sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
53e8a03231e3243510c24f3c96e911f7f95f99b607b25492e2831beccede7a5f | Perl | 338 | 10 | @files1 = <IC_[0-9]_toML.txt.ru.class.arff>;
@files2 = <IC_[0-9][0-9]_toML.txt.ru.class.arff>;
@files=(@files1,@files2);
system("export CLASSPATH=/work/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file\n";
system("java -Xmx3000m weka.classifiers.functions.SMO -t $file -x 10 > $file.svmbin.... |
9b236148bb28af82685f820959cd9940d36e8cfc85baf309b2fb2c938460502a | Perl | 339 | 16 | @f=<*fasta>;
for($c1=0;$c1<=$#f;$c1++){
$i=@f[$c1];
chomp $i;
@t=split(/\./,$i);
$in=@t[0];
for($c2=$c1+1;$c2<=$#f;$c2++){
$j=@f[$c2];
chomp $j;
@t=split(/\./,$j);
$jn=@t[0];
print "$in\t$jn\n";
system("/home/animesh/export/kmer/trunk/Linux-amd64/bin/atac.pl -dir $in.$jn.atac -id1 $in -seq1 $i -id2 $jn... |
90408de11fe6625a46e6974577347d3b5c772e89df5e17a6d62ce9cc57fe38e0 | Perl | 345 | 17 | $file=shift;
open(F,$file);
while($l=<F>){
chomp $l;
@tmp=split(/\s+/,$l);
if(@tmp[1] eq "c"){
$lenmatdiff=abs(@tmp[6]-@tmp[10]);
$matlen{@tmp[10]}=@tmp[6];
$totlen+=@tmp[10];
#print "$lenmatdiff\t@tmp[6]-@tmp[10]\n";
}
}
for $key ( sort {$b<=>$a} keys %matlen) {
$acclen+=$key;
print "$key\t$matlen{$key}... |
00ab3e00323a6b47db7e968ef00970401170dfa0c8816bd54b888a35cb4ee4e7 | Perl | 346 | 22 | while(<>){
chomp;
@t=split(/\s+/);
$lp=$l;
$l++;
my $gl;
my $glp;
for($c=0;$c<=$#t;$c++){
if($l-$lp>1){print "STEP";}
if(@t[$c]=~/^gi/){
#print "$l,@t[$c]\t";
$gl.=@t[$c];
}
if(@t[$c]=~/^[1-9]/){
#print "$l,@t[$c]\t";
$glp.=@t[$c];
}
}
$glh{$gl}=$glp;
print "\n";
}
foreach $w (keys %glh)... |
100f7a6f5fbb81b1a579c2ee1658e8772d5383a8c0833c7ef518a4852bbd7ba2 | Perl | 348 | 9 | #!/usr/bin/perl
use Bio::SeqIO;
$in = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta');
$out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL');
# note: we quote -format to keep older perl's from complaining.
while ( my $seq = $in->next_seq() )
{
$o... |
78d9b6124aee8b108271659e4a8f40d648756bfdcc5f07a31bf1d16c2471c05c | Perl | 350 | 9 | @files = <IC*.txt>;
system("export CLASSPATH=/work/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file\n";
system("perl txt2csv.pl $file > $file.csv");
system("java weka.core.converters.CSVLoader $file.csv > $file.arff");
system("java weka.filters.unsupervised.attribute.RemoveUseless -i $fi... |
0defe0e0445f20b414615c84e416fdad0c0174cc38c0c7c7452776f9d59c00a9 | Perl | 351 | 19 | #! /usr/bin/perl -w
use strict;
use warnings;
use File::Temp "tempfile";
#use POSIX qw(tmpnam);
my ($input1, $input2, $mode, $out_file1) = @ARGV;
my ($fh, $file1) = tempfile();
my ($fh1,$file2) = tempfile();
`sort $input1 > $file1`;
`sort $input2 > $file2`;
`comm $mode $file1 $file2 > $out_file1`;
`... |
365b38b10d81ab304f48dc969cbde4f7c43f8473dafdfd15da0ef22a4e3f06f7 | Perl | 352 | 10 | use Bio::SeqIO;
my $ntfile = shift(@ARGV);
my $seqin = Bio::SeqIO->new(-file => "$ntfile" , '-format' => 'Fasta');
while ( my $seq = $seqin->next_seq() ) {
$seq->id =~ /ref\|(\S+)\|(\S+)/;
my $id=$1;
my $name = "$id.fa";
my $seqout = Bio::SeqIO->new(-file => ">$name" , '-format' => 'Fasta');
... |
0d0b1bea3ffe9e79f514b920e6066296528bc4c6788a645c7c4e37778c8462e0 | Perl | 362 | 20 | $numSlots =$nproc;
while (@jobs) {
while ($numSlots && @jobs) {
--$numSlots;
$nj = @jobs;
unless (fork()) {
$job = shift @jobs;
print "child running at slot $numSlots\n";
print "$job\n";
exec $job;
}
shift @jobs;
}
wait;
++$numSlots;
}
while ($numSlots... |
1a5acbe71865574f234f22e9604dc3c37ae3c222cfc42b74a05f54d8ebea1b73 | Perl | 371 | 13 | while(<>){
chomp;
@t1=split(/\s+/);
for($cc=0;$cc<=$#t1;$cc++) {
if(@t1[$cc]=~/^V/){
push(@tall,@t1[$cc]);
}
}
}
close F;
@utall = grep !$seen{$... |
7c467103759e192f7e68509c723ad357376a74aec58160ac9ad7b44b6e741fc8 | Perl | 379 | 11 | @th=qw/0 0 0/;
@ta=qw/0 1 0/;
@ts=qw/1 0 0/;
$a=sqrt((@th[0]-@ta[0])**2 + (@th[1]-@ta[1])**2 + (@th[2]-@ta[2])**2);
$b=sqrt((@ts[0]-@ta[0])**2 + (@ts[1]-@ta[1])**2 + (@ts[2]-@ta[2])**2);
$c=sqrt((@th[0]-@ts[0])**2 + (@th[1]-@ts[1])**2 + (@th[2]-@ts[2])**2);
$s=(1/2)*($a+$b+$c);
$area=sqrt($s*($s-$a)*($s-$... |
cf3274f52b2b4d2c7b8b75eab8ea3fa359a59f38b759042bffec8d8eb04b19ae | Perl | 379 | 18 | #!/usr/bin/perl
open F1,"ricecontigAC109365.fas";
open (FILEOUT1, ">AC109365.fas.1");
open (FILEOUT2, ">AC109365.fas.2");
while($l=<F1>)
{
chomp($l);
$li=$li.$l;
}
@seq=split(//,$li);
$len=@seq;
for($c=0;$c<=($len/2+100);$c++)
{$seq1=$seq1.@seq[$c];}
for($cc=($len/2-100);$cc<=$len;$cc++)
{$seq2=$seq2.@seq... |
96594c1347fe11965625454c028e4924ac63d93650676296724d3221cc2620ec | Perl | 380 | 20 | #!/usr/bin/perl
system("ls /user1/ -1>t1.txt");
open F1,"t1.txt";
while($l1=<F1>){
chomp $l1;
@t1=split(/\s+/,$l1);
#foreach (@t1) {$c++;print "$c\t$_\n";}
$n1=@t1[0];
print "$n1\n";
system("ls /user1/$n1/ -1>t2.txt");
open F2,"t2.txt";
while($l2=<F2>){
chomp $l2;
@t2=split(/\s+/,$l2);
$n2=@t2[0];... |
a14865856d54b3d0a9f3f6bb0aa2825454c13d2d0f325c7916be1566c749f199 | Perl | 383 | 13 | #!c:/perl/bin/perl.exe
#hellowww
#a perl program that draws a web page.
print "Content-type: text/html", "\n\n"; #MIME header.
print "<HTML>", "\n";
print "<HEAD>";
print "<TITLE>Perl meets the World Wide Web</TITLE>", "\n";
print "</HEAD>", "\n";
print "<BODY>", "\n";
print "<H1>Hello, World!</H1>", "\n";
pr... |
33b535ba3ba7ac16ff6c50f3198d72ab528acebb788f2401a3217673e3fc5c62 | Perl | 384 | 17 | fact(x) is 1 :- x is 0, fact(x) is 1 :- x is 1, fact(x) is x*fact(x-1) :- x>1.
fact2(0, 1).
fact2(X, Y):- X1 is X - 1, fact2(X1, Y1), Y is X*Y1.
fact(N, F) :- fac(N, 1, 1, F).
fac(N, P, F, R1) :- N > P, P1 is P+1, R is F*P1, fac(N, P1, R, R1).
fac(N, N, F, F).
factorial(0,F,F).
factorial(N,A,F) :-
N > 0,
... |
e1040f82d198353f342a45c3ee15fe60a59eb27afba3531dc091ce6331081ca4 | Perl | 388 | 22 | #!/usr/local/bin/perl -w
# group tag lines by row, optimizing setrow invocations
my $row = -1;
my %rows;
while (<>) {
if (/^\s*((-|\d|\.)*\d+)\s+setrow/) {
$row = $1;
next;
}
$rows{$row} .= $_;
}
my($key, $val);
for $key (sort {$a <=> $b} keys %rows) {
$val = $rows{$key};
unless ($val =~ /^\s+$... |
1164b72016a761349d28f22ada815324ddaea58e599e03934681d7ab1ee987cf | Perl | 389 | 11 | while(<>){
if($c>21655585){exit}
if($_=~/^>/){$c++;if($c>2430650 && $c<21655585){print;}}
else{if($c>2430650 && $c<21655585){print;}}
}
#2430651:>FPCYWBM01BDMRD length=395 xy=0448_0743 region=1 run=R_2009_01_16_05_58_49_
#[animesh@korgpil animesh]$ grep "^>" allruns.fasta | grep -n "FR1250U01EEQZ9"
#21655585:>FR1250U... |
15f826e68b0b412818019ed706dccf6cf5a90d36c492f7a67799076dbba734c9 | Perl | 389 | 29 | $ctg="7180001513595";
$rs=3729;
$re=6566;
while(<>){
chomp;
@t=split(/\t/);
if($ctg eq @t[1]){
$start=@t[2];
$end=@t[3];
if($start>$end){
$tmp=$start;
$start=$end;
$end=$start;
}
$read{@t[0]}++;
if($read{@t[0]}==1){
for($c=$start;$c<=$end;$c++){
$depth{$c}++;
}
}
}
}
foreach (keys %dept... |
c84092ec7af8c1d4bcfd0dee341a0a8081e3e312d0e2f36bcdc855ca0a02001c | Perl | 391 | 10 | @files = <IC*toML.txt>;
system("export CLASSPATH=/work/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file\n";
system("perl txt2csvclass.pl $file > $file.class.csv");
system("java weka.core.converters.CSVLoader $file.class.csv > $file.class.arff");
system("java weka.filters.unsupervised.att... |
64f3e3e718f0d2fc33996aea4a4b2b077e935c1c2308f4bf2bf6ceb00ae6b9a7 | Perl | 392 | 34 | #!/usr/bin/perl
$f1=shift@ARGV;
$f2=shift@ARGV;
open(F1,$f1);open(F2,$f2);
while($l1=<F1>)
{
chomp($l1);
push(@1,$l1);
}
while($l2=<F2>)
{
chomp($l2);
push(@2,$l2);
}
foreach $t1(@1)
{foreach $t2(@2)
{if($t1 eq $t2)
{$n++;
}
}
if($n == 0)
{
print "$t1 is unique\n";
}
else
{
print "$t1 is repeated... |
f6ced6812052ce7204b813976e65b10e5beb065a5254f57421b526f64852a73a | Perl | 393 | 15 | #!/usr/bin/perl
use strict;
use warnings;
use DateTime::Format::Natural;
my $parse = DateTime::Format::Natural->new();
while (1) {
print 'Input date string: ';
chomp(my $input = <STDIN>);
my $dt = $parse->parse_datetime(string => $input, lang => 'en', debug => 0);
printf("%02s.%02s.%4s ... |
f15a0af800afde28b808bd95907a54741a8ce1809006ec23fd1d143fb7379307 | Perl | 398 | 26 | $file2=shift @ARGV;
open(F2,$file2);
$fout="$file2.rv.csv";
open(FO,">$fout");
while($l=<F2>){
$l=~s/^\s+//;
$l=~s/\s+$//;
@t=split(/\,/,$l);
$line++;
if($line==1){
for($c=0;$c<$#t;$c++){
$cp=$c+1;
print FO"V$cp,";
}
print FO"LI\n";
}
for($c=0;$c<$#t;$c++){
$out=@t[$c]+0;
print FO"$out,";
}... |
7fbd90feaab84b894ee52b75ca99180919b976a945cd84cd731b9e64d6059683 | Perl | 420 | 27 | $f1=shift @ARGV;
chomp $f1;
$f2=shift @ARGV;
chomp $f2;
open(F1,$f1);
open(F2,$f2);
open(F,">readanno.txt");
while(<F1>){
chomp $_;
@t1=split(/\s+/,$_);
$c1{@t1[0]}=$_;
}
while(<F2>){
chomp $_;
@t2=split(/\s+/,$_);
$c2{@t2[0]}=$_;
}
foreach $r1 (keys %c1) {
$c++;
foreach $r2 (keys %c2) {
... |
7fb34435b089ca6f383cba0de6fddc146c92424b5b77f21b4819c96214d09051 | Perl | 434 | 11 | @files=<ung2*xml>;
for($c=0;$c<=$#files;$c++){
print "$files[$c]\n";
open(F,">$files[$c].mgf");
print F"BEGIN IONS\nPEPMASS=3467\nCHARGE=1+\n";
system("grep \"<mass>\" $files[$c] | sed -r \'s/<|>/ /g\' | awk '{print \$2}' > tm");
system("grep \"<absi>\" $files[$c] | sed -r \'s/<|>/ /g\' | awk '{print \$2}' > ti");... |
20a748d912a503ba94b4fdee764ddebe0d7fbd457a10c9e20c890019812e130c | Perl | 436 | 17 | #!/usr/bin/perl -w
use Parallel::ForkManager;
use LWP::Simple;
my $pm=new Parallel::ForkManager(10);
for my $link (@ARGV) {
$pm->start and next;
my ($fn)= $link =~ /^.*\/(.*?)$/;
if (!$fn) {
warn "Cannot determine filename from $fn\n";
} else {
$0.=" ".$fn;
print "Getting $fn from $link\n... |
50e7a4cb5ab6ce275ab2754397882aef6b373332e316d76f687043046676382e | Perl | 457 | 22 | @files=<IC_*_toML.txt.class.arff.72fold.lr.txt>;
for($c=0;$c<=$#files;$c++) {
$file=@files[$c];
#print "Processing file # $c $file,";
@fname=split(/\./,$file);
print "@fname[0],";
open(F,$file);
while(<F>){
chomp;
@t1=split(/\s+/);
for($cc=0;$cc<=$#t1;$cc++) {
if(@t1[$cc]=~/^FC/){
push... |
b018d81252726022b79ee86e18cd75bf62ea535db8b2c60fb93bc56e5f06e170 | Perl | 461 | 30 | #!/usr/bin/perl
#print "enter file name \n";
#$file=<>;
#chomp;
open F1,"xen";
while($l=<F1>)
{
if($l=~/^>/)
{$lname=$lname.$l;}
else{
chomp($l);
$length=length($l);
#print "$length\n";
$li=$li.$l;
}
}
@seq=split(//,$li);
$len=@seq;
#print "$len\n";
for($c=0;$c<$len;$c=$c+200000){
for($cc=$c;$cc<... |
9dc3e870810ef076063490cc9df968e29cc252ced7742cd99f76585f8236740b | Perl | 463 | 18 | %append 2 lists
append([],A,A).
append([A|X],Y,[A|T]):- append(X,Y,T).
%reverse a list into another list
rev([],[]).
rev([H|T],L):-rev(T,Z),append(Z,[H],L).
%a palindrome is a list that is the same as its reverse
palin(X):- rev(X,Y),same(X,Y).
%same checks that each list contains the same elements
%not... |
2f51f854a2075d791f7e769d47a6d5556c98045c15c64d16bfbd02e4c6468bcd | Perl | 468 | 19 | #! /usr/bin/perl -w
use strict;
use warnings;
# a wrapper for head for use in galaxy
# headWrapper.pl [filename] [# lines to show] [output]
die "Check arguments" unless @ARGV == 3;
die "Line number must be an integer\n" unless $ARGV[1]=~ m/^\d+$/;
open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!... |
1872181453cc2d3b88e13e8ca7ed57b295587c8ad0dc0ab4053b5a1ddc63c845 | Perl | 476 | 17 | use CGI;
open (OUT,">>test.out") || die;
$records = 5;
foreach (0..$records) {
my $q = new CGI;
$q->param(-name=>'counter',-value=>$_);
$q->save(OUT);
}
close OUT;
# reopen for reading
... |
367a110e72a505642ccaeeaee5e423c8317c8ebd5a55ebd8bdd74bcf225d6fc8 | Perl | 480 | 20 | [
# homology description for set1, referred by --url1
{ 'ortholog_one2one' => 1,
'ortholog_one2many' => 2,
'ortholog_many2many' => 3,
'inparalog' => 4 }
,
# homology description for set2, referred by --url2
{ 'ortholog_one2one' => 1,
'apparent_ortholog_one2one' => 2,
'ortholog_one2many' => 3,
'ortholog_many... |
c3502446c3a3cc5413ba9207a4c553d701d056945f0277f42c18003a9f98bbce | Perl | 480 | 19 | while ($record = getRecord(\*STDIN)){
my ($rec, $fields, $recs) = parseRecord($record);
if ($rec eq "FRG"){
my $sq = $$fields{seq};
my $nm = $$fields{src};
my @lines = split('\n', $nm);
$nm = join('',@lines);
if ($nm =~ /^\s*$/){
$nm = $$fields{acc};
}
@lines = split('\n', $sq);
$sq ... |
cc89263bc16294029dd7d24506813593ccf9e40f4d6339fb6206cbb4da0627f8 | Perl | 481 | 12 | #!/usr/bin/perl
my $p_ppm3 = $ARGV[0];
my $p_cdpkgs = $ARGV[1];
my $p_pdpkgs = "http://ActivePerlEE.ActiveState.com/packages/5.8.4";
Win32::SetChildShowWindow(0) if defined &Win32::SetChildShowWindow;
#system("$p_ppm3 repo add \"ActivePerl Enterprise Edition Package Repository\" $p_pdpkgs");
system("$p_ppm3... |
be31fc78775ab73c4f1cc8286d7a53a2682bbb147f75c356e22e994de5d7dbec | Perl | 485 | 18 | print "Initial probabilities:\n";
foreach $state (sort keys %pi) {
print "P($state)=$pi{$state}\n";
}
print "\n\nEmission probabilities:\n";
foreach $state (sort keys %b) {
foreach $sym (sort keys %{$b{$state}}) {
print "P($sym|$state)=$b{$state}{$sym}\n";
}
}
print "\n\nTransition probabilities... |
3eef0a17d0303d16d8cac6045a80c5e419d823254f18e8f5bb09a061bdbc656a | Perl | 489 | 24 | #!/usr/bin/perl
$file=shift @ARGV;
open(F,$file);
while($l=<F>){
$c++;
chomp $l;
@t=split(/\s+/,$l);
push(@flist,@t[1]);
if($max<@t[1]){$max=@t[1]}
print "$c\t@t[1]\t$max\n";
}
$fo=$file.".pgm";
open(FO,">$fo");
$time=time;
$csqrt=int(sqrt($c));
print FO"P2\n# Created by crtpng.pl at $time\n$csqrt ... |
51642985432e840002fcd3cbd77fd32b4d82978323486f71f707ccefade99878 | Perl | 493 | 25 | use strict;
my $f = shift @ARGV;
my $break=1000;
open (F, $f) || die "can't open \"$f\": $!";
my $seq="";
while (my $line = <F>) {
if ($line !~ /^>/){
$line=~s/\s+//g;
chomp $line;
$seq=$seq.uc($line);
}
}
close F;
my $len=length($seq);
for(my $cnt=0;$cnt<=$len;$cnt+=$break){
my ... |
807672bb158874dcaa965cebdcbcfe6cf652252aaa6680cf6226e5422ea7c923 | Perl | 501 | 23 | #!/usr/bin/perl
print "What is the filename containing the sequences? ";
$name = <STDIN>;
chomp($name);
print "The sequence filename is $name \n";
#
open (FILENAME, $name) ||
die "can't open $name: $!";
$seq = "";
while ($line = <FILENAME>) {
chomp ($line);
if ($line =~ /^>/){
$line =~ s/>//;... |
3b4411b43c11ec185a0d1f0c877ca23617a2780349e0efe770209eaf4238c4a7 | Perl | 502 | 25 | #!/usr/bin/perl -w
$cnt = 0;
$mt="\n";
while (<>) {
$cnt++;
if (/^\s*$/ && $lastbrack) {
printf "%5d< %s", $cnt, $_;
}
if (/^\s*[\}]$/ && $lastempty) {
printf "%5d> %s", $cnt-1, $mt;
}
if (/^\s*[\{]\s*$/) {$lastbrack=1}
else {$lastbrack=0}
if (/^\s*\/\//) {next}
if (/\S.*[\{]/) {... |
6a2bd4dcf6c76707c84bf74d6c64a8260c7d51d56b8e245eb0e5cb137440a09b | Perl | 509 | 19 | while(<>){
chomp;
@t=split(/\s+/,$_);
if(@t[3] ne "NA" and @t[4] ne "NA" and @t[3] ne "" and @t[4] ne ""){
$c++;
$name_gene="\$MIRA$c";
print "\tmy $name_gene = \$ftr->new(-start=>@t[3],-end=>@t[4]);\n";
push(@name,$name_gene);
}
}
print "\tmy \$t = \$panel->add_track(\n";
print "\t\ttranscript... |
ef0a88ef252828de6cae528b760832dd3ce11bdcae5b2cb430e26e5653f60d96 | Perl | 509 | 31 | $f1=shift @ARGV;
chomp $f1;
$f2=shift @ARGV;
chomp $f2;
open(F1,$f1);
open(F2,$f2);
open(F,">$f1.$f2.out");
while(<F1>){
chomp $_;
@t1=split(/\s+/,$_);
$c1{@t1[0]}=$_;
}
while(<F2>){
chomp $_;
@t2=split(/\s+/,$_);
$c2{@t2[0]}=$_;
}
foreach $r1 (keys %c1) {
$c++;$cc=0;
foreach $r2 (keys %c2)... |
7c8512fa05845b222239747761b22be303ed782d5751597d3e60bf2c12237056 | Perl | 519 | 19 | #!/usr/bin/perl
while(<>){chomp;split(/\s+/);$c++;$dictast{length(@_[0])}.=">s.$c\n@_[0]\n";}
foreach $w (sort {$b<=>$a} keys %dictast){
open(FI,">temp.blast.in");
print "Blasting $w length word(s) file\n";
print FI"$dictast{$w}";
close FI;
#system("cp 1T32.A.fas temp.blast.in");
system("blastcl3 -p blast... |
356599c6db8c1cffe06c40be96fd215f74eef2a411e44651216fe5025b7b5859 | Perl | 531 | 22 | while(<>){
chomp;
@t=split(/,/);
@n=split(/vs/,$t[0]);
push(@ns1,$n[0]);
push(@ns2,$n[1]);
$m{"$n[0]-$n[1]"}="$t[1]-$t[2]-$t[7]";
}
%seen = (); @ns1 = grep { ! $seen{ $_ }++ } @ns1;
%seen = (); @ns2 = grep { ! $seen{ $_ }++ } @ns2;
for($c1=0;$c1<=$#ns1;$c1++){
if($c1==0){print "GI , ";for($c=0;$c<=$#ns2;$c++){pr... |
71ca6c0bf9f7de7d18e584fefc854e28a5738712ea009da798bf08c7bffe100e | Perl | 543 | 20 | #-bash-3.2$ head Pwgs6dhmovlcod.posmap.mates.good
#190m01
#-bash-3.2$ head Pwgs6dhmovlcod.posmap.frgscf.sorted.distpair
open(F2,"Pwgs6dhmovlcod.posmap.frgscf.sorted.distpair");
open(F1,"Pwgs6dhmovlcod.posmap.mates.good");
#2 22a15 7180001551862 7180001551862 474899 417089 475515 417809 r f 57810
while(<F1>){chomp;$_=~s... |
2b2df2e5c977291f2f6e15089b9da0f21c2fd6454075736fe27936219dcd374a | Perl | 546 | 30 | use strict;
use warnings;
my %f1;
open(F1,$ARGV[0]);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
my @t1=split(/\t/,$l1);
$f1{$t1[0]}=$l1;
}
close F1;
open(F2,$ARGV[1]);
while(my $l1=<F2>){
chomp $l1;
$l1=~s/\r//g;
my @t1=split(/\t/,$l1);
my $midx=0;
fore... |
2c31baff9966727f5a5903dd513942e69673275227e384ecc9743b49576749b9 | Perl | 554 | 22 | use blib; # we're inside the dist tree
use PDL; # this must be called before (!) 'use Inline Pdlpp' calls
use PDL::NiceSlice; # only used to demonstrate how to switch off below
use Inline Pdlpp; # the actual code is in the __Pdlpp__ block below
$a = sequence 10;
print $a(0:4),"\n";
print $a->inc->(0:4),"\n";... |
fd24d6d0461ac20f7b03147b48bb9e60b4da0e7f90582627f70a292cd33d3917 | Perl | 560 | 32 | use strict;
use warnings;
use Text::ParseWords;
my %seqn;
my $f1=shift @ARGV;
open(F1,$f1);
while(my $l1=<F1>){
if($l1=~/^>/){
$l1=~s/^>//;
$l1=~s/\,//;
my @tmp1=split(/ /,$l1);
#print "$tmp1[0]=$tmp1[5]\n";
$seqn{$tmp1[0]}=$tmp1[5];
}
}
close F1;
my $f2=shift @ARGV;
open(F2,$f2);
#my $l;
whil... |
d3220338fba6b84af8b8b68e2d67e178ab85db96f4cea557e44ad330c57b1c0c | Perl | 561 | 18 | memberof(X, [X|T]).
memberof(X, [H|T]) :- memberof(X,T).
%calculates the intersection of 2 sets represented as lists
%calculates an empty list if there is an empty intersection; otherwise
%calculates a list of the elements in the intersection
intersect([],Y,[]).
intersect([H|T],Y,[H|Z]) :- memberof(H,Y), inte... |
4e748f69260e12d9fa33d1caa077151597d37186795fa50623811bb480f0882e | Perl | 572 | 22 | print "SNNS pattern definition file V3.2\n";
print "generated at Thu Sep 30 15:58:23 2010\n\n\n";
$num=shift @ARGV;
$ni=6;
$no=11;
chomp $num;
@base=qw/-1 0 1/;
print "No. of patterns : $num\n";
print "No. of input units : $ni\n";
print "No. of output units : $no\n\n";
$numc=1;
while($numc<=$num){
print "#Input patter... |
6735dd21a9d80fb7e2eec85e383e12d3aa402ef3d0e3bb8927ad64b049bd752f | Perl | 594 | 22 | #104j22.f 7180001536277 4184 4563 r
#209f14.r 7180001536287 394 1100 r
#-bash-3.2$ grep "^[0-9]" Pwgs6dhmovlcod.posmap.frgscf.sorted | wc
while(<>){if($_=~/^[0-9]/){
chomp;
@tmp=split(/\s+/);
$scf{@tmp[0]}=@tmp[1];
$bp{@tmp[0]}=@tmp[2];
$ep{@tmp[0]}=@tmp[3];
$ortn{@tmp[0]}=@tmp[4];
... |
fcc096f4cff32eaedd886acd92893809ede21ecc5852451f11f569183d2364dd | Perl | 594 | 17 | #!/usr/bin/perl
#>625E1AAXX100810:1:100:10000:10271/1
#>SOLEXA16:0008:2:1:1138:15204#0/1
while ($line = <>) {
chomp ($line);
@tmp=split(/\:|\#|\//,$line);
if ($line =~ /^>/){
$libstring="@tmp[1]";
$template=$libstring."_@tmp[4]_@tmp[5... |
1a508fe29af5f2f4af1c9f3470d4a81f0cb1e2fd66441e79c152e0c67d3cbb3e | Perl | 596 | 24 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
@organism=qw/chick danre fugu mouse xentr bovin ptro macaca/;
foreach $org (@organism) {
print "Org- $org\t";
$filein="align2d_".$org.".py";
system("mod9v3 $filein");
print "Finish Prog - align2d\t";
$filein="model-single_".$org.".py";
system("mod9v3 $filein... |
8ca66c398ae0f6a1d35a6be28800e12c548077174a2ce15e4e189253836db42b | Perl | 598 | 23 | use strict;
use warnings;
use lib '/scratch/misc/parallel/Parallel';
use LWP::Simple;
use Parallel::ForkManager;
system("ls -1 *.fas > list.tmp");
my $command="est2genome";
my $genome="NC_010336.fna";
my @tasks;
open(F,"list.tmp");
while(<F>){chomp;push(@tasks,$_);}
close F;
my $... |
dc2f3c552d42a2996802e610c2b52adbecc3fa4bb31ebdfd1951770a7290c6a5 | Perl | 601 | 26 | #!/usr/bin/perl
$th=0.99;
$fcovmat=shift @ARGV;
open(FCM,"$fcovmat");
while($l=<FCM>){
chomp $l;
push(@fcm,$l);
}
close FCM;
$fo=$fcovmat."pos.out";
open(FO,">$fo");
for($c1=0;$c1<=$#fcm;$c1++){
@t=split(/\t/,@fcm[$c1]);
for($c2=$c1+1;$c2<=$#t;$c2++){
if((@t[$c2]<-($th)||@t[$c2]>($th))&&@t[$c2]!=-1&... |
8c7e351b86d59d5127a4721732edc8bf9d3d356f08c5e81659c03e29324b69d2 | Perl | 603 | 16 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::SeqIO;
my $infile = shift @ARGV;
my $infileformat = pir;
my $outfile = shift @ARGV;
my $outfileformat = fasta;
my $seq_in = Bio::SeqIO->new('-file' => "<$infile",
'... |
0a433f1552374442cb5aad43f4193f4e6d5cbc1527e1f84370efd38d65bbdd2b | Perl | 617 | 16 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::SeqIO;
my $infile = shift @ARGV;
my $infileformat = shift @ARGV;
my $outfile = shift @ARGV;
my $outfileformat = shift @ARGV;
my $seq_in = Bio::SeqIO->new('-file' => "<$infile",
... |
9fbfcdb2972b6954e62ff27f235e71b928421814c32cae4a9b8c8879b6fec09a | Perl | 618 | 7 | system("/usit/titan/u1/ash022/site/454apps/bin/runAssembly -fi t6 -o codbac181n17RA -g codbac181n17.fna");
system("/usit/titan/u1/ash022/site/454apps/bin/runAssembly -fi t6 -o codbac24g13RA -g codbac24g13.fna");
system("/usit/titan/u1/ash022/site/454apps/bin/runAssembly -fi t6 -o codbac29j5RA -g codbac29j5.fna");... |
45b2dab3e21211f8086b2f77d4184824cda2807539c3901f9c83a12249961fff | Perl | 622 | 26 | $file2=shift @ARGV;
open(F2,$file2);
$fout="$file2.csv";
open(FO,">$fout");
while($l=<F2>){
$l=~s/^\s+//;
$l=~s/\s+$//;
@t=split(/\t/,$l);
$line++;
if($line==1){
for($c=0;$c<$#t;$c++){
$cp=$c+1;
... |
e41f68118a3832284a96e69080ea7f1d157cb108db15614001d08f1a7d542765 | Perl | 628 | 22 | #!/usr/bin/perl -w
use strict;
use Archive::Zip qw(:CONSTANTS :ERROR_CODES);
use IO::String;
use IO::File;
# test writing to a scalar
my $zipContents = '';
my $SH = IO::String->new($zipContents);
my $zip = Archive::Zip->new();
my $member = $zip->addString('a' x 300, 'bunchOfAs.txt');
$member->desiredCompr... |
94e6db842137295495ea65bbcf4fd534d2d0dc5fac2a32711d91bb00f966f58f | Perl | 631 | 36 | #!/usr/bin/perl
$f=shift @ARGV;
open(F,$f);
while($line=<F>){
$c++;
print "$line\t$c\n";
if($c == 1){
@namez=split(/\,/,$line);
}
}
undef %saw;
@au = grep(!$saw{$_}++, @namez);
close F;
$fo=$f;
$fileemit=$fo.".emit";
open(FE,">$fileemit");
foreach $audi (@au){
@temp=split(/\<|\>/,$audi... |
14af871a8e906f6aec1c1276e6deba548742ee5873873bfb61abe3dcb017192a | Perl | 637 | 28 | #!/usr/bin/perl
# Examines an ATAC file for overlaps in the first assembly.
use strict;
my $lastBeg = 0;
my $lastEnd = 0;
my $thisBeg = 0;
my $thisEnd = 0;
open(F, "grep B34LC:0 boxfiller_out_v2.blocks_covLT.8_filtered.matches.atac | sort -k6n |");
while (<F>) {
print $_;
my @vals = split '\s+', $_;
$t... |
6965288022458882265eef09a7f445844696ce532afbbd127e91375c13bd5d31 | Perl | 640 | 23 | use strict;
use lib '/home/ash022/Desktop/bac2fish/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my @db_adaptors = @{ $registry->get_all_DBAdaptors() };
foreach my ... |
f25f6c6043805bf57dde716f2139bd45d9422ab3449caae320d14128d6db2f0f | Perl | 643 | 25 | #!/usr/bin/perl
$f1=shift @ARGV;chomp $f1;
if (!$f1) {print "\nUSAGE: \'perl program_name filename_2_b_transposed\'\n\n";exit;}
open F1,$f1||die"cannot open $f1";
$c1=0;
$f2=$f1.".trp.csv";
open(F2,">$f2");
while($l1=<F1>){
chomp $l1;
$l3=$l1;$l3=~s/\s+//g;$l3=~s/\,//g;
if($l3 eq ""){next;}... |
1ab177e2544cd6ae73a6d7842a0f3e780b9185d8d055fa173aef8891eec45368 | Perl | 645 | 25 | $currDir = `pwd`;
chomp $currDir;
$projdir=$currDir;
$projdir=~s/\/assembly//;
$perlscript="editcg.pl";
$cgf=$projdir."/assembly/454ContigGraph.txt";
$csf=$projdir."/assembly/454AllContigs.*";
do{
$cnt++;
$ef="edit".$cnt;
$editcom=$projdir."/assembly/".$ef;
system("perl $perlscript $cgf > $editcom");
if($cnt==100){syst... |
7bb9cd345593aeb579ba7a95f0bc8ef57e1cec646937e4e0f4a33daaf709c1da | Perl | 651 | 23 | $file=shift;
open(F,$file);
while($l=<F>){
chomp $l;
@tmp=split(/\s+/,$l);
if(@tmp[1] eq "c"){
$lenmatdiff=abs(@tmp[6]-@tmp[10]);
$lenmatch=int(@tmp[6]+@tmp[10]/2);
if(@tmp[6]<@tmp[10]){$small=@tmp[6]}
else{$small=@tmp[10]}
$totlen+=$small;
$... |
804d745e62bdfb8e5bb759778b4d4ddd6fbab7b2828e52728a563af800160642 | Perl | 654 | 27 | $file=shift;
$chunk=50000;
open(F,$file);
while(<F>){
$c++;
if($c==1){$header=$_;}
else{@seq[$c]=$_}
}
close F;
for($c1=2;$c1<$#seq;$c1+=$chunk){
$fn++;
$fo="$file.$fn.out";
open(FO,">$fo");
print FO"$header";
for($c2=0;$c2<$chunk;$c2++){
print FO"@seq[$c1+$c2]";
}
system("java -Xmx30000m weka.core.converte... |
dcce4f91a908bf21964ffaa9d702b11c7aa3a669897225ba3933daab0aa266b6 | Perl | 658 | 11 | @files2 = <IC_[0-9][0-9].txt.ru.class.arff>;
system("export CLASSPATH=/work/ash022");
for($c=49;$c<=57;$c++) {
$file=@files2[$c];
print "Processing file # $c $file\n";
#system("java -Xmx3000m weka.attributeSelection.GainRatioAttributeEval -i $file -x 10 > $file.graeclass.txt ");
#system("java -Xmx3000m weka.attr... |
e1c49c1b3529b6b55e048c6a89900c9160d8d6b4150764924e32894fea7d2f58 | Perl | 659 | 31 | $f=shift @ARGV;
open(F1,$f);
while(<F1>){
@t=split(/\t/);
$ctgmin{@t[1]}=Inf;
$ctgmax{@t[1]}=-Inf;
}
open(F2,$f);
while(<F2>){
chomp;
@t=split(/\t/);
$start=@t[2];
$end=@t[3];
if($start>$end){
$tmp=$start;
$start=$end;
$end=$start;
}
if($ctgmin{@t[1... |
8c9f57f04370881d09f4bec9ef661d066bb1a3eeae09c5ff03263b574d8fbd34 | Perl | 665 | 33 | #!/usr/bin/perl
open f1,"tab.txt" || die "cant open";
$lc=0;
while($line=<f1>)
{
chomp $line;
push(@seq,$line);
}
$lc=@seq;
#rint $lc;
for($lii=0;$lii<$lc;$lii++){$li=@seq[$lii];
$li =~ s/\s+/\t/g;
$li =~ s/\t//;
@elem=split(/\t/,$li);
$len=@elem;
for ($cc=0;$cc<$len;$cc++)
{$tree[$lii][$cc]=@elem[$cc... |
eb603295e2f06584b1f153edb31a7ede2693deedcace8b1bd6fa2371c8b4c21b | Perl | 669 | 29 | while(<>){chomp;$l++;
if(/^>/){$_=~s/\>tp\|//g;$_=~s/\s+/\|/;$nm=$_;print ">ustp|$nm\n";$wnt=0;}
elsif(/\*/){#print "$_\n";
$fnd = index($_,'*',0);
#if($fnd>0){
print substr($_,0,$fnd),"\n";
while ($fnd!=-1) {
if($fnd>0&&$fnd>$st&&$wnt>0){print substr($_,$st+1,$fnd-$st-1),"\n";}
print ">ustp|L$l-S$st-E$fnd-$nm\n";
$st=... |
6fee9d1813de39676b80aadbb6d7b13a910d17e9899e18f440204aab63455854 | Perl | 670 | 31 | my $f1 = shift @ARGV;
open (F1, $f1) || die "can't open \"$f1\": $!";
use strict;
use Text::ParseWords;
my %nh;
my %ph;
my $cntt;
my $thr=0.05;
while (my $line = <F1>) {
$line =~ s/\r//g;
chomp $line;
my @tmp=parse_line('\t',0,$line);
my @tmpp=split(/-/,$tmp[0]);
if($tmp[2]<$thr){
$nh{$tmpp[1]}++;
$ph{$tmpp[1... |
6dfaa7362659bd2e17278ee83c3be20ee61aff2efe6e13399039b5444ec89297 | Perl | 672 | 29 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
#>codbac-190o01.fb140_b1.SCF length=577 sp3=clipped
while(<>){
if($_=~/^>/){
$cnt++;
my @tmp=split(/\s+/,$_);
my $namestr=substr($tmp[0],8,8);
my $namesubstr=substr($tmp[0],8,6);
$hitname{$namesubstr}++;
$hitpos{$name... |
064d2e2a897b6324c93c8c37dc7458fa3cf56a775c0088b34f6ab8592c99d360 | Perl | 678 | 7 | system("/usit/titan/u1/ash022/site/454apps/bin/runMapping -o codbac181n17RMS GenomeScaffoldsPure.fna codbac181n17.fna");
system("/usit/titan/u1/ash022/site/454apps/bin/runMapping -o codbac24g13RMS GenomeScaffoldsPure.fna codbac24g13.fna");
system("/usit/titan/u1/ash022/site/454apps/bin/runMapping -o codbac29j5RMS Genom... |
cee33ff520531954da1c55529db3cb77be5ce7e00500c862dad5eb0a62019fe0 | Perl | 696 | 36 | #!/usr/bin/perl
use Bio::SeqIO;
#$seq = "";
open(FILEHANDLE,"noncodnegregap1.txt") ||
die "can't open $name: $!";
while ($line = <FILEHANDLE>){
chomp($line);
if ($line =~/\s+/)
{
push(@arr,$line) ;
}
}
print "@arr \n";
foreach $line(@arr) {
@b=split(/\s+/,$li... |
392144aa8017584948125a56360d0955b9021b500b1a677de2e699ceca58795d | Perl | 697 | 29 | #!/usr/bin/perl
#
# wordwrap.pl --- does word wrap
#
while (<>) {
if (/^#/) { # don't word wrap comments
print;
next;
}
next if (/^$/); # skip blank lines
$linelen = 0;
split;
while (defined($word = shift @_)) {
$word =~ s#\$\(srcdir\)/\.\./version.h#\$\(top_srcdir\)/version.h#;... |
3b0b2f9da954b7c2a29298556b1b083496645299462ec8b684bcd882131b82f2 | Perl | 707 | 29 | use blib;
use PDL; # this must be called before (!) 'use Inline Pdlpp' calls
use Inline Pdlpp; # the actual code is in the __Pdlpp__ block below
$a = sequence 10;
print $a->inc,"\n";
print $a->inc->dummy(1,10)->tcumul,"\n";
__DATA__
__Pdlpp__
# a rather silly increment function
pp_def('inc',
Pa... |
cbae865aa5c361d506b10a0168ae52dbc3fc0d94b3a1d5c68842c0a3e0caed27 | Perl | 708 | 29 | use strict;
my $leng=shift @ARGV;
my $length=4;
my $sample=100;
use Math::NumberCruncher;
my @base=qw/A T G C/;
for(my $len=0;$len<=$leng;$len+=$leng/$sample){
my $lengen;
my $str;
my @temp;
while($lengen<$len){
$str.=$base[int(rand(4))];
$lengen++;
}
print length($str),"\t";
while($str =~ /GA... |
f7464d601689bc9631feb6f787ad6dec52aad70d865c710ad656910a45c68405 | Perl | 715 | 21 | #!/bin/perl -w
# Getting Entry, Chain, Residue, and Atom objects given a PDB file
use Bio::Structure::IO;
use strict;
my $file = shift or die "No PDB file\n";
my $structio = Bio::Structure::IO->new(-file => $file);
my $struc = $structio->next_structure;
for my $chain ($struc->get_chains) {
my $chainid... |
669742e1e3e67fac09c99f6433f10f7640b3e3aa19f348c41bae327b950e518e | Perl | 723 | 36 | #!/usr/bin/perl
use strict;
use warnings;
my $f1=shift @ARGV;chomp $f1;
my $thr=shift @ARGV;
my %seqh;
my $seqc;
open F1,$f1||die"\nUSAGE: \'perl program_name filename_2B_scanned\'\n\n";
while(my $l1=<F1>){
$l1=~s/\r|\n|$//g;
if($l1!~/^>/){
$seqh{$seqc}.=$l1;
}
else{$l1=~s/\>|sp\|//g;$seqc=$l... |
1f8f57f70ffd4aec7a64b2159d44c0755e588565021fb73a0b4f212dba7f8d9e | Perl | 726 | 26 | use strict;
use warnings;
use lib '/scratch/misc/parallel';
use LWP::Simple;
use Parallel::ForkManager;
system("ls -1 *.fas > list.tmp");
my $command="blastcl3";
# my $genome="NC_010336.fna";
my @tasks;
open(F,"list.tmp");
while(<F>){chomp;push(@tasks,$_);}
close F;
my $tasksize= ... |
81134747f68e9c580fea513f41a97ff70533029ae39811513c224e0f6e653ba9 | Perl | 727 | 32 | use strict;
use warnings;
use WWW::Mechanize;
my $query=shift @ARGV;
chomp $query;
my %collurl;
my $purl = 'http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q='.$query;
my $contentrec=MURL($purl);
sub MURL{
my $url=shift;
my $mech = WWW::Mechanize->new();
$mech->get( $url );
my @links = $mech->links... |
867426774a8415557419dbf36a1097d7e82bbfb0a9ec39d9064d6b271876a48c | Perl | 731 | 33 | use lib '/xanadu/project/codgenome/GraphViz/lib';
use lib '/xanadu/project/codgenome/IPC-Run/lib';
use GraphViz;
$g = GraphViz->new();
while(<>){
@t1=split(/\s+/);
if(@t1[0] eq "C"){
$v1="C.".@t1[1];
$v2="C.".@t1[3];
$e1=@t1[2];
$e2=@t1[4];
$readcnt=@t1[5];
$node{$v1}++;
$node{$v2}++;
$l... |
ff6f6fd5e8d93e2149ab06b93deb5594c6206a4ba0e7d1411a717c6232003647 | Perl | 731 | 32 | #codbac62j4-3p22.rp2_b1.SCF1
$file=shift @ARGV;chomp $file;
$fileo1="$file.f.fna";
$fileo2="$file.r.fna";
$filesing="$file.single.fna";
open(F,$file);
open(FF,">$fileo1");
open(FR,">$fileo2");
open(FS,">$filesing");
while(<F>){
chomp;
if($_=~/^>/){
@tmp=split(/\./,$_);
@tmp[0]=~s/\>//g;
$name{@tmp[0]}++;
if(@tmp[1]... |
4fe56b7740621d6fc74200278ef544ac99b91577015bdf6cf5864e6ea47c0f40 | Perl | 738 | 39 | use strict;
use Text::ParseWords;
open(F1,$ARGV[0]);
open(F2,$ARGV[1]);
my %id;
my %val;
my $prot=1;
my $abd=2;
while(my $l=<F1>){
chomp $l;
$l=~s/\r//g,
my @tmp=parse_line(',',0,$l);
$id{$tmp[$prot]}++;
}
close F1;
while(my $l2=<F2>){
chomp $l2;
$l2=~s/\r//g,
my @tmp2=parse_line(',',0,$l2)... |
cd91facced69877a8ee3311cb41f0a0b0fa95af61fb5fda3b7dd9261db278b61 | Perl | 743 | 29 | #!/usr/local/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
# by Jason Stajich
#
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
# the output stream for your seqs, this can be a file
# instead or STDOUT, see the Bio::SeqIO module for info
my $seqout = new Bio::SeqIO(-fh => \*STDOU... |
4855a630524bf6493a6ee2e9eabb600fbdc0ee25591f197cfa7584d0392b241f | Perl | 747 | 26 | use strict;
use warnings;
use lib '/usit/titan/u1/ash022/';
use lib '/xanadu/home/ash022/libwww-perl-5.832/lib';
use lib '/xanadu/home/ash022/URI-1.40';
use LWP::Simple;
use Parallel::ForkManager;
#system("ls -1 *.fas > list.tmp");
#my $command="est2genome";
#my $genome="NC_010336.fna";
my @tasks;... |
3be2ce4abe313bba6c95a0944c69aa74a579cf69ae7f7c27f1bb0b4cfc16632b | Perl | 749 | 29 | #!/usr/local/bin/perl -w
use lib '/home/fimm/ii/ash022/bioperl';
use lib '/home/fimm/ii/ash022/bioperl/IO-String';
use Bio::DB::GenBank;
use Bio::SeqIO;
#use Bio::SeqIO;
use strict;
my $cnt;
while(<>){
chomp $_;
my @tmp=split(/\s+/,$_);
foreach my $n (@tmp){if($n=~/^NC/){$cnt++;conv($n,$cnt);}... |
04f7d4f0fc024a1de5ba640f431601a753d383d169be07cb2151c8d04c7522f6 | Perl | 754 | 33 | $main_file_pattern=shift @ARGV;
chomp $main_file_pattern;
open(F,$main_file_pattern)||die "can't open";
while ($line = <F>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
$snames=~s/\s+/ /g;
$snames=~s/^\s+//g;
@ty=split(/\s+/,$snames);
push(@seqname,@ty[0])... |
bb6910035575128df9bebbcdb51b4f340a578ca21e899867c0ce20b253d5ef2d | Perl | 754 | 34 | #!/usr/local/bin/perl
# makes GFF stuff for a contig.
BEGIN {
push(@INC,"../modules");
push(@INC,"../../bioperl-live");
}
use CGI;
use Bio::EnsEMBL::DBSQL::Obj;
use strict;
my $q = new CGI;
print $q->header();
#print "content-type: text\n\n";
my $contigid = $q->param('contig');
my @featu... |
c37b59c3cca33712c10746d946ba8f7ed3fb9161f797dfc8dd9fea111775c6e9 | Perl | 759 | 25 | use strict;
use warnings;
use lib '/usit/titan/u1/ash022/';
use lib '/xanadu/home/ash022/libwww-perl-5.832/lib';
use lib '/xanadu/home/ash022/URI-1.40';
use LWP::Simple;
use Parallel::ForkManager;
#system("ls -1 *.fas > list.tmp");
#my $command="est2genome";
#my $genome="NC_010336.fna";
my @tasks;... |
10a23e0af9a54d10ed74fc5815c6e47d9da7f228eb64cdf0513a8537dd87e36b | Perl | 762 | 20 | @files=<*>;
foreach $f (@files){
if(-d $f){
@sff=<$f/*.sff>;
foreach $sf (@sff){
@tmp=split(/\//,$sf);
print "converting $sf\t$f\n";
# system("/usit/titan/u1/ash022/clc-assembly-cell-3.2.0-linux_64/tofasta -o @tmp[1].$f.fastq $sf");
... |
79591ed187cb30db7d902cf6934974440ec6cb60336387ec4eb443c62516369b | Perl | 765 | 34 | #!/perl/user/bin/perl
use Bio::SeqIO;
use Bio::Seq;
open(FILEHANDLE,"base") ||
die "can't open $name: $!";
while ($line=<FILEHANDLE>) {
chomp($line);
if ($line =~ /\.\./)
{
push(@table,$line) ;
}
#print "$line \n";
}
foreach $a(@table) {
@b=split(/\.\./,$a);
... |
79fe5a6743a93a974219f6059da7d309f6c07bee57c31f8dd9d96968c8bed6ec | Perl | 770 | 13 | @files = <dl*.arff>;
system("export CLASSPATH=/work/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file\n";
system("java -Xmx3000m weka.classifiers.meta.ClassificationViaRegression -t $file -c 1 > $file.10fold.lr.txt ");
system("java -Xmx3000m weka.classifiers.functions.SMO -... |
b35b996c05e102430c5350fdeea969d7d720a86e94fdbfe6bb1b9d014796780e | Perl | 772 | 30 | #!/usr/bin/perl -w
use Bio::Seq;
use Bio::Index::Fasta;
$out = Bio::SeqIO->new(-file => ">>seq" , '-format' => 'Fasta');
print "File with list of genescan identified genes? ";
$filename = <STDIN>;
open (FILENAME,$filename) || die " cannot open $filename: $!";
$dir="/home/andrew/exhome";
$db="eh2x";
$dbob... |
b836f13e79d55b473d6c08b75cf46404f8b2f66e12ac7f496fb1126541f4b848 | Perl | 772 | 35 | use warnings;
use strict;
open(F1,$ARGV[0]);
open(F2,$ARGV[1]);
my @list=<F1>;
my @gop=<F2>;
@list = sort { uc($a) cmp uc($b) } @list;
@gop = sort { uc($a) cmp uc($b) } @gop;
my $cnt=0;
my %match;
for(my $c1=0;$c1<=$#list;$c1++){
$list[$c1]=~s/\n|\r//g;
for(my $c2=$cnt;$c2<=$#gop;$c2++){
$gop[$c2... |
addd930e30fd0eb3c77e6ee10c476528bb992d4beed3fc46105c7c9b64e97c07 | Perl | 782 | 29 | use strict;
use lib '/home/ash022/Desktop/bac2fish/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $genome=shift @ARGV;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my $line;
my $gn;
my $tgcnt;
my $ttcnt;
my $slice_adapto... |
59dfa2a17a196629196bf06f095ef0d822587c2f2221c3211b6ccd6e6fa76a8c | Perl | 783 | 16 | @files = <svm_mat_lex.csv.class.csv.inddisvox.txt.uniq.extftr.csv>;
system("export CLASSPATH=/usit/titan/u1/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file CSV2ARFF\n";
system("java weka.core.converters.CSVLoader $file > $file.class.arff");
print "Processing file # $c $file LR\n";
syst... |
f0e108a06bdaf5ffc470a87b1d26edbc71731186f35254ca40bfa5d0d120680b | Perl | 783 | 33 | #!/usr/bin/perl -w
use strict;
use XML::Simple qw(:strict);
use LWP::UserAgent;
use Data::Dumper;
# Create a user agent
my $ua = LWP::UserAgent->new();
# Construct URL for entry
my $url = 'http://www.ebi.ac.uk/Tools/picr/rest/getMappedDatabaseNames';
# Perform the request
my $response = $ua->get($url);
# Check for ... |
b2c7a6136f69224d462dd88dfab2091285d78a2e3bc6c9b46861f44950afd70f | Perl | 787 | 42 | #!/usr/bin/perl -w
# jkb 12/12/95
# Usage: html_index.pl DOCUMENT_toc.html
# Builds $ARGV.index Their use is as follows:
#
# $ARGV.index contains a mapping of node names to urls. The show_help Tcl
# command reads this file.
#$last = "";
#@sub = ();
$name = $ARGV[0];
$name =~ s/_toc.html//;
open(INDEX, "> $name.inde... |
b163dadcfe8beeeb8f57deb99aa534d4ee0099aff11e9028db864b31908b916b | Perl | 788 | 29 | #!usr/bin/perl
use strict;
use LWP::UserAgent;
print "ENTER THE FILE NAME CONTAINING 4 LETTER PDB
ENTRIES :";
my $input=<STDIN>;
chomp $input;
unless(open(INP,$input))
{print" ERROR IN OPENING THE FILE $input: $!\n";exit;}
my @ids=<INP>;
close INP;
foreach my $pdb_id(@ids)
{
chomp $pdb_id;
$pdb_id=~ tr/... |
201421f48cc36c0cc2e9ce959f231049cd17f8c3d27291b8324b22ac795e7eda | Perl | 794 | 25 | #!/bin/perl
use lib "/work/assembly/walenzbp/projects/scripts";
use libBri;
while (!eof(STDIN)) {
my %p = &libBri::readPolish(*STDIN);
if (defined($p{'raw'})) {
my $status = "$p{'numMatches'}-$p{'numMatchesN'}-$p{'percentID'}-$p{'matchOrientation'}-$p{'strandPrediction'}";
my $st = 0;
... |
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