
while getopts "o:td:" flag
do
case $flag in
d) delim=$OPTARG;;
t) delim="\t";;
o) outer="-a $OPTARG";;
?) exit;;
esac
done
# Delete the flagged arguments:
shift $(($OPTIND -1))
# two input files
f1="$1"
f2="$2"
# cols from the input files
col1="$3"
col2="$4"
join "$outer" -t "$delim" -1 "$col1" -2 "$col2" <(sort "$f1") <(sort "$f2")
and two files
$ cat file1
c c1
b b1
$ cat file2
a a2
c c2
b b2
Why does the last command fail? Thanks.
$ equijoin2 -o 2 -d " " file1 file2 1 1
a a2
b b1 b2
c c1 c2
$ equijoin2 -o 1 -d " " file1 file2 1 1
b b1 b2
c c1 c2
$ equijoin2 -d " " file1 file2 1 1
join: extra operand '/dev/fd/62'
|
"$outer" is a quoted scalar variable so it always expands to one argument. If empty or unset, that still expands to one empty argument to join (and when you call your script with -o2, that's one -a 2 argument instead of the two arguments -a and 2).
Your join is probably GNU join in that it accepts options after non-option arguments. That "$outer" is a non-option argument when empty as it doesn't start with - so is treated as a file name and join complains about the third file name provided which it doesn't expect.
If you want a variable with a variable number of arguments, use an array:
outer=()
...
(o)
outer=(-a "$OPTARG");;
...
join "${outer[@]}"
Though here you could also do:
outer=
...
(o)
outer="-a$OPTARG";;
...
join ${outer:+"$outer"} ... <(sort < "$f1") <(sort < "$f2")
Or:
unset -v outer
...
(o)
outer="$OPTARG";;
...
join ${outer+-a "$outer"} ...
(that one doesn't work in zsh except in sh/ksh emulation).
Some other notes:
join -t '\t' doesn't work. You'd need delim=$'\t' to store a literal TAB in $delim
Remember to use -- when passing arbitrary arguments to commands (or use redirections where possible). So sort -- "$f1" or better sort < "$f1" instead of sort "$f1".
arithmetic expansions are also subject to split+glob so should also be quoted (shift "$((OPTIND - 1))") (here not a problem though as you're using bash which doesn't inherit $IFS from the environment and you're not modifying IFS earlier in the script, but still good practice).
| Why do I have "join: extra operand '/dev/fd/62'" error? |
1,560,507,233,000 |
I have two files with columns separated by tab and I want to merge them
file a01
a= b=
c= d=
e= f=
g= h= i=
j= k= l=
m= n= 0=
file b01
1 2
3 4
5 6
7 8 9
10 11 12
13 14 15
desired output
a=1 b=2
c=3 d=4
e=5 f=6
g=7 h=8 i=9
j=10 k=11 l=12
m=13 n=14 0=15
but when I run the command
join a01 b01
it returns nothing
I don't know what I am doing wrong
thanks in advance
|
That's simply not how the joincommand works - it joins lines based on a common (matching field) - which your input files don't have.
You could do something like this using paste and awk:
paste a01 b01 | awk '{n=NF; for (i=n/2;i>0;i--) {$i = $i""$(i+n/2); NF--}} 1'
a=1 b=2
c=3 d=4
e=5 f=6
g=7 h=8 i=9
j=10 k=11 l=12
m=13 n=14 0=15
| join returns nothing |
1,560,507,233,000 |
I asked a similar question yesterday (Merging two tables including multiple ocurrence of column identifiers) but ran into a problem with unique lines.
I would like to merge two tables based on column 1:
File 1:
1 today
1 green
2 tomorrow
3 red
File 2:
1 a lot
1 sometimes
2 at work
2 at home
2 sometimes
3 new
4 a lot
5 sometimes
6 at work
Desired output (file 3):
1 today a lot
1 today sometimes
1 green a lot
1 green sometimes
2 tomorrow at work
2 tomorrow at home
2 tomorrow sometimes
3 red new
I came up with the following:
awk -F '[\t]' -v OFS='\t' '{i=$1;$1=x} NR==FNR{A[i]=$0;next} A[i]{print i,$0A[i]}' file2 file1 > file3
However, it gives me only:
1 today sometimes
2 tomorrow sometimes
3 red new
Please note that the solutions in the previous thread (join and awk) would give me a combination of the 2 files including all lines. I would like to have only the lines of file 1 (column 1 as the identifier) but report all matching occurrences in file 2.
Edit:
columns are tab separated
Real File 1:
fig|395961.4.peg.2627 Bacteria Cyanobacteria unknown unknown 1795
(Column1: fig... Column2: Bacteria... Column3 1795)
Real File 2:
fig|1000561.3.peg.1838 Cysteine desulfurase (EC 2.8.1.7) Test - Thiamin Cofactors, Vitamins, Prosthetic Groups, Pigments
(Column1: fig... Column2: Cysteine... Column3 Test...)
|
I would do this in Perl:
#!/usr/bin/env perl
use strict;
my (%file1,%file2);
## Open the 1st file
open(A,"file1");
while(<A>){
## Remove trailing newlines
chomp;
## Split the current line on tabs into the @F array.
my @F=split(/\t/);
## This is the tricky part. It adds fields 2-last
## to the hash $file1. The value of this hash is an array
## and the keys are the 1st fields. This will result in a list
## of all 1st fields and all their associated columns.
push @{$file1{$F[0]}},@F[1..$#F];
}
## Open the 2nd file
open(B,"file2");
while(<B>){
## Remove trailing newlines
chomp;
## Split the current line on tabs into the @F array.
my @F=split(/\t/);
## If the current 1st field was found in file1
if (defined($file1{$F[0]})) {
## For each of the columns associated with
## this 1st field in the 1st file.
foreach my $col (@{$file1{$F[0]}}) {
print "$F[0]\t$col\t@F[1..$#F]\n";
}
}
}
You could golf it into a (long) one-liner:
$ perl -lane 'BEGIN{open(A,"file1"); while(<A>){chomp; @F=split(/\t/);
push @{$k{$F[0]}},@F[1..$#F];} }
$k{$F[0]} && print "$F[0]\t@{$k{$F[0]}}\t@F[1..$#F]"' file2
1 today green a lot
1 today green sometimes
2 tomorrow at work
2 tomorrow at home
2 tomorrow sometimes
3 red new
If you're working with huge files, let it run a while.
| Merging two tables including multiple ocurrence of column identifiers and unique lines |
1,560,507,233,000 |
I have 2 set of files.
File one contains ID's
ex:
1111
2222
6666
3333
4444
File two contains ID and username:
1873 Neil
1111 Roger
7632 Tim
3333 Oscar
8723 Greg
4444 Roy
6666 Patrick
I want to extract the ID and username, but only the ones that has the same ID as in file 1.
I did the normal grep -f file1 file2, on two test files I made, with few Id's such as the ones i just posted. However, when i apply this to the two proper files, where file1 contains 3500 ID's and File2 contains 12000 ID's + Username, instead of extracting the 3500 lines that occur in both files, it extracts 12000 lines.
However, with the 2 test files, and a few dummy ID's it will only extract the correct ids and leave the others.
Any tip on what's wrong?
|
Try doing this using join instead of grep, this will be more suitable :
$ join <(sort file1) <(sort file2)
1111 Roger
3333 Oscar
4444 Roy
6666 Patrick
If your shell lack process substitutions <( ), you can do :
sort file1 > new_file1
sort file2 > new_file2
join new_file1 new_file2
Doc said :
join writes to standard output a line for each pair of input lines that have identical join fields.
See http://www.gnu.org/software/coreutils/manual/html_node/join-invocation.html
Notes :
The file need to be sorted on the sort key for join to work properly, that's why we uses some file descriptors in the background using process substitutions
See http://mywiki.wooledge.org/ProcessSubstitution , or http://mywiki.wooledge.org/BashFAQ/024 for a common use.
| Matching two files for similar first line |
1,560,507,233,000 |
I want to compare two CSV files with the following format. They not have headers. I want to compare them by a specific column (in this case, the 2nd one).
The source CSV files around 4-5GB, so loading them into memory is won't work.
If there's no matching column in old.csv, than every new line written into out.csv.
This 2nd column will be a html link, for the shake of simplicity, here one word only.
My question is it possible to achieve the same result with sed, awk, join, or grep?
old.csv
"person"|"john"|"smith"
"person"|"anne"|"frank"
"person"|"bob"|"macdonald"
"fruit"|"orange"|"banana"
"fruit"|"strawberry"|"fields"
"fruit"|"ringring"|"banana"
new.csv
"person"|"john"|"smith"
"person"|"anne"|"frank"
"person"|"bob"|"macdonald"
"fruit"|"orange"|"banana"
"fruit"|"strawberry"|"fields"
"glider"|"person"|"airport"
"fruit"|"ringring"|"banana"
"glider"|"person2"|"airport"
diff.py
#!/usr/bin/env python3
"""
Source: https://gist.github.com/davidrleonard/4dbeebf749248a956e44
Usage: $ ./csv-difference.py -d new.csv -s old.csv -o out.csv -c 1
"""
import sys
import argparse
import csv
def main():
parser = argparse.ArgumentParser(description='Output difference in CSVs.')
parser.add_argument('-d', '--dataset', help='A CSV file of the full dataset', required=True)
parser.add_argument('-s', '--subset', help='A CSV file that is a subset of the full dataset', required=True)
parser.add_argument('-o', '--output', help='The CSV file we should write to (will be overwritten if it exists', required=True)
parser.add_argument('-c', '--column', help='A number of the column to be compared (0 is column 1, 1 is column 2, etc.)', required=True, type=int)
args = parser.parse_args()
dataset_file = args.dataset
subset_file = args.subset
output_file = args.output
column_num = args.column
with open(dataset_file, 'r') as datafile, open(subset_file, 'r') as subsetfile, open(output_file, 'w') as outputfile:
data = {row[column_num]: row for row in csv.reader(datafile, delimiter='|', quotechar='"')}
subset = {row[column_num]: row for row in csv.reader(subsetfile, delimiter='|', quotechar='"')}
data_keys = set(data.keys())
subset_keys = set(subset.keys())
output_keys = data_keys - subset_keys
output = [data[key] for key in output_keys]
output_csv = csv.writer(outputfile, delimiter='|', quotechar='"', quoting=csv.QUOTE_ALL)
for row in output:
output_csv.writerow(row)
if __name__ == '__main__':
main()
sys.stdout.flush()
Which is generating out.csv
"glider"|"person"|"airport"
"glider"|"person2"|"airport"
|
Super simple with awk:
$ awk -F'|' 'NR == FNR {old[$2]; next} !($2 in old)' old.csv new.csv
"glider"|"person"|"airport"
"glider"|"person2"|"airport"
That stores the 2nd field of the old.csv file in the array named "old", and then for the new.csv file, it will print records where the 2nd field is not in the "old" array.
It is true that this will not respect any pipe character within quotes. For that, I like ruby's csv module:
ruby -rcsv -e '
old_col2 = []
old_data = CSV.foreach("./old.csv", :col_sep => "|") do |row|
old_col2 << row[1]
end
CSV.foreach("./new.csv", :col_sep => "|") do |row|
if not old_col2.include?(row[1])
puts CSV.generate_line(row, :col_sep => "|", :force_quotes => true)
end
end
'
| Merging two CSV compared by a specific column only |
1,560,507,233,000 |
I've been trying to use awk to merge two files when they have the same first column. Here are my example files:
FileA.txt
A2M 1
A4GALT 11
AAAS 35
AAGAB 7
FileB.txt
A4GALT 2
AAAS 17
AAGAB 7
As you can see, the second file is missing the entry for A2M. If I am missing an entry, then I want the entry to read 0 in the final output. As so:
A2M 1 0
A4GALT 11 2
AAAS 35 17
AAGAB 7 7
My lab mate suggested that I use awk since join isn't working properly for me. With some help, I've come up with this awk command:
awk -F "\t" 'FNR==NR {h[$1] = $2;next} BEGIN{ OFS = "\t"} {print $0,$2?h[$1]:"0"}' FileB.txt FileA.txt
However, my output does not output the 0 when there isn't a match in FileB.txt and instead prints nothing. Any idea about what's going wrong?
|
If you join two files, it's a job for join:
join -1 1 -2 1 -a 1 -o 1.1 -o 1.2 -o 2.2 -e "0" FileA.txt FileB.txt
Where:
-1 1 -2 1 defines the fields to join (in both files the 1st)
-a 1 to force join to print the unpairable lines from FileA.txt
-o 1.1 1.2 2.2 is the output format
and -e "0" defines the value to store in an empty field
The output:
A2M 1 0
A4GALT 11 2
AAAS 35 17
AAGAB 7 7
| Merge lines with matching first column |
1,560,507,233,000 |
I have a requirement of comparing the first column between 2 pipe delimited files and if they match, I need to replace the 3rd Column in File 1 with 4th Column in File 2.
File 1:
111|xyz|23345
222|abc|123
333|xyz|45667
444|xyz|5432
555|xyz|8976
File 2:
111|xyz|344|rtms
222|abc|222|xyzw
666|xyz|ggg|abde
888|xyz|ff|nnnn
333|xyz|dd|abde
444|xyz|vv|nnnn
555|xyz|bbb|uuyytt
Output File:
111|xyz|rtms
222|abc|xyzw
333|xyz|abde
444|xyz|nnnn
555|xyz|uuyytt
|
One-liner without the need for awk and a temporary file:
join -t '|' -j1 -o 1.1 1.2 2.4 <(sort -t'|' -k1,1 file1) <(sort -t '|' -k1,1 file2)
Using both join and awk:
First, sort file2 based on 1st field and save it it file2.sort
sort -k 1 file2 > file2.sort
Now, using "|" as the delimiter, join file1 and file2.sort. Then again using "|" as the delimiter, extract the necessary column using awk.
join -t '|' file1 file2.sort | awk -F "|" ' {print $1"|"$2"|"$6}'
THe output will be:
ron@ron:~$ join -t '|' file1 file2.sort | awk -F "|" ' {print $1"|"$2"|"$6}'
111|xyz|rtms
222|abc|xyzw
333|xyz|abde
444|xyz|nnnn
555|xyz|uuyytt
| Compare 1st Column in 2 Files and Replace 3rd Column of File 1 with 4th Column of File 2 |
1,350,877,526,000 |
I am having some issues with a script that is using join to join two files. Eaxmple input files contains lines like this:
Here are the input file and the output of the join command:
D:\work\BuildScripts\3C>cat D:\temp\aaa.txt
hzapplications\adn\adn4\adn4density\adn4_idd_module.cpp,83
hzapplications\adn\adn4\adn4density\adn4dencalmodule.cpp,73
hzapplications\adn\adn4\adn4density\adn4denimagemodulerm.cpp,111
hzapplications\adn\adn4\adn4density\adn4denimagemodulert.cpp,202
hzapplications\adn\adn4\adn4density\adn4densityanqmodules.cpp,445
hzapplications\adn\adn4\adn4density\adn4densityappl.cpp,378
hzapplications\adn\adn4\adn4density\adn4densityappl.h,50
hzapplications\adn\adn4\adn4density\adn4densityevrmodules.cpp,272
hzapplications\adn\adn4\adn4density\adn4densitykernel.cpp,490
hzapplications\adn\adn4\adn4density\adn4densitykernel.h,65
hzapplications\adn\adn4\adn4density\adn4densitysecimgmodule.cpp,209
hzapplications\adn\adn4\adn4density\adn4densitysecimgmodule.h,70
hzapplications\adn\adn4\adn4density\adn4densitysecmodule.cpp,218
hzapplications\adn\adn4\adn4density\adn4densitysecmodule.h,70
hzapplications\adn\adn4\adn4density\adn4dphimodules.cpp,610
hzapplications\adn\adn4\adn4density\adn4dphimodulesrt.cpp,115
hzapplications\adn\adn4\adn4density\adn4rhomodulesrt.cpp,102
D:\work\BuildScripts\3C>cat D:\temp\bbb.txt
hzapplications\activect\ptc\ictsx01\ictsx01_bootuptask.cpp,1
hzapplications\activeps\iola\acquisition\iola_acqmodule.cpp,4
hzapplications\activeps\iola\simulation\iola_simmodule.cpp,3
hzapplications\activeps\iolr\simulation\iolr_simmodule.cpp,1
hzapplications\activeps\iolr\task\iolr_poweron200vhitask.cpp,1
hzapplications\activeps\iolr\task\iolr_poweron200vlowtask.cpp,1
hzapplications\activeps\iolr\task\iolr_poweronnrlvtask.cpp,1
hzapplications\activeps\iolr\task\iolrtaskcommon.cpp,2
hzapplications\adn\adn4\adn4density\adn4densitykernel.cpp,1
hzapplications\adn\adn4\adn4equipment\adn4adseelem.cpp,1
hzapplications\adn\adn4\adn4equipment\adn4collar.cpp,1
hzapplications\adn\adn4\adn4equipment\adn4tool.cpp,2
hzapplications\adn\adn6c\adn6cequipment\adn6ccollar.cpp,1
hzapplications\adn\adn8\adn8equipment\adn8tool.cpp,1
hzapplications\adn\adn8\adn8neutron\adn8neutronkernel.cpp,1
hzapplications\adn\adn8d\adn8ddensity\adn8ddensitykernel.cpp,1
hzapplications\adn\adn8d\adn8dequipment\adn8dtool.cpp,1
D:\work\BuildScripts\3C>join --ignore-case -1 1 -2 1 -t"," -o "1.1,1.2,2.2" -e "0" -a 1 D:\temp\aaa.txt D:\temp\bbb.txt
hzapplications\adn\adn4\adn4density\adn4_idd_module.cpp,83,0
hzapplications\adn\adn4\adn4density\adn4dencalmodule.cpp,73,0
hzapplications\adn\adn4\adn4density\adn4denimagemodulerm.cpp,111,0
hzapplications\adn\adn4\adn4density\adn4denimagemodulert.cpp,202,0
hzapplications\adn\adn4\adn4density\adn4densityanqmodules.cpp,445,0
hzapplications\adn\adn4\adn4density\adn4densityappl.cpp,378,0
hzapplications\adn\adn4\adn4density\adn4densityappl.h,50,0
hzapplications\adn\adn4\adn4density\adn4densityevrmodules.cpp,272,0
hzapplications\adn\adn4\adn4density\adn4densitykernel.cpp,490,0
hzapplications\adn\adn4\adn4density\adn4densitykernel.h,65,0
hzapplications\adn\adn4\adn4density\adn4densitysecimgmodule.cpp,209,0
hzapplications\adn\adn4\adn4density\adn4densitysecimgmodule.h,70,0
hzapplications\adn\adn4\adn4density\adn4densitysecmodule.cpp,218,0
hzapplications\adn\adn4\adn4density\adn4densitysecmodule.h,70,0
hzapplications\adn\adn4\adn4density\adn4dphimodules.cpp,610,0
hzapplications\adn\adn4\adn4density\adn4dphimodulesrt.cpp,115,0
hzapplications\adn\adn4\adn4density\adn4rhomodulesrt.cpp,102,0
D:\work\BuildScripts\3C>
The expected output is that this particular line is joined like so:
hzapplications\adn\adn4\adn4density\adn4densitykernel.cpp,490,1
Any suggests are most welcome. I am using the unxutils package on windows, this is the exact version:
D:\work\BuildScripts\3C>join --version
join (GNU textutils) 2.0
Written by Mike Haertel.
Copyright (C) 1999 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
|
It turns out that --ignore-case is the problem. It has an effect even when there are no uppercase letters because it treats all lowercase letters as uppercase, causing them to jump to the other side of the characters that are between the uppercase and lowercase in ASCII order: [\]^_
In normal sorted order, iolrt comes after iolr_ but in --ignore-case order they are reversed.
The sort command needs the -f option to produce the correct order. (In addition to -t, and -k1,1)
| Using join with two files fails on larger file sizes |
1,350,877,526,000 |
My files:
file1.txt
=========
key1
key1
key1
key1
key2
key2
key3
key3
key3
key4
key4
file2.txt
=========
key1 22
key2 23
key3 24
Expected Output :
==================
key1 22
key1 22
key1 22
key1 22
key2 23
key2 23
key3 24
key3 24
key3 24
All solutions that I found does not duplicate matches strings.
awk '{a[$1]=a[$1]" "$2} END{for(i in a)print i, a[i]}'
join -a 1
What needs to be modified in this approaches to result in a left outer join?
|
Awk solution:
awk 'NR==FNR{ a[$1]=$2; next }$1 in a{ $2=a[$1]; print }' file2.txt file1.txt
The output:
key1 22
key1 22
key1 22
key1 22
key2 23
key2 23
key3 24
key3 24
key3 24
Or simply with join command:
join -o1.1,2.2 file1.txt file2.txt
| LEFT (OUTER) JOIN [duplicate] |
1,350,877,526,000 |
I have many files like following in a directory "results"
58052 results/TB1.genes.results
198003 results/TB1.isoforms.results
58052 results/TB2.genes.results
198003 results/TB2.isoforms.results
58052 results/TB3.genes.results
198003 results/TB3.isoforms.results
58052 results/TB4.genes.results
198003 results/TB4.isoforms.results
For eg: TB1.genes.results file looks like following:
gene_id transcript_id(s) length effective_length expected_count TPM FPKM
ENSG00000000003 ENST00000373020,ENST00000494424,ENST00000496771,ENST00000612152,ENST00000614008 2206.00 1997.20 1.00 0.00 0.01
ENSG00000000005 ENST00000373031,ENST00000485971 940.50 731.73 0.00 0.00 0.00
ENSG00000000419 ENST00000371582,ENST00000371584,ENST00000371588,ENST00000413082,ENST00000466152,ENST00000494752 977.15 768.35 1865.00 14.27 37.82
ENSG00000000457 ENST00000367770,ENST00000367771,ENST00000367772,ENST00000423670,ENST00000470238 3779.11 3570.31 1521.00 2.50 6.64
ENSG00000000460 ENST00000286031,ENST00000359326,ENST00000413811,ENST00000459772,ENST00000466580,ENST00000472795,ENST00000481744,ENST00000496973,ENST00000498289 1936.74 1727.94 1860.00 6.33 16.77
ENSG00000000938 ENST00000374003,ENST00000374004,ENST00000374005,ENST00000399173,ENST00000457296,ENST00000468038,ENST00000475472 2020.10 1811.30 6846.00 22.22 58.90
ENSG00000000971 ENST00000359637,ENST00000367429,ENST00000466229,ENST00000470918,ENST00000496761,ENST00000630130 2587.83 2379.04 0.00 0.00 0.00
ENSG00000001036 ENST00000002165,ENST00000367585,ENST00000451668 1912.64 1703.85 1358.00 4.69 12.42
ENSG00000001084 ENST00000229416,ENST00000504353,ENST00000504525,ENST00000505197,ENST00000505294,ENST00000509541,ENST00000510837,ENST00000513939,ENST00000514004,ENST00000514373,ENST00000514933,ENST00000515580,ENST00000616923 2333.50 2124.73 1178.00 3.26 8.64
Other files also has the same columns. To join all "genes.results" with "gene_id" and "expected_count" columns into one text file I gave the following command.
paste results/*.genes.results | tail -n+2 | cut -f1,5,12,19,26 > final.genes.rsem.txt
[-f1 (gene_id), 5 (expected_count column from TB1.genes.results), 12 (expected_count column from TB2.genes.results),
19 (expected_count column from TB3.genes.results), 26 (expected_count column from TB4.genes.results)]
"final.genes.rsem.txt" has, selected gene_id and expected_count columns from every file.
ENSG00000000003 1.00 0.00 3.00 2.00
ENSG00000000005 0.00 0.00 0.00 0.00
ENSG00000000419 1865.00 1951.00 5909.00 8163.00
ENSG00000000457 1521.00 1488.00 849.00 1400.00
ENSG00000000460 1860.00 1616.00 2577.00 2715.00
ENSG00000000938 6846.00 5298.00 1.00 2.00
ENSG00000000971 0.00 0.00 6159.00 7069.00
ENSG00000001036 1358.00 1186.00 6196.00 7009.00
ENSG00000001084 1178.00 1186.00 631.00 1293.00
My question is - As I have only few samples I gave the column number in the command [like this in "cut" -f1,5,12,19,26]. What I should do if I have more than 100 samples. How can I join them with required columns?
|
GNU awk is used. I put this command in the bash script. It will be more convenient.
Usage: ./join_files.sh or, for pretty printing, do: ./join_files.sh | column -t.
#!/bin/bash
gawk '
NR == 1 {
PROCINFO["sorted_in"] = "@ind_num_asc";
header = $1;
}
FNR == 1 {
file = gensub(/.*\/([^.]*)\..*/, "\\1", "g", FILENAME);
header = header OFS file;
}
FNR > 1 {
arr[$1] = arr[$1] OFS $5;
}
END {
print header;
for(i in arr) {
print i arr[i];
}
}' results/*.genes.results
Output (I created three files with the same content for testing)
$ ./join_files.sh | column -t
gene_id TB1 TB2 TB3
ENSG00000000003 1.00 1.00 1.00
ENSG00000000005 0.00 0.00 0.00
ENSG00000000419 1865.00 1865.00 1865.00
ENSG00000000457 1521.00 1521.00 1521.00
ENSG00000000460 1860.00 1860.00 1860.00
ENSG00000000938 6846.00 6846.00 6846.00
ENSG00000000971 0.00 0.00 0.00
ENSG00000001036 1358.00 1358.00 1358.00
ENSG00000001084 1178.00 1178.00 1178.00
Explanation - the same code with comments added. Also, look at the man gawk.
gawk '
# NR - the total number of input records seen so far.
# If the total line number is equal 1
NR == 1 {
# If the "sorted_in" element exists in PROCINFO, then its value controls
# the order in which array elements are traversed in the (for in) loop.
# else the order is undefined.
PROCINFO["sorted_in"] = "@ind_num_asc";
# Each field in the input record may be referenced by its position: $1, $2, and so on.
# $1 - is the first field or the first column.
# The first field in the first line is the "gene_id" word;
# Assign it to the header variable.
header = $1;
}
# FNR - the input record number in the current input file.
# NR is the total lines counter, FNR is the current file lines counter.
# FNR == 1 - if it is the first line of the current file.
FNR == 1 {
# remove from the filename all unneeded parts by the "gensub" function
# was - results/TB1.genes.results
# become - TB1
file = gensub(/.*\/([^.]*)\..*/, "\\1", "g", FILENAME);
# and add it to the header variable, concatenating it with the
# previous content of the header, using OFS as delimiter.
# OFS - the output field separator, a space by default.
header = header OFS file;
}
# some trick is used here.
# $1 - the first column value - "gene_id"
# $5 - the fifth column value - "expected_count"
FNR > 1 {
# create array with "gene_id" indexes: arr["ENSG00000000003"], arr["ENSG00000000419"], so on.
# and add "expected_count" values to it, separated by OFS.
# each time, when the $1 equals to the specific "gene_id", the $5 value will be
# added into this array item.
# Example:
# arr["ENSG00000000003"] = 1.00
# arr["ENSG00000000003"] = 1.00 2.00
# arr["ENSG00000000003"] = 1.00 2.00 3.00
arr[$1] = arr[$1] OFS $5;
}
END {
print header;
for(i in arr) {
print i arr[i];
}
}' results/*.genes.results
| How to join files with required columns in linux? |
1,350,877,526,000 |
I have two very large text files with space-delimited fields:
File1
527858 51 2 27.92464882 8.63E-07
570289 82 2 30.12532071 2.87E-07
571034 90 2 29.26089611 4.43E-07
571033 90 2 28.56723908 6.26E-07
452403 104 2 28.27577506 7.24E-07
351390 100 2 28.16226794 7.67E-07
527858 50 2 27.92464882 8.63E-07
File2
527858 rs435
570289 rs564
571034 rs654
571033 rs345
452403 rs665
351390 rs787
527858 rs435
output:
rs435 51 2 27.92464882 8.63E-07
rs564 82 2 30.12532071 2.87E-07
rs654 90 2 29.26089611 4.43E-07
rs345 90 2 28.56723908 6.26E-07
rs665 104 2 28.27577506 7.24E-07
rs787 100 2 28.16226794 7.67E-07
rs435 50 2 27.92464882 8.63E-07
Compare the first column of file1 and file2 and replace the first column of file1 with names in 2nd column of file2.
|
Here's the same basic idea as the awk in Archemar's answer, implemented in Perl:
$ perl -lane '$#F>1?print"$l{$F[0]} @F[1..$#F]":($l{$F[0]}=$F[1])' file2 file1
rs435 51 2 27.92464882 8.63E-07
rs564 82 2 30.12532071 2.87E-07
rs654 90 2 29.26089611 4.43E-07
rs345 90 2 28.56723908 6.26E-07
rs665 104 2 28.27577506 7.24E-07
rs787 100 2 28.16226794 7.67E-07
rs435 50 2 27.92464882 8.63E-07
Explanation
-lane: the -l adds a newline to each print call and removes trailing newlines from each line of input. The -a makes perl act like awk: it will automatically split each input line into the array @F. So, the 1st field will be $F[0], the second $F[1] etc. The -n tells perl to read its input file(s) line by line and apply the script given with -e to each of them.
$#F>1? ... : ... : this is a C-style conditional operator. The general format is condition ? foo : bar which means "if condition is true, do foo and if it isn't, do bar. The $#F is the number of array indices in the array @F. Since arrays begin at 0, a value of 1 means an array with two elements. So, this will execute the first block (print ..., see below) if there are more than 2 elements in the array, which will only be true for file1.
($l{$F[0]}=$F[1]) : this is executed for each line of file2, for each line with less than 3 fields. It populates the hash %l, whose keys are the numerical first fields of file2 and whose values are the associated rsIDs.
print"$l{$F[0]} @F[1..$#F]" : print the rsID saved in the hash %l for this first field ($l{$F[0]}), a space, and then the rest of the fields in this line ($F[1..$#F]).
Personally, I would probably use the awk solution or, at worst, the perl one I provided since they don't need the files to be sorted. However, since you tagged with join, here's how to do it using that tool:
$ join -o 2.2 1.2 1.3 1.4 1.5 <(sort file1) <(sort file2)
rs787 100 2 28.16226794 7.67E-07
rs665 104 2 28.27577506 7.24E-07
rs435 50 2 27.92464882 8.63E-07
rs435 50 2 27.92464882 8.63E-07
rs435 51 2 27.92464882 8.63E-07
rs435 51 2 27.92464882 8.63E-07
rs564 82 2 30.12532071 2.87E-07
rs345 90 2 28.56723908 6.26E-07
rs654 90 2 29.26089611 4.43E-07
| match columns and replace |
1,350,877,526,000 |
I have an invnentory file with a group of servers defined
[prod]
prod1 ansible_host=10.10.2.30
prod2 ansible_host=10.10.2.40
prod3 ansible_host=10.10.2.50
prod4 ansible_host=10.10.2.60
I want to define a variable that concatenates all servers in prod group delimited by comma.
lets say variable is list, variable should contain values like
list: "prod1_IP,prod2_IP,prod3_IP,prod4_IP"
list: "10.10.2.30,10.10.2.40,10.10.2.50,10.10.2.60"
one could easily put these manually, but catch is, list is supposed to expand in different scenrios.
I guess one can use hostvars[item].ansible_host with for loop. but not sure how
|
The playbook below does the job
- hosts: prod
gather_facts: false
tasks:
- block:
- set_fact:
list1: "{{ ansible_play_hosts_all|product(['_IP'])|map('join')|
join(',') }}"
- debug:
var: list1
- set_fact:
list2: "{{ ansible_play_hosts_all|map('extract', hostvars, 'ansible_host')|
join(',') }}"
- debug:
var: list2
run_once: true
gives
list1: prod1_IP,prod2_IP,prod3_IP,prod4_IP
list2: 10.10.2.30,10.10.2.40,10.10.2.50,10.10.2.60
| how to fetch ansible inventory & populate in an ansible variable? |
1,350,877,526,000 |
I've been trying to merge two big files based on two key columns (Chromosome and Position) and I found out that the most efficient way seems to be awk.
A sample of how my files look like is:
file1.txt
Gene_ID Chromosome Position Fst
ENSG00000141424 18 33688658 0
ENSG00000141424 18 33688669 0
ENSG00000141424 18 33688681 0
ENSG00000141424 18 33688683 0.0111734
ENSG00000141424 18 33688720 0
ENSG00000141424 18 33688726 0
ENSG00000141424 18 33688743 0
ENSG00000141424 18 33688745 0
ENSG00000141424 18 33688763 0
And the other file:
file2.txt
Chromosome Start End Ref Alt RS_ID
1 10019 10020 TA T rs775809821
1 10020 10020 A - rs775809821
1 10055 10055 - A rs768019142
1 10055 10055 T TA rs768019142
1 10108 10108 C T rs62651026
1 10109 10109 A T rs376007522
1 10128 10128 A AC rs796688738
1 10128 10128 - C rs796688738
1 10139 10139 A T rs368469931
1 10144 10145 TA T rs144773400
I want to get a third file looking like this:
Gene_ID Chromosome Position RS_ID Fst
ENSG00000141424 18 33688658 rs1504554... 0
I've tried using awk and I think the syntax is OK but what I get is a file containing file1.txt and file2.txt concatenated.
awk 'FS=" "; OFS=" ";NR=FNR{A[$1,$2]=$6;next}{$5=A[$2,$3];print}' file1.txt file2.txt > file3.txt
Any ideas of what I might be doing wrong?
|
A few correction of your code should fix it
awk 'NR==FNR{A[$1,$2]=$6;next}{$5=A[$2,$3];if($5!="")print}' file2.txt file1.txt
NR==FNR instead of NR=FNR is the condition when awk runs through the first file file2.txt
On the second run when NR!=FNR we print out the line if there exists a join key in A
The default field separator for awk is already a whitespace, so no need to specify them here
| Joining two files based on two key columns awk |
1,350,877,526,000 |
I want to join two files according to number in the file, two number same file
Toyota model1
BMW model2
Benz model3
BMW model4
BMW model5
Benz model6
Benz model7
and second file
class C model1
class E model2
class A model3
class W model4
class W model5
class C model6
class A model7
I want to join the two file according to the number, like this, joining each model number with each other in one file.
Toyota class C model1
BMW class E model2
Benz class A model3
BMW class W model4
BMW class W model5
Benz Class C model6
Benz Class A model7
after that delete the 'model' string
My code,
sort -V file1 > new_file1
sort -V file2 > new_file2
join newfile1 new_file2 > result.txt
sed 's/model[(1-9)]//g' result.txt > result_1.txt
the problem I'm getting an Error while joining the files
join: file1.txt:10: is not sorted: 03Benz model 249
join: file2.txt:4: is not sorted: BMW model 2
what if I want to count frequency after that
( this pair happen in the text 2 times) after joined
Toyota class C 1
BMW class E 1
Benz class A 2
BMW class W 2
Benz Class C 1
|
Use join.
It looks like changing the first space character in the file to something other than space will be sufficient to convert the file whitespace-delimited records.
Here's an implementation that replaces the first space with % and then joins on the second column of each file.
$ cat file2 | sed -e 's/ /%/' | join -1 2 -2 2 - file1
or
$ <file2 sed -e 's/ /%/' | join -1 2 -2 2 - file1
which produces
model1 class%C Toyota
model2 class%E BMW
model3 class%A Benz
model4 class%W BMW
model5 class%W BMW
model6 class%C Benz
model7 class%A Benz
If you need to convert it to a tab-delimited format, you can use tr.
tr ' %' '\t '
| How to Sort and join according to Number/Counter inside the file? |
1,350,877,526,000 |
I'm trying to be a bit effective and need a script or command solution.
Say I make a file with 2 columns, or two files with one column, whichever is easier:
AA1 B2 ZZ1 YYY XX1
AA2 B2 ZZ2 YYY XX2
AA3 B3 ZZ3 YYY XX3
AA4 B4 ZZ4 YYY XX4
ZZ5 YYY XX5
ZZ6 YYY XX6
ZZ7 YYY XX7
There is an uneven number of entries. Now, I want to make a new file (preferably with some other input as well, though lets start here) that takes every value in the first column and combines that with every value in the second column (they will always have unequal number of lines) and outputs results as:
AA1 B2 ZZ1 YYY XX1
AA1 B2 ZZ2 YYY XX2
[...]
AA4 B4 ZZ1 YYY XX1
AA4 B4 ZZ2 YYY XX2
So, cycle through all values in column 1 in order, combining them with each value in column 2 in order.
|
Assuming you have the following files:
$ cat file1
ZZ1 YYY XX1
ZZ2 YYY XX2
ZZ3 YYY XX3
ZZ4 YYY XX4
ZZ5 YYY XX5
ZZ6 YYY XX6
ZZ7 YYY XX7
$ cat file2
AA1 B2
AA2 B2
AA3 B3
AA4 B4
Then use this awk:
awk 'FNR==NR{a[c++]=$0} FNR!=NR{for(i in a){print $0,a[i]}}' file1 file2
FNR==NR applies only to the first file file1
a[c++]=$0 fills an array called a with the contents of file1
FNR!=NR applies only to the second file file2
for(i in a) loops trough array a...
print $0,a[i] ...and print the line from file2 and the contents of the array.
The outout:
AA1 B2 ZZ1 YYY XX1
AA1 B2 ZZ2 YYY XX2
AA1 B2 ZZ3 YYY XX3
AA1 B2 ZZ4 YYY XX4
AA1 B2 ZZ5 YYY XX5
AA1 B2 ZZ6 YYY XX6
AA1 B2 ZZ7 YYY XX7
AA2 B2 ZZ1 YYY XX1
AA2 B2 ZZ2 YYY XX2
AA2 B2 ZZ3 YYY XX3
AA2 B2 ZZ4 YYY XX4
AA2 B2 ZZ5 YYY XX5
AA2 B2 ZZ6 YYY XX6
AA2 B2 ZZ7 YYY XX7
AA3 B3 ZZ1 YYY XX1
AA3 B3 ZZ2 YYY XX2
AA3 B3 ZZ3 YYY XX3
AA3 B3 ZZ4 YYY XX4
AA3 B3 ZZ5 YYY XX5
AA3 B3 ZZ6 YYY XX6
AA3 B3 ZZ7 YYY XX7
AA4 B4 ZZ1 YYY XX1
AA4 B4 ZZ2 YYY XX2
AA4 B4 ZZ3 YYY XX3
AA4 B4 ZZ4 YYY XX4
AA4 B4 ZZ5 YYY XX5
AA4 B4 ZZ6 YYY XX6
AA4 B4 ZZ7 YYY XX7
| Combine columns using awk? (Or other suggestions) |
1,350,877,526,000 |
I have 'FileA':
10 10011300 10011301 T C
10 10012494 10012495 G A
10 10028691 10028692 A T
10 10093496 10093497 G A
10 10102457 10102458 C T
10 10103252 10103253 G C
10 10122271 10122272 T C
10 10128778 10128779 T C
10 10130299 10130300 C A
10 10148307 10148308 G A
and I have files 1-22:
1 10177 rs367896724
1 10235 rs540431307
1 10352 rs555500075
1 10505 rs548419688
1 10506 rs568405545
1 10511 rs534229142
1 10539 rs537182016
1 10542 rs572818783
1 10579 rs538322974
1 10616 rs376342519
As you might be able to tell, I am dealing with genetic data. What I want to do is every time columns 1 and 3 from FileA match columns 1 and 2 from files 1-22, columns 1, 2 and 3 from files 1-22 (or columns 1 and 3 from FileA and column 3 from files 1-22) are printed into a text file with the number shared between FileA and files 1-22 in column 1 as the text file's name.
So far, I'm stuck on sorting the files to be able to invoke join. FileA keeps giving me an error, even though I am trying to sort it exactly the same way I was successfully able to sort files 1-22.
Essentially, what I am hoping for is a tutorial to do exactly the thing I am trying to do here. I have checked with multiple different sources and have attempted this several times to no avail.
Commands I have used:
sort -k 1,1 FileA.txt
join -j 1 File1.txt FileA.txt > output.txt
EDIT:
Here's a sample of the desired output
18 3320671 rs375411568
18 3320673 rs550898405
18 3320676 rs73366565
18 3320704 rs536519819
18 3320720 rs118037107
18 3320736 rs566910986
18 3320755 rs567626849
18 3320786 rs183777311
18 3320860 rs528977928
18 3320887 rs577743595
18 3320897 rs530122744
It looks very similar to the earlier example of files 1-22, and that's because it is essentially the same thing. I want for matches between columns 1 and 3 from FileA with columns 1 and 2 of the file x (x being any one file of a series of files numbered 1-22; in this example, 18), a line corresponding with the matching line of file x appears and is saved in output.txt.
|
Okay, I actually forgot I asked this question but someone just upvoted this post and I have since figured it out so I'll go ahead and post the answer.
For the first snippet of output I listed above,
10 10011300 10011301 T C
10 10012494 10012495 G A
10 10028691 10028692 A T
10 10093496 10093497 G A
10 10102457 10102458 C T
10 10103252 10103253 G C
10 10122271 10122272 T C
10 10128778 10128779 T C
10 10130299 10130300 C A
10 10148307 10148308 G A
all I needed to do was use the following awk command,
cat [inputfile.txt] | awk '{print $1"_"$3"\t"$4"\t"$5}' | sort -k1,1 > outputfileA.txt
The output would look like this and all rows would be sorted by the first column:
10_10011301 T C
10_10012495 G A
10_10028692 A T
10_10093497 G A
I would also do the same thing for the second snippet of code,
1 10177 rs367896724
1 10235 rs540431307
1 10352 rs555500075
1 10505 rs548419688
1 10506 rs568405545
and use a similar awk command to generate another file:
cat [inputfile.txt] | awk '{print $1"_"$2"\t"$3}' | sort -k1,1 > outputfileB.txt
Resulting in:
1_10177 rs367896724
1_10235 rs540431307
1_10352 rs555500075
1_10505 rs548419688
1_10506 rs568405545
Since both of these output files have one column in common, and those columns are sorted identically, we could then invoke the join command:
join -1 1 -2 2 outputfileA.txt outputfileB.txt | tr ' ' '\t' > outputfileC.txt
tr ' ' '\t' translates all whitespaces into tabs in the output. All lines with identical matches between the first column of the first file and the first column of the second file are written into the output file, which might look something like this:
1_101850899 A C rs138958619
1_101856556 T C rs191666242
1_101867058 C T rs188447998
1_101874381 A C rs143747209
1_101877269 G A rs186149522
1_101878704 C A rs192815769
1_101885657 G T rs150829467
1_101891797 T G rs141886478
1_101893793 T A rs182950692
1_101897192 T C rs189527356
I hope I explained that well. Let me know if I need to clarify anything.
| How do I compare one text file against about two dozen other text files and print out certain columns of each line whenever there is a match? |
1,350,877,526,000 |
I am trying join two files by one common column (1ª) between two file (File1 and file2), resulting in file 3, but the resultant file is not working. Can someone help me?
I used this command:
awk 'NR==FNR {h[$1] = $0; next} {print h[$1],$0}' file1 file2 > file3
File 1.
1 1767 0 1986 28061997 1 1 1 0 29031998 972 34176 9 1 9 9 55 97 42 1 0
2 1876 0 1986 25051995 1 1 1 0 22072000 952 30438 1 1 3 9 1009 95 25 4 0
3 5878 0 1986 16071996 1 1 1 0 22071997 963 30438 4 1 3 9 1009 96 40 4 0
File 2:
1 0 5 8 25031998 2 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 BX1001337 AX54651 BR909511 0
2 0 53 8 19021996 2 8 22031996 6 8 27051996 1 14 27051996 2 7 27051996 2 15 27051996 2 8 21021997 2 8 22031997 6 8 20041997 1 14 20041997 3 15 20041997 3 8 22071997 6 8 28091998 1 14 28091998 4 15 28091998 4 8 25061999 2 8 22091999 6 8 7032000 1 14 7032000 5 15 7032000 3 16 7032000 1 11 1071995
923 11 1101995 924 11 1011996 931 18 1011996 93 11 1041996 932 11 1071996 933 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 11 1041998 952 17 1041998 1005 11 1071998 953 17 1071998 1007 11 1101998 954 11 1011999 961 18 1011999 96 11 1041999 962 17 1041999 1009 11 1071999 963 17 1071999 1007 11 1101999 964 17 1101999 1003 11 1012000 971 18 1012000 97 17 1012000 1005 11 1042000 972 11 1072000 973 BR1001881 AX62116 BR872756 0
3 0 6 8 12041997 2 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 BR1003576 AX52602 BR830819 0
File3. It’s working wrong.Is putting the file 2 in 2ª line..
1 1767 0 1986 28061997 1 1 1 0 29031998 972 34176 9 1 9 9 55 97 42 1 0
1 1 0 5 8 25031998 2 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 BR1001337 AX54651 BR909511 0
2 1876 0 1986 25051995 1 1 1 0 22072000 952 30438 1 1 3 9 1009 95 25 4 0
2 4 0 53 8 19021996 2 8 22031996 6 8 27051996 1 14 27051996 2 7 27051996 2 15 27051996 2 8 21021997 2 8 22031997 6 8 20041997 1 14 20041997 3 15 20041997 3 8 22071997 6 8 28091998 1 14 28091998 4 15 28091998 4 8 25061999 2 8 22091999 6 8 7032000 1 14 7032000 5 15 7032000 3 16 7032000 1 11 1071995
923 11 1101995 924 11 1011996 931 18 1011996 93 11 1041996 932 11 1071996 933 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 11 1041998 952 17 1041998 1005 11 1071998 953 17 1071998 1007 11 1101998 954 11 1011999 961 18
1011999 96 11 1041999 962 17 1041999 1009 11 1071999 963 17 1071999 1007 11 1101999 964 17 1101999 1003 11 1012000 971 18 1012000 97 17 1012000 1005 11 1042000 972 11 1072000 973 BR1001881 AX62116 BR872756 0
3 5878 0 1986 16071996 1 1 1 0 22071997 963 30438 4 1 3 9 1009 96 40 4 0
3 4 0 6 8 12041997 2 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 BR1003576 AX52602 BR830819 0
File3. I would like that:
1 1767 0 1986 28061997 1 1 1 0 29031998 972 34176 9 1 9 9 55 97 42 1 0 0 5 8 25031998 2 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 BR1001337 AX54651 BR909511 0
2 1876 0 1986 25051995 1 1 1 0 22072000 952 30438 1 1 3 9 1009 95 25 4 0 0 53 8 19021996 2 8 22031996 6 8 27051996 1 14 27051996 2 7 27051996 2 15 27051996 2 8 21021997 2 8 22031997 6 8 20041997 1 14 20041997 3 15 20041997 3 8 22071997 6 8 28091998 1 14 28091998 4 15 28091998 4 8 25061999 2 8 22091999 6 8 7032000 1 14 7032000 5 15 7032000 3 16 7032000 1 11 1071995 923
11 1101995 924 11 1011996 931 18 1011996 93 11 1041996 932 11 1071996 933 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 11 1041998 952 17 1041998 1005 11 1071998 953 17 1071998 1007 11 1101998 954 11 1011999 961 18 1011999 96 11 1041999 962 17 1041999 1009 11 1071999 963 17 1071999 1007 11 1101999 964 17 1101999 1003 11 1012000 971 18 1012000 97 17 1012000 1005 11 1042000 972 11 1072000 973 BR1001881 AX62116 BR872756 0
3 5878 0 1986 16071996 1 1 1 0 22071997 963 30438 4 1 3 9 1009 96 40 4 0 0 6 8 12041997 2 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 BR1003576 AX52602 BR830819 0
|
Try this one liner!.
awk 'FNR==NR{A[$1]=$0;next}{line="";for(i=2;i<=NF;i++)line=line $i" ";sub(" $","",line);if ($1 in A)print A[$1]" "line;}' file1.txt file2.txt > file3
Out
1 1767 0 1986 28061997 1 1 1 0 29031998 972 34176 9 1 9 9 55 97 42 1 0 0 5 8 25031998 2 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 BX1001337 AX54651 BR909511 0
2 1876 0 1986 25051995 1 1 1 0 22072000 952 30438 1 1 3 9 1009 95 25 4 0 0 53 8 19021996 2 8 22031996 6 8 27051996 1 14 27051996 2 7 27051996 2 15 27051996 2 8 21021997 2 8 22031997 6 8 20041997 1 14 20041997 3 15 20041997 3 8 22071997 6 8 28091998 1 14 28091998 4 15 28091998 4 8 25061999 2 8 22091999 6 8 7032000 1 14 7032000 5 15 7032000 3 16 7032000 1 11 1071995 923 11 1101995 924 11 1011996 931 18 1011996 93 11 1041996 932 11 1071996 933 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 11 1101997 944 11 1011998 951 18 1011998 95 11 1041998 952 17 1041998 1005 11 1071998 953 17 1071998 1007 11 1101998 954 11 1011999 961 18 1011999 96 11 1041999 962 17 1041999 1009 11 1071999 963 17 1071999 1007 11 1101999 964 17 1101999 1003 11 1012000 971 18 1012000 97 17 1012000 1005 11 1042000 972 11 1072000 973 BR1001881 AX62116 BR872756 0
3 5878 0 1986 16071996 1 1 1 0 22071997 963 30438 4 1 3 9 1009 96 40 4 0 0 6 8 12041997 2 11 1101996 934 11 1011997 941 18 1011997 94 11 1041997 942 11 1071997 943 BR1003576 AX52602 BR830819 0
Saves in A lines from file1 by first column, starts reading file2, skips first column and saves fields in line, if first column in A concatenates both lines in one line and prints.
| How join two files by one common column (1ª) between two file (File1 and file2)? |
1,350,877,526,000 |
I have two unsorted files, each with two columns. For any line in file1 whose column1 value matches that of any line in file2, but whose column 2 values differ, I want to print the column 1 value and each column 2 value.
If data from column1 in file 1 does not exist in file2 it can be discarded. I do not need to preserve the sort order in the output file.
file1:
2222,b2
4444,d4
1111,a1
3333,c3
5555,e5
file2:
2222,8f
5555,e9
4444,7c
3333,c3
OUTPUT file:
2222,b2,8f
4444,d4,7c
5555,e5,e9
|
Read the 2nd file, save the content into an array (key = 1st field, value = 2nd field) then read the 1st file and check if 1st field is a common key and if the corresponding 2nd field is different. If the result is positive, print the key and the two values:
awk 'BEGIN{FS=OFS=","}NR==FNR{z[$1]=$2;next}
{if (z[$1] && (z[$1]!=$2)){print $0, z[$1]}}' file2 file1
| If column 2 of file2 is diferent than column2 of file1 print column1 from file1 and column2 from both files |
1,350,877,526,000 |
file1.txt (50 lines)
TERYUFV00000010753
TERYUFV00000009526
file2.txt (500 lines)
TERYUFV00000009526 refids_739_known_8/10_target
TERYUFV00000018907 refids_12023_known_21/22_target
TERYUFV00000010753 refids_11775_known_1/1_target
Output.txt
TERYUFV00000010753 refids_11775_known_1/1_target
TERYUFV00000009526 refids_739_known_8/10_target
Compare file1.txt (has 50 lines) with file2.txt (has 500 lines), get the list from file2.txt which are identical to file1.txt.
I tried both join & fgrep command and it outputs empty file
|
fgrep -f file1.txt file2.txt
Here we are obtaining search pattern from file1.txt and searching it in file2.txt.
As the text is fixed we are using fgrep for faster search operation.
| compare two files get identical list |
1,350,877,526,000 |
I have a CSV file that is like this
name;address;phone;email
John;123 La Sierra;555-121212;[email protected]
Nick;456 La Bongaa;555-121232;[email protected]
Carl;789 La Fountain;553-121212;[email protected]
and I want to remove the last entry making it be like
name;address;phone;
John;123 La Sierra;555-121212;
Nick;456 La Bongaa;555-121232;
Carl;789 La Fountain;553-121212;
The last ; has to be kept there but the last field removed.
I have found this code on a question of mine and adapted to this case
perl -000ne '@f=split(/;/); print join(";",@f[0..2]) , "\n"' myFile.csv
I thought it would split by ; and then join just fields 0, 1 and 2 but it is not working.
file command gives me this result about myFile.csv
UTF-8 Unicode text, with CRLF line terminators
The file contains accented characters that I think may interfere with this.
Any ideas?
|
Since I'm not sure you want a perl code so much, here is a similar awk code:
awk -F';' -v OFS=';' '{ $NF=""; print }' data.csv
=> This code empties the last field of each line ($NF=""). Input fields (-F\;) and output fields (OFS=';') are said to be separated with ";".
The same with sed:
sed 's/[^;]*$//' data.csv
=> This substitutes (s/.../.../) the longest sequence of characters that is not a ";" ([^;]*) at the end of the line ($) with nothing.
The same with grep:
grep -o '.*;' data.csv
=> grep regular expressions are greedy by default, that means that they match the longest sequence possible. Here .*; hence means "the longest sequence of characters that ends with a ";". The -o option outputs what is matched instead of the whole line.
Finally, a perl equivalent would be (thanks to @steeldriver):
perl -F';' -lpe '$F[-1]=""; $_ = join ";", @F' data.csv
=> It works similarly to awk, the joining being explicit here.
| Removing a field from a comma delimited text with accented chars |
1,350,877,526,000 |
I have two files--file1 and file2 that I want to join but some fields are missing in second file for which I want to insert string 'null'. One requirement is that the keys must be in the same order as in file1.
The input files and expected output result are as below:
file1.txt file2.txt
a 7 nah a anau
b 0 blah c bau
c 5 bah d cau
d 1 gah
e 0 hah
Expected output result:
a 7 nah anau
b 0 blah null
c 5 bah bau
d 1 gah cau
e 0 hah null
|
join + sort solution:
join -o1.1,1.2,1.3,2.2 -a1 -e"null" <(sort file1.txt) <(sort file2.txt)
The output:
a 7 nah anau
b 0 blah null
c 5 bah bau
d 1 gah cau
e 0 hah null
| Join two files, keep key order of first file and fill missing values with string 'null' |
1,350,877,526,000 |
I used the sort command to numerically sort file1.txt.
~]# sort -n -o file1.txt file1.txt
0 Barack
50 George
60 Ronald
100 Bill
The sort check command states the file is not sorted.
~]# sort -c file1.txt
sort: file1.txt:4: disorder: 100 Bill
I manually modify the file and place "100 Bill" second.
~]# cat file1.txt
0 Barack
100 Bill
50 George
60 Ronald
Now, the sort check command produces no stdout or stderr, meaning the file is properly sorted. Once properly sorted, I can now join the files. It seems that the first character is being used to know if the file is sorted instead of the entire integer.
sort -c file1.txt
Is there a way to sort the file so that "100 Bill" is on line 2? I cannot do this manually, as the real application of this issue deals with hundreds of lines of text processed by a daily job.
|
If you want to use a file with join, you need to make sure it’s sorted lexicographically on the join key, which means you shouldn’t use -n with sort. You can always sort the result of the join operation again numerically.
When you run sort -c, you need to specify the same sorting parameters as you used to sort the file: so if you want to check whether a file is sorted numerically, run sort -c -n.
Thus in your case, run sort -o file1.txt file1.txt to sort the file lexicographically for use with join (using the first field as the join field).
| Numeric sort fails to properly sort file |
1,350,877,526,000 |
I have two CSV files and am trying to merge them based on the first column in the first file matching the third column in the second file. They lines are not sorted.
file1.csv:
android,1,2
osx,2,5
file2.csv:
Converting,:Developer::|[E],android,Exact,,,,8,31
Converting,:Developer::|[E],osx,Exact,,,,8,31
Converting,:Developer::|[E],windows,Exact,,,,8,31
and would desire the following output.csv:
Converting,:Developer::|[E],android,Exact,,,,8,31,1,2
Converting,:Developer::|[E],osx,Exact,,,,8,31,2,5
Converting,:Developer::|[E],windows,Exact,,,,8,31,,
I have tried every example of
awk -F',' 'FNR==NR.....
that I could find on here but just cant seem to get it right.
|
You could use join for this
join -1 1 -2 3 -t ',' -a 2 -o 2.{1..9} 1.{2..3} <(sort file1.csv) <(sort file2.csv)
-1 and -2 specifies which field from the files to compare
-t specifies the seperator to use for the fields
-a 2 says to print lines in <file2> that do not match
-o configures the output based on <file>.<field>
| Compare columns from two CSVs and merge on matches |
1,350,877,526,000 |
I have 2 files and want to inner join them using awk. This is written using sql server :
SELECT [file1.column1],[file2.column2] FROM file1
INNER JOIN file2 on file2.column1 = file1.column5;
This is the file i want to join:
file1 :
file2:
so the key is column5 file1 and column1 file2.
How to write them in awk language?
Your help will be useful for me to learn this awk.
|
One way:
join -t"|" -1 5 -2 1 -o 1.1 2.2 file1 file2
-1 5 - Use the 5th column of file1
-2 1 - Use the 1st column of file2
-o 1.1 2.2 - Print as output 1st column of 1st file, 2nd column of 2nd file
| How to join 2 files based one key and selected some specific column? |
1,350,877,526,000 |
I have several lists with two fields - first field contain an URL, 2nd field an email-address (an account). The 2nd field is the same for all entries in a list.
I concatenate the lists to one list, and sort it by the 1st field. Most entries are unique, but some are duplicates or triplicates (ie. the URL was in the list for multiple accounts).
Is there a command or script that I can use to join the duplicates, so the 2nd field became a list of accounts when required?
For example:
url1 acct2
url2 acct1
url3 acct1
url3 acct2
url4 acct2
url4 acct3
url4 acct5
...
Should become:
url1 acct2
url2 acct1
url3 acct1 acct2
url4 acct2 acct3 acct5
...
|
With sort + awk pipeline:
sort -k1,1 file \
| awk 'url && $1 != url{ print url, acc }
{ acc = ($1 == url? acc FS:"") $2; url = $1 }END{ print url, acc }' OFS='\t'
Sample output:
url1 acct2
url2 acct1
url3 acct1 acct2
url4 acct2 acct3 acct5
| List sorted on 1st field, how can I join 2nd field on lines where 1st field is the same? |
1,350,877,526,000 |
I am a novice programmer. I am using unix's join command to self-join couple long files together.
join -j30 test test2
col1 col2 ... col30 col1 col2 ... col30
A B ZZZ ^M A B ZZZ
I am getting this ^M character in my output.
Why is it there? and How would I remove it?
EDIT:
Below is a screenshot of my part of my output
|
The ^M means you are bringing over/editing file in Windows.
Use the dos2unix command over the files to convert them to Unix text mode.
DOS uses carriage return and line feed "\r\n" as a line ending, while Unix uses just line feed "\n". The ^M are a visual representation of the "extra" \r characters.
To install the dos2unix command, do (on Debian-based distros):
sudo apt-get install dos2unix
or in a Mac (MacPorts):
sudo port install dos2unix
Alternatively, you can also do it with sed as in:
sed 's/\r$//' dosfile.txt > unixfile.txt
| How to fix unix `join` command inserting ^M between join columns? -Unix |
1,350,877,526,000 |
I'm struggling with this task:
I have two files:
file1 looks like:
102 13.342
103 7.456
105 6.453
107 3.567
108 4.210
file2 looks like:
0 098 0 0 0 -9 x
0 099 0 0 0 -9 x
0 100 0 0 0 -9 x
0 101 0 0 0 -9 x
0 102 0 0 0 -9 x
0 103 0 0 0 -9 x
0 104 0 0 0 -9 x
0 105 0 0 0 -9 x
0 106 0 0 0 -9 x
0 106 0 0 0 -9 x
0 107 0 0 0 -9 x
0 108 0 0 0 -9 x
And I want a file3 that looks like
0 098 0 0 0 -9 x
0 099 0 0 0 -9 x
0 100 0 0 0 -9 x
0 101 0 0 0 -9 x
0 102 0 0 0 13.342 x
0 103 0 0 0 7.456 x
0 104 0 0 0 -9 x
0 105 0 0 0 6.453 x
Basically, I want to join file1 and file2 by matching first and second fields in file1 and file2 respectively, keeping mismatches, and also, substituting the value of the sixth field in file2 with the value of the second field in file1 in each matching line...
I know this task is related with the use of:
join -a1 -a2 -o 1.2 whatsoever. But cannot figure it out how to continue... Also considering awk
|
When there are so many fields involved I tend to prefer awk:
$ awk 'NR==FNR{a[$1]=$2; next}{if($2 in a){$6=a[$2]}}1;' file1 file2
0 098 0 0 0 -9 x
0 099 0 0 0 -9 x
0 100 0 0 0 -9 x
0 101 0 0 0 -9 x
0 102 0 0 0 13.342 x
0 103 0 0 0 7.456 x
0 104 0 0 0 -9 x
0 105 0 0 0 6.453 x
0 106 0 0 0 -9 x
0 106 0 0 0 -9 x
0 107 0 0 0 3.567 x
0 108 0 0 0 4.210 x
Explanation
NR==FNR{a[$1]=$2; next} : NR is the current line number and FNR is the current line number of the current file. When processing more than one file, the two will be equal only while the 1st file is being read. a[$1]=$2 uses the st field as a key to an array whose value is the 2nd field. Thenextskips to the next line. So, this will save all values fromfile1into the arraya`.
if($2 in a){$6=a[$2]} : now we're reading the 2nd file. If the second field of this line is present in the array a, set the 6th field ($6) to be whatever was stored in a for the second field.
1; : this is shorthand for "print this line".
| Joining two files matching two columns with mismatches and in each matching line, substitute second column from file 1 into 6th column in file 2 |
1,350,877,526,000 |
Imagine that we have two for example files. The first file is filled with unique names of employees created by combining the first two characters of the first name and the last 2 characters of the last name. Example : Peter Smith - Peht
First file contains :
Peht
Mawo
Stso
Makr
Bavo
The second file contains recordings about them when they logged into the system. ( Obviously there are also employees that are not listed in file1. )
The second file:
Mawo 21.4.2016 17:49
Peht 21.4.2016 17:58
Mawo 22.4.2016 7:58
Wato 22.4.2016 7:59
Stso 22.4.2016 8:02
Bavo 22.4.2016 8:15
Bane 22.4.2016 9:01
Bavo 23.4.2016 9:12
Mawo 23.4.2016 9:24
Dalo 23.4.2016 9:54
Peht 23.4.2016 9:58
Grma 24.4.2016 10:00
I need to find out how many times employes from file1 connected to
the system ( file2 ).
What is the best way of doing that? The only solution which came to my mind is to make some 2 loops and for each name from file1 loop the whole file2 then grep names, ask if the names match if yes then count++. Could anyone give me some elegant solution for this problem using for example awk if it's possible?
|
Something simple like:
mapfile -t names < file1
for name in "${names[@]}"
do
echo "${name}" $(grep -c "^$name " file2)
done
Will provide output like:
Peht 2
Mawo 3
Stso 1
Makr 0
Bavo 2
The grep string says to anchor the username at the beginning (^) of the line, and enforce a trailing space after the line.
| Elegant way of counting how many times patterns from a file occur in another file |
1,350,877,526,000 |
I would like to create a simple bash function to use for my convenience. Following the answer given at: Joining bash arguments into single string with spaces I've been able to mash up this small piece of code:
function gcm {
msg="'$*'"
eval "git commit -m ${msg}"
}
Now, this example is very convenient for commit messages like "Hello, it's me" (simple set of word characters that is), but when I wan't a commit message like: "[WIP] Halfway trough code.", I get an error message as follows:
zsh: no matches found: [WIP]
Would you please clarify for me what is happening in the background and why this snippet fails?
|
ZSH is delightfully free of the word-splitting behaviour seen in other shells (unless for some bizarre reason the SH_WORD_SPLIT option has been turned on), so there is no need to use strange double-quoting constructs.
% (){ print -l $* } a b c
a
b
c
% (){ print -l "$*" } a b c
a b c
% (){ local msg; msg="$*"; print -l $msg } a b c
a b c
%
Thus, the following should suffice:
function gcm {
local msg
msg="$*"
git commit -m $msg
}
Globbing may be disabled by quoting strings like [WIP] as '[WIP]', or perhaps via a noglob alias:
% function blah { print -l "$*" }
% alias blah='noglob blah'
% blah [de] *blah*
[de] *blah*
%
| ZSH, concatenate passed in arguments into a single string |
1,350,877,526,000 |
I'm trying to join two files removing duplicate head row and take only 1 last row
for example:
File1.txt
head1
data1
data2
tail8
File2.txt
head1
data3
data4
tail9
results desired in file3.txt:
head1
data1
data2
data3
data4
tail8 or rail9 doesn't matter
I try first this to remove duplicate head:
awk '!seen[$0]++' file1.txt file2.txt > file3.txt
second command is:
awk 'NR > 1 { print prev } { prev = $0 }' file3.txt > file4.txt
but result is with tail in the middle of file4.txt, not to the end
head1
data1
data2
tail8
data3
data4
Any idea? Thank you in advance
|
$ awk 'NR==FNR{ if (NR>1) print prev; prev=$0; next } FNR>1' file1 file2
head1
data1
data2
data3
data4
tail9
| Merge two file skip last row of 1 file with awk |
1,350,877,526,000 |
I have a text file with format word @@@ type @@@ sentence on every line, sorted by 'word' in ascending order. Some lines however are not unique and they begin with the same word as the previous line, ie see word1 below:
...
word0 @@@ type2 @@@ sentence0
word1 @@@ type1 @@@ sentence1
word1 @@@ type1 @@@ sentence2
word1 @@@ type1 @@@ sentence3
word1 @@@ type2 @@@ sentence4
word2 @@@ type1 @@@ sentence5
...
I want to join the lines that have the same word and type combination into one, by appending the sentences, so the file results in:
...
word0 @@@ type2 @@@ sentence0
word1 @@@ type1 @@@ sentence1 ;;; sentence2 ;;; sentence3
word1 @@@ type2 @@@ sentence4
word2 @@@ type1 @@@ sentence5
...
The word and type fields have no whitespace.
|
Assuming your input is sorted on both word and type fields as it appears from your posted sample input:
$ cat tst.awk
BEGIN { FS=" @@@ "; ORS="" }
{ curr = $1 FS $2 }
curr != prev {
printf "%s%s", ORS, $0
prev = curr
ORS = RS
next
}
{ printf " ;;; %s", $NF }
END { print "" }
$ awk -f tst.awk file
word0 @@@ type2 @@@ sentence0
word1 @@@ type1 @@@ sentence1 ;;; sentence2 ;;; sentence3
word1 @@@ type2 @@@ sentence4
word2 @@@ type1 @@@ sentence5
The above will work using any awk in any shell on every UNIX box, only stores 1 line at a time in memory, and will produce output in the same order as the input.
| Merge following portions of lines into current line in a 3 column file |
1,350,877,526,000 |
I have a table A:
1 n m n ...
2 m n m ...
3 n m n ...
4 m n m ...
5 n m n ...
I have a table B:
1 A
3 B
5 C
I want to join the column 2 of table B with table A by matching column 1 of both tables, without removing the unique lines in table A to get the following (for no matches write a "NA"):
1 A n m n ...
2 NA m n m ...
3 B n m n ...
4 NA m n m ...
5 C n m n ...
|
From man join
-a FILENUM
also print unpairable lines from file FILENUM, where FILENUM is
1 or 2, corresponding to FILE1 or FILE2
-e EMPTY
replace missing input fields with EMPTY
so
join -a1 -e 'NA' -o 0,2.2,1.2,1.3,1.4 A B
1 A n m n
2 NA m n m
3 B n m n
4 NA m n m
5 C n m n
| Join without removing unique lines in Linux |
1,350,877,526,000 |
I have two files:
File1.txt
30 40 A T match1 string1
45 65 G R match2 string2
50 78 C Y match3 string3
File2.txt
match1 60 add1 50 add2
match2 15 add1 60 add2
match3 20 add1 45 add2
and I want to obtain an output that looks like so:
30 40 A T match1 string1 60 add1
45 65 G R match2 string2 15 add1
50 78 C Y match3 string3 20 add1
I want to append column 2 and column 3 from file2.txt to the end of file1.txt if there is a match in column 5 from file1.txt.
I've tried to use this join command:
join -1 5 -2 1 -a 1 -o 1.1 -o 1.2 -o 1.3 -o 1.4 -o 1.5 -o 1.6 -o 2.2 -o 2.3 file1.txt fil2.txt
However, this only seems to print the columns from the first file. Is there any other solutions other than join to tackle this problem?
|
I found a solution:
awk -F "\t" 'FNR==NR {a[$1] = $2 "\t" $3;next} $5 in a{print $0 "\t" a[$5]}' file2.txt file1.txt > outing.txt
| Joining columns from files if they contain a match in another column |
1,350,877,526,000 |
I have a file (file-1) that looks like this,
DIP-10097N|refseq:NP_416170|uniprotkb:P30015
DIP-10117N|refseq:NP_414973|uniprotkb:P08177
DIP-10168N|refseq:NP_418766|uniprotkb:P15005
DIP-10199N|refseq:NP_415632|uniprotkb:P30958
DIP-10358N|refseq:NP_418659|uniprotkb:P28903
DIP-10440N|refseq:NP_289596|uniprotkb:P20082
DIP-10441N|refseq:NP_417502|uniprotkb:P20083
DIP-10441N|refseq:NP_417502|uniprotkb:P20083
DIP-10467N|refseq:NP_415423|uniprotkb:P09373
DIP-10469N|refseq:NP_418386|uniprotkb:P32674
DIP-10562N|refseq:NP_418370|uniprotkb:P17888
DIP-10582N|refseq:NP_414864|uniprotkb:P77743
DIP-10592N|refseq:NP_415819|uniprotkb:P37344
and another (file-2) which looks like this,
DIP-10331N|refseq:NP_311078|uniprotkb:P12638 DIP-10117N|refseq:NP_414973|uniprotkb:P08177
DIP-10331N|refseq:NP_311078|uniprotkb:P12638 DIP-10840N|refseq:NP_414640|uniprotkb:P10408
DIP-1025N|refseq:NP_414574|uniprotkb:P00968 DIP-10097N|refseq:NP_416170|uniprotkb:P30015
DIP-10467N|refseq:NP_415423|uniprotkb:P09373 DIP-10097N|refseq:NP_416170|uniprotkb:P30015
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10117N|refseq:NP_414973|uniprotkb:P08177
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10750N|refseq:NP_289799|uniprotkb:P02410
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10757N|refseq:NP_288150|uniprotkb:P02421
In output I want to print the contents of file-1 plus the value in either column of file-2 that has the same value as that of file-1 in the other column. Like this,
DIP-10097N|refseq:NP_416170|uniprotkb:P30015 DIP-1025N|refseq:NP_414574|uniprotkb:P00968
DIP-10097N|refseq:NP_416170|uniprotkb:P30015 DIP-10467N|refseq:NP_415423|uniprotkb:P09373
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10117N|refseq:NP_414973|uniprotkb:P08177
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10750N|refseq:NP_289799|uniprotkb:P02410
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10757N|refseq:NP_288150|uniprotkb:P02421
DIP-10117N|refseq:NP_414973|uniprotkb:P08177 DIP-10331N|refseq:NP_311078|uniprotkb:P12638
DIP-10467N|refseq:NP_415423|uniprotkb:P09373 DIP-10097N|refseq:NP_416170|uniprotkb:P30015
Is there a way I can do it using awk or grep.
Any help would be highly appreciated.
|
This is wide known operation in awk — collect array from key-file then use the array to operate with second file values
awk '
FNR==NR{
A[$2] = A[$2] " " $1
next
}
$1 in A{
for(i=1;i<=split(A[$1], B);i++)
print $1 B[i]
}
' file2 file1
Or a little bit shorter:
awk '
FNR==NR{
A[$2] = A[$2] $2 " " $1 "\n"
next
}
$1 in A{
printf "%s", A[$1]
}
' file2 file1
Other variant
grep -f <(cat -E file1) file2 |
sed 's/\(\S*\)\s*\(\S*\)/\2\t\1/' |
sort
At last easiest (as for me):
join -2 2 file1 <(sort -k2 file2)
| Comapring columns in 2 files and printing the values that differ |
1,350,877,526,000 |
I'm trying to join two simple files in Solaris 5.8 Version as below:
~/temp/s: cat 1
work1 a 8058 51
work2 b 15336 51
~/temp/s: cat 2
8058 77-11:29:32 /apps/sas
15336 100-12:23:49 /local/hotfix
~/temp/s: join -1 3 -2 1 1 2
8058 work1 a 51 77-11:29:32 /apps/sas (The other line is missing from the output)
The output only contains one record where it should be two. I'm really not sure where it went wrong.
Is there any way we may get all the records in the output?
|
I think this might be a bug with join. I just tried it on Fedora 14 using this version of join:
$ join --version
join (GNU coreutils) 8.5
Example
$ join -1 3 -2 1 1 2
8058 work1 a 51 77-11:29:32 /apps/sas
15336 work2 b 51 100-12:23:49 /local/hotfix
Alternative
You could use awk to do this:
$ awk 'NR==FNR{_[$3]=$3;next}$1 in _{print _[$1],$0}' 1 2
8058 8058 77-11:29:32 /apps/sas
15336 15336 100-12:23:49 /local/hotfix
| Join command gives incorrect output? |
1,350,877,526,000 |
I have two files
file 1 contains
2*J=0 EXP= 0.00000
2*J=4 EXP= 1.27911
2*J=8 EXP= 1.57613
2*J=12 EXP= 1.69134
2*J=10 EXP= 2.72705
2*J=16 EXP= 4.55689
2*J=20 EXP= 5.62138
file 2 contains
2*J=0 EXC= 0.00000
2*J=8 EXC= 1.21836
2*J=4 EXC= 1.59642
2*J=12 EXC= 1.78359
2*J=10 EXC= 2.69484
2*J=16 EXC= 7.24518
2*J=20 EXC= 7.32688
I want to join the two files such that the output will be
2*J=0 EXP= 0.00000 EXC= 0.00000
2*J=4 EXP= 1.27911 EXC= 1.59642
2*J=8 EXP= 1.57613 EXC= 1.21836
2*J=12 EXP= 1.69134 EXC= 1.78359
2*J=10 EXP= 2.72705 EXC= 2.69484
2*J=16 EXP= 4.55689 EXC= 7.24518
2*J=20 EXP= 5.62138 EXC= 7.32688
|
with GNU awk, we can control how the output is sorted:
joiner.awk
#!/usr/bin/env -S gawk -f
FILENAME == ARGV[1] {
f1[$1] = $2 OFS $3
sort_key[$1] = $3
next
}
{
f2[$1] = $2 OFS $3
}
function sorter(idx1, val1, idx2, val2) {
return sort_key[idx1] - sort_key[idx2]
}
END {
PROCINFO["sorted_in"] = "sorter"
for (key in f1)
print key, f1[key], f2[key]
}
Then
$ gawk -f joiner.awk file1 file2
2*J=0 EXP= 0.00000 EXC= 0.00000
2*J=4 EXP= 1.27911 EXC= 1.59642
2*J=8 EXP= 1.57613 EXC= 1.21836
2*J=12 EXP= 1.69134 EXC= 1.78359
2*J=10 EXP= 2.72705 EXC= 2.69484
2*J=16 EXP= 4.55689 EXC= 7.24518
2*J=20 EXP= 5.62138 EXC= 7.32688
The "PROCINFO" magic is documented: https://www.gnu.org/software/gawk/manual/html_node/Controlling-Array-Traversal.html
| Join two files ordered numerically according to second column |
1,350,877,526,000 |
I am trying to compare second columns of two text files and print the first columns of both files if match.
I have tried the below awk codes but it was no use
1) awk 'NR==FNR {a[$2]=$2; next} {print $1,a[$1]}' nid8.txt nid9.txt
2) awk 'NR==FNR {a[$2]=$2; next} {print $1, $1 in a}' nid8.txt nid9.txt
Example files:
nid8.txt:
1000 500
1001 501
1002 502
1003 503
1004 504
1005 505
nid9.txt:
2000 504
2001 502
2002 508
2003 505
2004 500
2005 501
Output:
1000 2004
1001 2005
1002 2001
1004 2000
1005 2003
|
You can use join here:
join -j 2 -o 1.1 2.1 <(sort -nk2,2 nid8.txt) <(sort -nk2,2 nid9.txt)
Use the second field -j 2 on both files as the keys.
and -output these fields:
first field from the first file 1.1
first field from the second file 2.1
join requires input files to be sorted, so we sort them on the second field that will be used as the key numerically sort -nk2,2 input.
Using awk which not require to have sorted inputs but load first input file into memory:
awk '!second_file{ my_array[$2]=$1; next }
($2 in my_array) { print $1, my_array[$2] }' nid8.txt second_file=1 nid9.txt
with my_array[$2]=$1 we are saving first column of first input file nid8.txt only where the keys are the second column of the same first file until second_file variable value is not set to 1 which cause !second_file expression value evaluate to false and won't execute that block for next input(s).
With ($2 in my_array) condition we checks if the second field exist in our array my_array or not, if that was exist then we print first field $1 (which is from the second file) and the value for that same key with my_array[$2] which contains the first field from the first file with the same key.
| Compare second column of two text files and print first columns of both files if match |
1,350,877,526,000 |
I would like to perform script below but without creation of intermediate files (lsfs.out, df.out) on IBM AIX with ksh
lsfs_out=`lsfs | sed -n '1d;p' | sort -b -k 3`
df_out=`df -k | sed -n '1d;p' | sort -b -k 7`
echo "$lsfs_out" > lsfs.out
echo "$df_out" > df.out
join -1 7 -2 3 df.out lsfs.out
The output of the first command is like below:
lsfs | sed -n '1d;p' | sort -b -k 3
/dev/hd4 -- / jfs2 4194304 -- yes no
/dev/hd11admin -- /admin jfs2 1048576 -- yes no
The output of the second command is:
df -k | sed -n '1d;p' | sort -b -k 7
/dev/hd4 2097152 836284 61% 9360 5% /
/dev/hd11admin 524288 523848 1% 7 1% /admin
I can't understand how to replace file names for "join" command with commands output.
What I was trying was useless. For example:
join -1 7 -2 3 <(echo "$df_out") <(echo "$lsfs_out")
ksh: 0403-057 Syntax error: `(' is not expected.
one more
join -1 7 -2 3 <`echo "$df_out"` <`echo "$lsfs_out"`
A file or path name is too long.
< some output >
Cannot find or open the file.
|
an awk solution (can be onelined of course)
(df -k ; lsfs ) |
awk 'FNR==1 {next; }
NF==7 { L[$7]=$0 ; next ; }
{ printf "%s %s\n",$0,L[$3];}'
where
FNR==1 {next; } filter header
NF==7 { L[$7]=$0 ; next ; } store df line indexed on filesystem
{ printf "%s %s\n",$0,L[$3];} print lsfs line and join with df's
this suppose no filesystem has a space in path (original problem also)
| How to join results of two commands in IBM AIX ksh |
1,350,877,526,000 |
I can't seem to get either grep or awk to do a relatively simple index pull of a list. I suspect it's because of adjacent duplicates in the index file, something I wouldn't have thought would cause an issue. Oddly looking for a solution online wasn't successful as all the queries I found are people who want to remove duplicates, not keep them!
The Index file looks like this with ~40k entries, many being sorted duplicates:
n0000003
n0000003
n0000008
n0000008
n0000017
n0000017
n0000017
n0000017
.....etc
And the search file looks like this, with ~10k unique entries of each identifier:
n0000003 216 -0.334 0.229 0.088 0.154
n0000008 16 0.117 0.200 0.508 0.621
n0000017 218 -0.353 0.196 0.042 0.084
...etc
What I need is output like this, with repeat output entries equaling the number of repeat index entries in the index file:
n0000003 216 -0.334 0.229 0.088 0.154
n0000003 216 -0.334 0.229 0.088 0.154
n0000008 16 0.117 0.200 0.508 0.621
n0000008 16 0.117 0.200 0.508 0.621
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
...etc
But instead both grep and awk give only one entry each (making it identical to the search file). I figured a grep could handle repeat duplicates no problem but I can't find a workaround.
These are commands I would have expected to work for example:
grep -f index.txt searchfile.txt > output.txt
awk -F'\t' 'NR==FNR{c[$1]++;next};c[$1]' index.txt searchfile.txt > output.txt
Any advice on how I could get grep or awk to output the proper number of repeats would be great!
Thanks so much!
Andrew
|
I don't think you can do this with grep, no, but you can in awk. The simplest approach I can think of is to store the contents of searchfile.txt in memory and then print its lines each time you see an index:
$ awk -F'\t' 'NR==FNR{c[$1]=$0;next}{if(c[$1]){print c[$1]}}' searchfile.txt index.txt
n0000003 216 -0.334 0.229 0.088 0.154
n0000003 216 -0.334 0.229 0.088 0.154
n0000008 16 0.117 0.200 0.508 0.621
n0000008 16 0.117 0.200 0.508 0.621
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
If both files are sorted on the index, you can also use join:
$ join -t$'\t' searchfile.txt index.txt
n0000003 216 -0.334 0.229 0.088 0.154
n0000003 216 -0.334 0.229 0.088 0.154
n0000008 16 0.117 0.200 0.508 0.621
n0000008 16 0.117 0.200 0.508 0.621
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
n0000017 218 -0.353 0.196 0.042 0.084
| Is it possible to use grep or awk to report duplicate output lines corresponding to repeating entries in an index file? |
1,350,877,526,000 |
I would like to join data from two CSV files based on matching column information. The data to match is from File1.csv column 5, and File2 column 1, and i want to append the information from File2 column 2 upon match, and if no match leave empty double quotes.
File1.csv
"Z","P","W","K","1","1.18.24.59"
"S","K","D","X","9","1.14.19.238"
"R","M","P","Y","8","1.15.11.21"
"B","D","0","U","5","1.9.20.159"
"R","E","W","Q","6","135.0.0.1"
"K","D","K","R","9","1.9.74.13"
File2.csv
"65.9.7.19","374 22 53"
"1.9.74.13","123 256 51"
"1.18.24.59","23 25 41"
"1.15.11.21","98 77 8291"
"1.14.19.238","8827 145 8291"
"1.9.20.159","283 1 5734"
Desired Output
"Z","P","W","K","1","1.18.24.59","23 25 41"
"S","K","D","X","9","1.14.19.238","8827 145 8291"
"R","M","P","Y","8","1.15.11.21","98 77 8291"
"B","D","0","U","5","1.9.20.159","283 1 5734"
"R","E","W","Q","6","135.0.0.1",""
"K","D","K","R","9","1.9.74.13","123 256 51"
|
Here's one solution, using awk. Tested on GNU awk 4.1.3.
$ awk -F, 'NR==FNR{a[$1]=$2}NR!=FNR{print $0","(a[$6]?a[$6]:"\"\"")}' file2.csv file1.csv
"Z","P","W","K","1","1.18.24.59","23 25 41"
"S","K","D","X","9","1.14.19.238","8827 145 8291"
"R","M","P","Y","8","1.15.11.21","98 77 8291"
"B","D","0","U","5","1.9.20.159","283 1 5734"
"R","E","W","Q","6","135.0.0.1",""
"K","D","K","R","9","1.9.74.13","123 256 51"
$
The NR==FNR{a[$1]=$2 matches the lines in file2, and adds them into an array, keyed on field #1.
The NR!=FNR then matches the lines in file1.
print $0"," prints the whole line from file1 followed by a comma.
(a[$6]?a[$6]:"\"\"") prints the corresponding contents of the array built earlier, but just "" if no entry found.
| Join two CSV files based on matching column data |
1,542,262,746,000 |
I have two csv files:
file1:
C1, 1, 0, 1, 0, 1
C2, 1, 0, 1, 1, 0
C3, 0, 0, 1, 1, 0
file2:
C3, 1.2
C1, 2.3
C2, 1.8
I want to merge these two files based on C column (which produces):
C1, 1, 0, 1, 0, 1, 2.3
C2, 1, 0, 1, 1, 0, 1.8
C3, 0, 0, 1, 1, 0, 1.2
And then remove the second last column (to produce):
C1, 1, 0, 1, 0, 2.3
C2, 1, 0, 1, 1, 1.8
C3, 0, 0, 1, 1, 1.2
|
You just have create a hash-map on the second file on the C column and use that on the first file as below. The actions right next FNR==NR applies to the first file specified at the end and the subsequent action happens on the last file. This is because of the special variables in awk, FNR and NR which track line numbers per file and across the files respectively.
awk -v FS="," -v OFS="," 'FNR==NR { unique[$1]=$2; next } $1 in unique { $NF=unique[$1]; }1' file2 file1
| Joining two csv files on common column and removing the second last column |
1,542,262,746,000 |
From coreutils' manual about join
-e string
Replace those output fields that are missing in the input with
string. I.e., missing fields specified with the -12jo options.
I don't understand the option at all. What do the following mean
"those output fields that are missing in the input"
"missing fields specified with the -12jo options"?
Thanks.
|
The slightly cryptic string -12jo refers to the four separate options -1, -2, -j and -o, of which the first three has to do with selecting what field in each file to join on and the last has to do with what fields from each file should be outputted. The -j option is an extension in GNU join and and -j n is the same as -1 n -2 n (where n is some integer).
The -e option comes into effect when you, with -a, request to get unpaired lines from one or both of the files that you join. An unpaired line will have missing data, as the line from one file did not correspond to a line in the other file. The -e option replaces those fields with the given string. Likewise, if you request, with -o, a field that does not exist on a particular line in a file, you would use -e to replace the empty values with a string.
Example: Two files that contain manufacturing costs and sales income for a number of products. Each file has the fields
Product ID
Product name
Some number
$ cat expenses.txt
1 teacup 5
2 spoon 7
3 bowl 10
$ cat sales.txt
1 teacup 30
2 spoon 24
To get the expenses and sales for all products, while replacing the number (from either the first or second file) that may be missing with the string NONE, I would do
$ join -a1 -a2 -o0,1.2,1.3,2.3 -e NONE expenses.txt sales.txt
1 teacup 5 30
2 spoon 7 24
3 bowl 10 NONE
Here, I use the -a option twice to request all lines from both files (a "full outer join" in SQL speak). The -o option is used to get specific fields from each file (field 0 is the join field, which is the first field in each file by default), and -e to specify the string NONE to replace missing value with.
As you can see, we get NONE as the "sales value" since the product with ID 3 was not mentioned in that second file.
| What does `join -e` mean? |
1,542,262,746,000 |
I'm trying to identify all lines in common based on the first column of one file. I'm using the following command:
awk '{print $1}' File1 | fgrep -wf - File2 >Out
File1:
M01605:153:000000000-B55NK:1:1101:10003:14536 chr1 150129998 A Rev 18
M01605:153:000000000-B55NK:1:1101:10007:14573 chr17 44166311 C 38 44166311
M01605:153:000000000-B55NK:1:1101:10007:14573 chr17 44166500 G Rev 34
M01605:153:000000000-B55NK:1:1101:10009:9160 chr8 16716272 G 35 16716395
M01605:153:000000000-B55NK:1:1101:10009:9160 chr8 16716336 A 37 16716337
M01605:153:000000000-B55NK:1:1101:10009:9160 chr8 16716336 A 38 16716459
M01605:153:000000000-B55NK:1:1101:10010:14111 chr8 89574844 A 38 89574844
M01605:153:000000000-B55NK:1:1101:10010:19939 chr3 181151945 T 36 181151945
M01605:153:000000000-B55NK:1:1101:10011:22802 chr17 43984669 A 34 43984765
M01605:153:000000000-B55NK:1:1101:10011:22802 chr17 43984669 A 38 43984689
File2:
M01605:153:000000000-B55NK:1:1101:10003:14536 2:N:0:1 GTTTGCGCCGATGTA
M01605:153:000000000-B55NK:1:1101:10003:4882 2:N:0:1 GCACTGTAAAAAGTA
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10007:5336 2:N:0:1 GTGTTTGTGTAGCTA
M01605:153:000000000-B55NK:1:1101:10008:14477 2:N:0:1 GGGCGGAGGTGAAGA
M01605:153:000000000-B55NK:1:1101:10009:18543 2:N:0:1 AGTTCGAGCGCAGTG
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10010:14111 2:N:0:1 CTGCGTACTGATAGC
M01605:153:000000000-B55NK:1:1101:10010:19939 2:N:0:1 TCCGTGGTGCCGGCA
M01605:153:000000000-B55NK:1:1101:10011:22802 1:N:0:1 TGAGTTCGGATAAAG
Out:
M01605:153:000000000-B55NK:1:1101:10003:14536 2:N:0:1 GTTTGCGCCGATGTA
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10010:14111 2:N:0:1 CTGCGTACTGATAGC
M01605:153:000000000-B55NK:1:1101:10010:19939 2:N:0:1 TCCGTGGTGCCGGCA
M01605:153:000000000-B55NK:1:1101:10011:22802 1:N:0:1 TGAGTTCGGATAAAG
Expected Out:
M01605:153:000000000-B55NK:1:1101:10003:14536 2:N:0:1 GTTTGCGCCGATGTA
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10010:14111 2:N:0:1 CTGCGTACTGATAGC
M01605:153:000000000-B55NK:1:1101:10010:19939 2:N:0:1 TCCGTGGTGCCGGCA
M01605:153:000000000-B55NK:1:1101:10011:22802 1:N:0:1 TGAGTTCGGATAAAG
Note the bolded lines are missing from the actual output generated and are what I want to be in the output file.
It seems like grep is running correctly, but then condensing all identical lines down into only one output line. Any suggestions?
|
That's exactly what the join command is made for: it joins two files based on a common field:
$ awk '{print $1}' File1 | join - File2
M01605:153:000000000-B55NK:1:1101:10003:14536 2:N:0:1 GTTTGCGCCGATGTA
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10007:14573 2:N:0:1 GGGGATAAGCGTTGC
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10009:9160 2:N:0:1 CAGAAGAGGTAATGT
M01605:153:000000000-B55NK:1:1101:10010:14111 2:N:0:1 CTGCGTACTGATAGC
M01605:153:000000000-B55NK:1:1101:10010:19939 2:N:0:1 TCCGTGGTGCCGGCA
M01605:153:000000000-B55NK:1:1101:10011:22802 1:N:0:1 TGAGTTCGGATAAAG
M01605:153:000000000-B55NK:1:1101:10011:22802 1:N:0:1 TGAGTTCGGATAAAG
Your files may be sorted numerically but not alphabetically, as expected by join. If join is complaining, slightly modify the command above to sort the input with GNU sort:
$ awk '{print $1}' File1 | sort | join - <(sort -k1,1 --stable File2)
As your second file seems to have duplicated lines (see coments), you may want to change the second sort command to sort -k1,1 --stable --unique File2 (still assuming you are using GNU sort, use uniq).
| Grep not returning identical matches from awk pipe |
1,542,262,746,000 |
I have two files each containing a timestamp and a count as follows
File1.txt
9 2016-06-22
3 2016-06-23
2 2016-06-24
1 2016-06-25
2 2016-06-26
2 2016-06-27
File2.txt
3 2016-06-23
2 2016-06-25
5 2016-06-27
I would like to created an output where it uses the date column (col-3) in both the files and create an joined output which is as follows.
Expected result:
9 2016-06-22
3 3 2016-06-23
2 2016-06-24
1 2 2016-06-25
2 2016-06-26
2 5 2016-06-27
Using paste command is very complex and involves manual effort to get the expected output.Can someone help me with this ?
Thank you.
|
The best solution is to use the join command:
join -j 2 -a 1 -e " " -o 1.1 2.1 1.2 File1.txt File2.txt
Not the more elegant solution, but if you want to learn shell-script this should do the job:
while read line1; do
file1_number=$(echo ${line1} | cut -d ' ' -f 1)
file1_date=$(echo ${line1} | cut -d ' ' -f 2)
line2=$(grep ${file1_date} File2.txt)
file2_number=$(echo ${line2} | cut -d ' ' -f 1)
if [[ -z "${file2_number}" ]]; then
file2_number=" "
fi
echo ${file1_number} "${file2_number}" ${file1_date}
done < File1.txt
| Joining two file data based on column comparision |
1,542,262,746,000 |
file1:
0000002|SLM DEV CORP |PO 857
0000003|S TOPPING |APT 19
0000004|JD BROS LTD |PO 118
0000005|ZKZ SERVICES |14699 CREDITVIEW RD
file2:
0000001|GTI CONSULTING |4513 GLADEBROOK CRES
0000002|SLM DEVELOPMENT CORP | SLM |PO BOX 857
0000003|S TOPPING |APT 19
0000004|JD PLETT BROS LTD |PO BOX 118
0000005|ZKZ SERVICES |ZKZ |14699 CREDITVIEW RD
expected output:
0000002|SLM DEVELOPMENT CORP | SLM |PO BOX 857
0000003|S TOPPING |APT 19
0000004|JD PLETT BROS LTD |PO BOX 118
0000005|ZKZ SERVICES |ZKZ |14699 CREDITVIEW RD
I have tried join command:
join -j1 1 -j2 1 -t'|' -o 1.1 2.2 2.3 file1 file2
Due to the pipe delimiter, I got wrong output. Also, I cannot use any other symbol as delimiter since any symbol can be available in column 2.
I need to match column 1 in file 2 and copy column 2 and 3 lengthwise.
I also tried looping column 1 data of file1 in file2 and getting the output but that takes too long since my files are very large.
|
Simple with awk, if the join field is unique:
awk -F"|" 'a[$1]++' file1 file2
-F"|" sets pipe as delimiter
a[$1]++ is a condition. When the condition is true, the line is printed. The condition becomes true, when the first field $1 appears more than one times.
If the join field is not unique:
awk -F"|" 'a[$1]++&&FNR!=NR' file1 file2
FNR!=NR: is also a condition that must be true. This applies only on the second file file2 which is processed. That condition could be removed, when you can guarantee that the first field in both files is unique.
| How to join two files by matching a column with an irregular number of columns? |
1,542,262,746,000 |
Is there an easy way to print all lines of a file1 (so that the output has the same number of lines as the input file1) but print a message such as NoMatch where the first entries of file1 does not match the first entries of file2?
file1:
Entry1 Entry2
a 2
b 3
c 4
d 5
file2:
a
b
b
a
d
d
Desired output:
Entry1
a 2
b 3
NoMatch 4
d 5
I am trying with
join -a1 -e "NoMatch" -11 -21 -o2.1 file1 file2
since I would like to keep the unpairable lines from file1 that do not match file2, and give a message for these cases as "no", but this keeps all of my records also in file2 (which contains duplicated records), what am I doing wrong? Could this be because my second file is tab delimited and my first file is space delimited?
Thanks so much for all the help...
|
With awk read file2 first and save $1 in seen[$1] then read file1 and if $1 wasn't "seen" replace it with NoMatch:
awk 'FNR==NR{seen[$1]++; next}
{(FNR==1 || ($1 in seen)) || $1="NoMatch"};1' file2 file1
If you prefer join, you need sorted input. You'll have to extract the header from file1 first, sort the remaining lines then join the result with the sorted file2:
{ head -n1; sort | join -j1 -a1 -e "NoMatch" -o 2.1 1.2 - <(sort file2); } <file1
and if needed, pipe everything to uniq to avoid duplicate lines:
{ head -n 1; sort | \
join -j1 -a1 -e "NoMatch" -o 2.1 1.2 - <(sort file2) | \
uniq; } <file1
| How do I print all records in file 1 but note the records that do not match file2? |
1,542,262,746,000 |
I have a tabular file like this which is my index:
a X001
a X002
a X003
b X002
c X006
z X007
z X008
z X001
I want to search the following single column file against that index and return each match from the second column of the index.
a
b
z
So the output from that search would be this:
X001
X002
X003
X002
X007
X008
X001
Edit: Here is exact info from my files (top 10 lines from each)
Index
10803548 COG4190
10803554 COG1476
10803555 COG1192
10803559 COG3385
10803567 COG0071
10803570 COG1695
10803571 COG0467
10803573 COG3883
10803574 COG0714
10803576 COG1192
File I am searching:
10956722
11497860
11497860
11497924
11497924
11497924
11497924
11497924
11497979
11497979
The Expected output of this search:
COG3704
COG1474
COG1474
COG2801
COG2801
COG2801
COG2801
COG2801
COG2223
COG2223
|
With join:
join -o1.2 <(sort -k1n index) <(sort -k1n file)
This will merge the two files at field number 1 and if they match, print the second field of the first file 1.2.
Or with awk:
awk 'FNR==NR{a[$1]=1} FNR!=NR&&a[$1]{print $2}' file index
The file file is loaded into an array a.
When the second file index in processed awk checks if the first field is in the array as index a[$1]. If yes, print the second field $2.
| Find multiple matches in a tabular file and print second column? |
1,542,262,746,000 |
I have 3 csv files I want to join by first column (id column)
Each file has the same 3 columns.
Row example :
id | timestamp | Name
3792318, 2014-07-15 00:00:00, "A, B"
When I join the 3 csv files with
join -t, <(join -t, csv1 csv2) csv3 > out.csv
The out.csv file doesn't have the same number of columns for each row, probably because the delimiter is a comma and some rows (like in the example above) have commas in the contents of the cell.
|
Obviously, using a csv parser would be better but if we can safely assume that
The 1st field will never contain a comma;
You only want the ids that are present in the 1st file (if an id is in file2 or file3 and not in file1 of you ignore it);
The files are small enough to fit in your RAM.
Then this Perl approach should work:
#!/usr/bin/env perl
use strict;
my %f;
## Read the files
while (<>) {
## remove trailing newlines
chomp;
## Replace any commas within quotes with '|'.
## I am using a while loop to deal with multiple commas.
while (s/\"([^"]*?),([^"]*?)\"/"$1|$2"/){}
## match the id and the rest.
/^(.+?)(,.+)/;
## The keys of the %f hash are the ids
## each line with the same id is appended to
## the current value of the key in the hash.
$f{$1}.=$2;
}
## Print the lines
foreach my $id (keys(%f)) {
print "$id$f{$id}\n";
}
Save the script above as foo.pl and run it like this:
perl foo.pl file1.csv file2.csv file3.csv
The script above can also be written as a one-liner:
perl -lne 'while(s/\"([^"]*?),([^"]*)\"/"$1|$2"/){} /^(.+?)(,.+)/; $k{$1}.=$2;
END{print "$_$k{$_}" for keys(%k)}' file1 file2 file3
| Merge CSV files with field delimiters also occuring inside quotes |
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