sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
65fcec94fe27947e6094331b321c560ac61f49930642709e002293a0469b66c4 | Perl | 1,154 | 33 | use warnings;use strict;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::Graph::NewickParser;
my $compara_dba = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-url => $ARGV[1]);
my $file = $ARGV[0];
my $newick_tree = qx"cat $file";
print "INPUT TREE:\n$newick_tree\n";
my $tree = Bio::EnsEMBL::Compa... |
3a2cda3f4e98c258026905ba236ed8d76589f5e94babbb3790fcfcc56dbee98d | Perl | 1,157 | 20 | system("export CLASSPATH=/work/ash022");
$file="selcomp.arff";
print "Processing file $file\n";
system("java -Xmx3000m weka.attributeSelection.GainRatioAttributeEval -i $file -x 10 > $file.graeclass.txt ");
system("java -Xmx3000m weka.attributeSelection.CfsSubsetEval -i $file -x 10 -s weka.attributeSelection.... |
3071655aeb7e29429da8ae27c1bfbee20975c79ce69e376dd648ee9d5bbdc445 | Perl | 1,163 | 21 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
99e68ba26bf91851fc41d0c00829f0f8016a592ae4de01fe890e5a208345e332 | Perl | 1,167 | 53 | use strict;
use warnings;
my %seqh;
my %seqm;
my $seqc;
my $f1=shift @ARGV;
open(F1,$f1);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
if($l1=~/^>/){$seqc=$l1;$seqc=~s/^>//;$seqc=~s/^(\w+).*$/$1/;}
else{$seqh{$seqc}.=uc($l1);}
}
close F1;
my $f2=shift @ARGV;
open(F2,$f2);
my $gn=shift @ARGV;
my... |
c74d0105e596a919177cea19722362659af66472daa7fa97e3def5d101909bb1 | Perl | 1,168 | 32 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
9c7068207d29da2d5f2234e4c7272110fb1cff8d362f8182647e5e4077903062 | Perl | 1,181 | 39 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
e15754d36d39585c2caa79982241e88b20a5d778cc6a94e9d629214b8e86691e | Perl | 1,189 | 41 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will ... |
0a154661549b3db8b10fb2677981061cc3cf3cff773fd6621374e4a589405b5b | Perl | 1,211 | 56 | use strict;
use warnings;
use Text::ParseWords;
my %seqh;
my %seqm;
my $seqc;
my $f1=shift @ARGV;
open(F1,$f1);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
if($l1=~/^>/){$seqc=$l1;$seqc=~s/^>//;}
else{$seqh{$seqc}.=uc($l1);}
}
close F1;
my $totseqlen=0;
foreach my $seq (keys %seqh){
$seqm{$se... |
9050c7bfedc8fd227dd153df153910587050e79229f19281d775eae92c34a3b2 | Perl | 1,211 | 28 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
0c12521a87fd1177743764a7d4b4cb704cf303c662751f4048cdadbd5b8911c3 | Perl | 1,227 | 63 | #user/bin/perl
$word = 'TATA';
$count1= $count2 =0;
print "Enter the sequence file name\n";
$name = <>;
chomp ($name);
open (IN, $name);
while ($line = <IN>)
{
if ($line =~ /^>/)
{
$linename = $line;
}
else
{
push (@seq, $line);
}
}
foreach $el (@seq)
{
# print "$el\... |
d429f9ac7505c91b1c479e9b7711359a40b31eeb176c2e1060d649f53297b774 | Perl | 1,232 | 27 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
2870ca8fe4086fbbe49baf776ffb5e36aaa8297ea7b94375494133ba89fe73a0 | Perl | 1,235 | 39 | #!/usr/bin/perl -w
use strict;
use Bio::Tools::Phylo::PAML;
use Bio::Root::IO;
my $parser = new Bio::Tools::Phylo::PAML(-file => shift,
-verbose => shift);
my $result = $parser->next_result;
my @otus = $result->get_seqs();
my $MLmatrix = $result->get_MLmatrix();
my $NGmatrix = $result->get_NGmatrix();
# ... |
c2e9765c0065e3bf7e1f57f384d0121b31c310cb6e69b4c3a6870e9c8c99394c | Perl | 1,239 | 47 | #!/usr/local/bin/perl
use CGI;
$query = new CGI;
print $query->header;
print $query->start_html;
print "<H1>what is the filename of the sequence containing file?</H1>\n" , $query->textfield('name',$name,50);
$name = <STDIN>;
chomp($name);
print "The sequence filename is $name \n";
open (FILENAME, $name) ||... |
815a68a29048a2b8b2bd631c269df3be4f493ca0ea774d09a0506b44d4453631 | Perl | 1,241 | 38 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
ad6e8caeef2248aa7d51f48fff7668303edded1ceba369f5d25dff840c5cafa4 | Perl | 1,243 | 44 | use strict;
use warnings;
my $f = shift @ARGV;
my $mut = shift @ARGV;
my $seq = shift @ARGV;
open FO,">$f.mutated.txt";
open FT,">$f.true.fasta";
open FF,">$f.false.fasta";
open F,$f;
my $l=0;
while(<F>){
if($l==0){print FO"Line\tSeqNum\tMatch\tExpectedAA\tPresentAA\tMutate2AA\tMutated\t$_";}
else{
m... |
01afdf2d1c4b4fcfdc77ed7aceb37c006170f347048a618f24e6687ce3112c1a | Perl | 1,246 | 40 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
1cdce096d5c2512839ec8b25cab5ccf38a910aadbf5dedf57ed80cd574166c54 | Perl | 1,248 | 55 | use strict;
use Text::ParseWords;
my $path = shift @ARGV;
my $pat = shift @ARGV;
my $i1 = shift @ARGV;
my @files=<$path/*$pat>;
my %mrna;
my %nc;
print "FileColumn$i1\t";
foreach my $f1 (@files){
my @tmp;
my @name;
my %pg;
my $lcnt;
my $fn=$f1;
$fn=~s/$path|$pat|\///g;
print "$fn\t";
o... |
dc958ac769437ecabc4dce2d8f8f309c0f25077b351386fe541586a9cbea4941 | Perl | 1,252 | 45 | #!/usr/bin/perl
sub hypotenuse {return sqrt ( ($_[0] ** 2) + ($_[1] ** 2) );}
$tree=hypotenuse(3,4);
#print "the hyp of 3 4 is $tree";
@numb=qw/q r w q e f r y/;
@numbs=qw/r q d r g h/;
$tree="hi how r ya\n";
@wear=split(//,$tree);
$len1=@numbs;
$len2=@numb;
if($len1>$len2)
{$xx=$len1;}
else
{$xx=$len2;}
... |
f15aeaa5f337040cd9c1adec05ca5a43d3817ccb510c5bfea482b5b6de6bd82c | Perl | 1,252 | 41 | #!/usr/bin/perl
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName GenomeFile\n\n\n";}
$fileas = shift @ARGV;$cp=0;$cnp=0;
#open (F1, $filess) || die "can't open \"$filess\": $!";
open (F2, $fileas) || die "can't open \"$fileas\": $!";
#while ( $line = <F1> ) {
# chomp ($line);
# push(@name1,$line);
# ... |
7d5a4880bd835cd2e769871e3e35a70d3868327c01850f5cafb87416067d752a | Perl | 1,254 | 54 | #!/usr/bin/perl -W
use strict;
use Bio::Perl;
use Bio::Tools::GFF;
my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
my $out = Bio::Tools::GFF->new(-fh => \*STDOUT, -gff_version => 2);
my $feature;
my @features = ();
#Record entries
while($feature = $gffio->next_feature()) {
push @features, $feat... |
c05d7619e510ddbac7b73c858cdee095184a2a0fff32b97b20c3fde3916e8c53 | Perl | 1,254 | 24 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6bbe394d4921e5f85e220f8babe60e4fbd7be7c0205c687cf73c8bad8fb9a6c3 | Perl | 1,265 | 37 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
e8f137e0a04bffd0c302bda3c58f66102cf2399433d4b2ecb374f86f43c404e5 | Perl | 1,271 | 21 | for($c=50;$c<=400;$c+=50){
print "Length $c\n";
system("/usit/titan/u1/ash022/mapasm454_source_11172009/applicationsBin/runAssembly -fi list.$c -o ecoli.assembly.low.$c *.sff");
}
__END__
-bash-3.2$ /usit/titan/u1/ash022/mapasm454_source_11172009/applicationsBin/runAssembly -fe list *.sff
Created assembly project di... |
ab9c2d8d9a04c76553dc54ccb1a1d3fa5e281faba60d4dce8e61d9f5e505184d | Perl | 1,280 | 21 | for($c=50;$c<=400;$c+=50){
print "Length $c\n";
system("/usit/titan/u1/ash022/mapasm454_source_11172009/applicationsBin/runMapping -fi list.$c -o ecoli.map.low.$c CP000948.fasta *.sff");
}
__END__
-bash-3.2$ /usit/titan/u1/ash022/mapasm454_source_11172009/applicationsBin/runAssembly -fe list *.sff
Created assembly p... |
dd90c49bb79b4f5a4fee874d4d5e65edee4ed750f1a1914b4052b0801f9feab1 | Perl | 1,284 | 43 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::Perl;
use Bio::SeqIO;
use strict;
my $window=35;
my $jump=22;
my $main_file=shift @ARGV;
my $fas_file=$main_file."_in.fasta";
open(FT,">$fas_file");
my ($wseqname,$wseq,$wseqlen)=get_other_source($main_file);
sub get_other_source{
my $foofile=shift;
... |
66221ab2e0821573aca66817b6c155ab1243a39a59c54798fb2e2ab1f02ccf0d | Perl | 1,286 | 24 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
1817e38f760e49f0c195fc51ae9d25e19d02d194b0c9bd560f56de5d5f34a524 | Perl | 1,292 | 50 | #>FTL1_1_1_0_507
$file=shift @ARGV;chomp $file;open(F,$file);
while(<F>){
chomp;
if($_=~/^>/){
$_=~s/\>//g;
@tmp=split(/\s+/,$_);
$n=@tmp[0];
$ncom{$n}=$_;
$name=$n;
$name=~s/R//g;
$name=~s/F//g;
$p{$name}++;
}
else{$seq{$ncom{$n}}=$_;}
}
open(FO1,">$file.1.fna");
open(FO2,">$file.2.fna");
open(FO3,... |
6542fc986efe1d9d05a81e64bf8c5fc65c1ab2f521655f155eb813e9495b6c95 | Perl | 1,296 | 63 | $input=shift @ARGV;
chomp $input;
$valtop=shift @ARGV;
chomp $valtop;
$appendi=$valtop;
open(F,$input);
$fo1=$input."$appendi.conc.csv";
$fo2=$input."$appendi.class.csv";
print "writing to file $fo1 and $fo2\n";
open(FOTP,">$fo1")or die $!;
open(FOTPC,">$fo2")or die $!;
while($lval=<F>){
chomp $lval;
@t=split(... |
4d23dcd3e69721d025ee6e7a7540e0677317d0eab526bae1ddfa3848006d62e3 | Perl | 1,299 | 55 | if( @ARGV ne 1){die "\nUSAGE\t\"ProgName SeqFile\t\n\n\n";}
$file1 = shift @ARGV;
open (F, $file1) || die "can't open \"$file1\": $!";
$seq="";
while ($line = <F>) {
if ($line =~ /^>/){
$c++;
chomp $line;
push(@seqname1,$line);
if ($seq ne ""){
push(@seq1,$seq);
$seq = "";
}
... |
c581a8fca829cb59a412bff1c57136bef2a6e5419b981088a46f84c026c614f4 | Perl | 1,299 | 59 | #!/usr/bin/perl
use strict;
use warnings;
use Text::ParseWords;
my $f1=shift @ARGV;chomp $f1;
my $p1=shift @ARGV;chomp $p1;
my $p2=shift @ARGV;chomp $p2;
my $p3=shift @ARGV;chomp $p3;
my $thr=shift @ARGV;
open F1,$f1||die"\nUSAGE:\'perl program_name filename_2B_scanned\'\n\n";
my $c1=0;
my $c2;
my @ma... |
97110cb2f52fd42be47adb432e0b2818bd7e6b67ef6347e1d3e9e8abdcd226eb | Perl | 1,304 | 34 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
5f9969382ea46bf4682411ff8d8cc89388a96b194cf13fb01d82238afc5c0adc | Perl | 1,305 | 51 | $file=shift @ARGV;chomp $file;
open (F,$file)||die "cant open :$!";
$seq="";
while ($line = <F>){
chomp ($line);
if ($line =~ /^>/){
$line =~ s/>//;
push(@seqname,$line);
if ($seq ne ""){
push(@seq,$seq);
$seq = "";
}
}... |
a87c9671e1a4466a4ceacfe3bf7b17fd34fddcf01ef73b877b7aa8b421194ec8 | Perl | 1,305 | 39 | #!/usr/bin/perl -w
# Count how many almost identical jumps there are in a library.
# Outputs to stdout a list of jumps with the number of identical ones found as the first column.
(@ARGV > 0) || die "You need the prefix as an argument";
$p = $ARGV[0];
print "$p\n";
system("ExtractJumpingReads IN=$p.annota... |
99b9f19fdc6bc853aa4604c39dd4d92b4299e76babdb9f0f7fda66692b360aca | Perl | 1,307 | 53 | % Morten Hordnes, guy001.
% Byttet kommentar tegn fra #
% til % da virket programmet, hvis jeg brukte #
% fikk jeg noen errors.
% Oppg A
maxAlignment(_,[],[]).
maxAlignment([],_,[]).
maxAlignment(Xs,Ys,Zs) :- findall(N,alig(Xs,Ys,N),L), max(L,Zs).
max([X],X).
max([H|T], E):- max(T,E), length(H,N1), length(H,N2) E1 <... |
ae84788d84cc39246438a230b15303198ea7bdab66c853d2a1f97fc76745686e | Perl | 1,326 | 72 | #!/usr/bin/perl
# Simple hack to merge multiple QC reports into one. Uses the first
# QC on the command line to figure out what fields exist, then writes
# a multiple column QC using those fields and data from all QC files
# on the command line.
use strict;
my @labels;
my %values;
my $s;
my $l;
m... |
064ba702c5056b898291c2bdaa6c4a494d928f34c59e43c95a0df27b1c9dd987 | Perl | 1,335 | 39 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
a8e9455ec3e6fdc8c2e68e6a0646279bee3a21c7372c7f23ed1cad671b74750c | Perl | 1,335 | 60 | $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])... |
38e7914bbbf9a555a4901b2935b01d129e51a7c855d0c346cd04f0ac46a16abc | Perl | 1,337 | 46 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::Perl;
use Bio::SeqIO;
use strict;
my $window=200;
my $jump=180;
my $main_file=shift @ARGV;
my $fas_file=$main_file."_in.fasta";
open(FT,">$fas_file");
my ($wseqname,$wseq,$wseqlen)=get_other_source($main_file);
sub get_other_source{
my $foofile=shift... |
1420ab71b125db44818d72b7c961fc299f4958aa58eec9b6d9441cdd9b873091 | Perl | 1,344 | 55 | my $f = @ARGV[0];
open (F1, $f) || die "can't open \"$f\": $!";
my $aa = @ARGV[1];
if($aa eq ""){die "provide the single letter code for the amino-acid to count \"$aa\": $!";}
use strict;
use Text::ParseWords;
my %nh;
my %seqc;
my %seqh;
my %ph;
my $cntt;
my $lc;
my $header;
my $seqc;
open(F1,$f);
while(my $l1=<F1>){
... |
5983b7664bf1d8db6d764b31e6ce79be639ec57e545854ab6f15c603426e96fd | Perl | 1,344 | 44 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
996e04afedfe362645dc91f787b4d7c7eda931d1845cc526485a2357a9cbd367 | Perl | 1,349 | 25 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
1c643ab52b6b6e4a1e21bcf2e234e9722a7cadb4461c71dc2775a7b29f3ab2ea | Perl | 1,351 | 44 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
fa2b3682d127fe9e298aea270d8a0aa3da536f2f32b8e0e7ae35b1ef6a9685f6 | Perl | 1,363 | 47 | #!/usr/bin/perl
#>codbac29j5-2o21.rp2_b1.SCF 883 0 883 SCF
#>codbac181n17-1a01.rp2_b1.SCF1 template=codbac181n171a01 dir=R library=codbac181n17
$file = shift @ARGV;
open(F2,$file);
while ($line = <F2>) {
if ($line =~ /^>/){
chomp ($line);
... |
a07e8c1809bd5df4718817a78f27cef65cdfca68adc5c86ee95603695b0ae115 | Perl | 1,366 | 75 | %chrname = (
189908151=>10,
189908152=>11,
189908153=>12,
189908154=>13,
189908155=>14,
189908156=>15,
189908157=>16,
189908158=>17,
189908159=>18,
189908160=>19,
189908150=>1,
189908162=>20,
189908163=>21,
189908164=>22,
189908165=>23,
189908166=>24,
189908167=>25,
189908161=>2,
189908168=>3,
189908169=>4,
189908170=>... |
619c1e8d9e1b77c0f85897a907371c6cdd67af0864ae69131d95f659d76ff121 | Perl | 1,369 | 60 | use strict;
use Text::ParseWords;
my $path = shift @ARGV;
my $pat = shift @ARGV;
my $i1 = shift @ARGV;
my $i2 = shift @ARGV;
my $i4 = shift @ARGV;
my $i8 = shift @ARGV;
my @files=<$path/*$pat>;
my %mrna;
my %nc;
print "FileColumn$i2\t";
foreach my $f1 (@files){
my @tmp;
my @name;
my %pg;
my $lcnt;
... |
a2b01de9f23fa991953f33076cd6baca328e51e726e2ec246672854d770483bb | Perl | 1,380 | 39 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
a52726f818d527b6279d5b9d82a6a8353c3977a88cea55b2a5f9538937b4fecf | Perl | 1,383 | 45 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
3bec609a1ccd61ece9ce659ed30c8f5589e062aca344431f829857c1a7f36f81 | Perl | 1,384 | 49 | use strict;
use warnings;
use Text::ParseWords;
my $f=shift @ARGV; #Mapped Uniprot File
my $c1=shift @ARGV; #Protein Sequence
my $c2=shift @ARGV; #Peptide Sequence
my $c3=shift @ARGV; #Modification column
my $c4=shift @ARGV; #Modification position
open(F,$f);
my $ln=0;
while(my $l=<F>){
chomp $l;$l=~s/\... |
d01665bdd12f4cf33a06c9f6abb87a762aabb25e42dadb69741af21b88d50f4c | Perl | 1,384 | 38 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
55e04555dfebe8c96cdc196a8ff0bbb2fff9f18c3c65e95c141e53d9138d8bac | Perl | 1,388 | 56 | use strict;
use Text::ParseWords;
open(F1,$ARGV[0]);
my $s1=$ARGV[1];
my $s2=$ARGV[2];
my $s3=$ARGV[3];
my $s4=$ARGV[4];
my $s5=$ARGV[5];
my %val1;
my %tm1;
my %val2;
my %tm2;
my %tm;
my $lc;
my $qt=0.05;
while(my $l=<F1>){
$lc++;
if($lc>1){
chomp $l;
$l =~ s/\r//g;
my @tmp1=parse_line(','... |
17f73365f4f1034f954eadc94305c58adf5b452d6a3be5b5493c900388e5832d | Perl | 1,390 | 42 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
7af6b2127a3ae574eca055b9c7361831923cd2c67c79500c41ac55e568ec5306 | Perl | 1,390 | 68 | use strict;
my $f1 = shift @ARGV;
my $i1 = shift @ARGV;
my $f2 = shift @ARGV;
my $i2 = shift @ARGV;
my @tmp;
my @name;
my %pg;
my %mrna;
my %nc;
my $lcnt;
open (F1, $f1) || die "can't open \"$f1\": $!";
while (my $line = <F1>) {
$lcnt++;
@tmp=split(/\t/,$line);
if ($lcnt>1&&$tmp[$i1]){
@name=split(/\... |
4d63e1215049b22d80e97347eca51cc3c896472586437bd727ed72ba1c893f14 | Perl | 1,400 | 50 | #!/usr/local/bin/perl -w
#
# hToTxt - read the definition of the UCSC chromColors from
# the source tree file chromColors.h and rearrange into
# a simple text file specifying each color hex value.
use strict;
my $argc = @ARGV; # arg count
if ( $argc != 1 ) {
print "usage: $0 <chromColors.h>\n";
exit(... |
9754f7fd625c6ff74f2cb929cdfaf6fdc919b7287440148a6cc06012c59a8119 | Perl | 1,402 | 57 | use strict;
use Text::ParseWords;
use Scalar::Util qw(looks_like_number);
my %vh;
my %nh;
my $cnt=0;
my $f1 = shift @ARGV;
my $idc=shift @ARGV;
open (F1, $f1) || die "can't open \"$f1\": $!";
my $lc;
while (my $line = <F1>) {
$lc++;
$line =~ s/\r//g;
$line=~s/\'/_p/g;
chomp $line;
my @tmp=parse_line('\t',0,$line... |
9c68a70bd998b7de5bdb742c2566e7b9d0d17a2c4c361d7068171bec75ad3f1d | Perl | 1,409 | 41 | while(<>){
chomp;
@tmp=split(/\s+/,);
@tmp[2] =~ s/\'//g;
@tmp[4] =~ s/\'//g;
if(@tmp[0]=~/[0-9]+/){
$tc++;
$cl{@tmp[0]}=@tmp[2];
#print "@tmp[0] @tmp[1] @tmp[2] @tmp[3] @tmp[4]\n";
}
if... |
dfc1eeeb2566efbca16c44af14ebdf4a5c974766c511f8341f3a7da8b1eeda79 | Perl | 1,414 | 44 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
8b674b09d5c944349654c9a73b1f7be5a2eb81fadddef257c7c52a4d38cd566e | Perl | 1,419 | 65 | use strict;
use Spreadsheet::Read;
my $id=0;
my %vh;
my %nh;
my %ch;
sub createhash{
my $f1 = shift;
my $data = ReadData ($f1);
my @lin=cell2cr($data->[1]{cell}[1][3]);#->[1]{$c};
my $line;
my $lc;
print "$f1\t$data\n";
#for(my $c=0;$c<=$#data;$c++){
for(my $c=0;$c<=10;$c++){
$lc++;
#$lc=$lin[1][1];
$li... |
9ad3d0d93aa7d2d830c19760fe742cdb96f01e3fc1739155cd5a7daa093f2e5c | Perl | 1,421 | 41 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
d2a02c6700dbb86a9e2f66d4d9fd81db2b842b6b96c81ecffd87cc4633daee05 | Perl | 1,428 | 26 | use strict;
use warnings;
my $file=shift @ARGV;
open F, "$file" or die "Can't open $file : $!";
while(my $l=<F>){
chomp $l;
$l=~s/\r//g;
my @t=split(/,/,$l);
print $t[0];
}
__END__
perl genloc.pl testmod.csv
email: sharma.animesh@gmail.com
perl matchlist.pl /cygdrive/... |
612d0beb1c7ac5af2814814b9271de4dc1ab0ba3702013e7ab1457e658691895 | Perl | 1,431 | 48 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::Perl;
use Bio::SeqIO;
use strict;
my $coverage=30;
my $window=35;
my $jump=5;
my $main_file=shift @ARGV;
my $fas_file=$main_file."_in.fasta";
open(FT,">$fas_file");
my ($wseqname,$wseq,$wseqlen)=get_other_source($main_file);
sub get_other_source{
my... |
54a1f6183e360c885baa594c2a67a62b75c36ecf10fa15a0d69c3504cd3668df | Perl | 1,436 | 45 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
db24cb7288767b0506e5a43131a0af91a9c9030d2b53a7b99162114d7c4c76aa | Perl | 1,450 | 81 | #!/perl/user/bin/perl
print "Enter the list of file names\n[ALL FILE NAMES SHOULD BE IN A SINGLE COLUMN\n";
$list = <>;
chomp($list);
open (IN, "$list")|| die "can`t open $!";
while ($line = <IN>)
{
chomp($line);
print "$line\n";
push (@files, $line);
}
open (OP, ">$list.csv");
print OP "... |
96167f84a193e75dac2c8737ccb0f0472558315ea823ec9e72cef47dc64132a8 | Perl | 1,456 | 71 | #!/usr/bin/perl
my $main_file=shift @ARGV;
open(FMFAS,$main_file)||die "can't open $main_file";
while ($line = <FMFAS>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
$snames=~s/\s+/\_/g;
push(@seqname,$snames);
... |
7cfe6675b3d32b2093bf9868555d9b65f49b4429abae9abdf2e7ac8a1cbb1cf4 | Perl | 1,458 | 66 | use strict;
use Text::ParseWords;
open(F1,$ARGV[0]);
my $unid=0;
my $s1=$ARGV[1];
my $s2=$ARGV[2];
my $lv=$ARGV[3];
my %nm;
my %id;
my %val1;
my %val2;
my $lc=0;
my %fnd;
my %hdr;
while(my $l=<F1>){
$lc++;
if($lc>$lv){
$l =~ s/\r|\n|\'//g;
my @tmp=parse_line(',',0,$l);
$nm{$tmp[$unid]}=$l;
... |
9f0240726c220f5328283f32c4fa4f495d2a4a73e2c0a68d6155da3d0075bb82 | Perl | 1,465 | 40 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
b2241d3786070e90425f7d20e87b77422d7e1ebabf083bc9da91694ec9f3ade8 | Perl | 1,465 | 50 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
5061f1da45a95daecaa211537c82604828ba951c01a0f124ee82699b6026ddb6 | Perl | 1,473 | 42 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
b46c5cfb0205e3f4b4f6f62df2c0e60988db23c2d09e2fbf7c62f4916f578a13 | Perl | 1,473 | 64 | use warnings;
use strict;
open(F1,$ARGV[0]);
open(F2,$ARGV[1]);
my $mc=$ARGV[2];
my $oc=$ARGV[3];
my $num=$ARGV[4];
if(!$ARGV[2]){$mc=0;}
if(!$ARGV[3]){$oc=$mc;}
if(!$ARGV[4]){$num=0;}
my @list=<F1>;
my @gop=<F2>;
if($num==0){
@list = sort { uc($a) cmp uc($b) } @list;
@gop = sort { uc($a) cmp uc($b) } @... |
89a4858dd16c86686365f7a77e1629c1c1c899b43155bdcd18178f6ef747fc36 | Perl | 1,475 | 47 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
66deb8d9a0aa4abccdfa856a2969b1091f77e22e6ea2c26edfd5d1e67ec44778 | Perl | 1,486 | 69 | use strict;
use Text::ParseWords;
my $path = shift @ARGV;
my $pat = shift @ARGV;
my $fpat = shift @ARGV;
my $i1 = shift @ARGV;
my @files=<$path/*$pat>;
my %mrna;
my %nc;
my %ir;
my %hp;
my %pepc;
my %pepcna;
my %pepc0;
print "FileColumn$i1\t";
foreach my $f1 (@files){
my @tmp;
my @name;
my %pg;
my $l... |
e79319c4f0fd2ac900a35881f5d1e1a2d50ba0396cbede5624f7a6edb07d999e | Perl | 1,491 | 59 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
0baa1bf390a9a6104ff5c11e59cd6c2b315e596ce2da599729611d12101f1d2d | Perl | 1,498 | 71 | # By Brandon S. Allbery
#
# This library is no longer being maintained, and is included for backward
# compatibility with Perl 4 programs which may require it.
#
# In particular, this should not be used as an example of modern Perl
# programming techniques.
#
# Suggested alternative: Cwd
#
#
# Usage: $cwd = ... |
6603259f59d43c849131addc5ac28ee2232d3bf68daf161aafc7b13046f762d5 | Perl | 1,500 | 52 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
56296ec1f605e1cb4e6d625fa7843da393951ddbaf10eebbe3e6579b05434100 | Perl | 1,507 | 47 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6848f6b6e7e6adec90176fcafe23a4f698cb10fec1467008736764a3099603e0 | Perl | 1,507 | 70 | $f1=shift @ARGV;
undef @seqname;undef @seq;
$seq="";
open(F1,$f1)||die "can't open";
while($line=<F1>){
#chomp ($line);
$line=~s/\n/ /g;
if ($line =~ /^>/){
@seqn=split(/\s+|\_/,$line);
$snamessplit=$line;
$snamessplit=~s/\s+/\_/g;
$snamessplit=~s/\_$//;
... |
797f224db74e3919e5b217dc876c7220d8a3d146a17556fa2925efdd3d288cda | Perl | 1,508 | 55 | use strict;
use warnings;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
my $user = 'ensro';
my $pass = undef;
my $dbname = 'mcvicker_chimp_agp';
my $port = 3350;
my $host = 'ecs4';
my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new
(-user => $user,
-host => $host,
-pass => $pass,
-dbname => $dbname,
-p... |
5155456d9c010f71e9c830089b2fc64698b4fcb52656a158400525eb4bd23f63 | Perl | 1,509 | 47 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
52993d45efb247a1460c4333e5b3e27ecc19cf35f965fc0b7ca5013dc5a133e4 | Perl | 1,509 | 58 | use warnings;
use strict;
my $f1=shift;
my $f2=shift;
open(F1,$f1);
open(F2,$f2);
my $mc1=0;
my @list=<F1>;
my @gop=<F2>;
@list = sort { uc($a) cmp uc($b) } @list;
@gop = sort { uc($a) cmp uc($b) } @gop;
my $cnt=0;
my %match;
my %mf;
my %mf1;
my %mf2;
my $title;
for(my $c1=0;$c1<=$#list;$c1++){
$li... |
727162d7afad147b7385f2d9a3557db9ee90a9b44454e5bfdbb2d0cf6cad7f22 | Perl | 1,509 | 55 | #!/usr/bin/perl
use strict;
use Bio::Graphics::Panel;
use Bio::Graphics::Feature;
chomp (my $CLASS = shift);
$CLASS or die "\nUsage: draw_contig.pl IMAGE_CLASS
\t- where IMAGE_CLASS is one of GD or GD::SVG
\t- GD generate png output; GD::SVG generates SVG.\n";
my $ftr = 'Bio::Graphics::Feature';
my $segm... |
f9bdbe6e142811d23613178c6e9f85dbd170c30222e60984e3be455e47a70c2e | Perl | 1,513 | 61 | if($#ARGV<1){
die "Usage: perl cluster_sort.pl file col_num, where file contains output from Tree with consensus sequences and motif scores added and col_num is the column with the score to use for the ranking (less is better)\n";
}
$file=$ARGV[0];
$col_num=$ARGV[1]-1;
open IN, $file;
$#details=$#bestscor... |
6ace860f675be71b79c8b3f2a67b3677bcc9d6abefa5ae9c6028dbb958fe16b4 | Perl | 1,544 | 50 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
c27778ad688669ee1c13a358c9eb4a2a4803ed0c473857d85e578766908c0383 | Perl | 1,551 | 44 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
5af6eb72e85ac13fe4d0b84c673b2c8531fcb001282638a6917fe49f4e5c7ab1 | Perl | 1,553 | 48 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
e050c9d1f1c9b0914c1209e312e4f7d9a1f03222a0cc7d14beef7d0c85a0ef03 | Perl | 1,554 | 54 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
2d23dc077c1955f52b817454998df1ff9ca6ca496519be2038e99909b84ef7fa | Perl | 1,563 | 52 | $file2=shift @ARGV;
open(F2,$file2);
$fout="$file2.class.csv";
open(FO,">$fout");
while($l=<F2>){
chomp $l;
$l=~s/^\s+//;
$l=~s/\s+$//;
@t=split(/\s+/,$l);
$line++;
if($line==1){
for($c=0;$c<$#t;$c++){
$cp=$c+1;
print FO"V$cp,";
}
print FO"CLASS\n";
}
for($c=0;$c<$#t;$c++){
$out=@t[$c]+0;
p... |
53b4fea4d313b84f7d9135c6b5487e1708b3a0a045ae7bb1454fa24b03776168 | Perl | 1,579 | 1 | /* instruction set
addc, subc, loadc -- (accumulator,constant)
add , sub , load , store -- (accumulator,addresses)
jumpEQ, jumpLE,... -- branch to locn by comparing
accumulator contents to zero.
jump -- unconditional branch to locn
...
Final assembler code is sequence of instr(op) or i... |
f46635382e108cec0b5f1fd957e2fd649775e08f0302bd258413913d4e7e7142 | Perl | 1,579 | 72 | $f1=shift @ARGV;
undef @seqname;undef @seq;
$seq="";
open(F1,$f1)||die "can't open";
while($line=<F1>){
chomp ($line);
if ($line =~ /^>/){
@seqn=split(/\s+|\_/,$line);
$snamessplit=$line;
$snamessplit=~s/\s+/\_/g;
$snames=$line;
c... |
9016946e13222bee9664c04f37fc23ebcc422ad5f74230e0d54dbaf58c717b8a | Perl | 1,581 | 63 | while(<>){
chomp;
$_=~s/
//g;
if($_=~/^>/){next}
else{$seq.=uc($_);}
}
sub rc {
my $dna = shift; # or my $dna = shift @_;
my $revcomp = reverse($dna);
$revcomp =~ tr/ACGTacgt][/TGCAtgca[]/;
return $revcomp;
}
sub fstr{
my $num_matches;
my $name=shift;
my $pep = s... |
b683cda239d42776e30cb55e3b69023f340cfcac3efe60b2a6b1fa87fec7294a | Perl | 1,599 | 88 | #!/usr/bin/perl
# gcd.pl sharma.animesh@gmail.com 2006/09/13 09:10:40
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $thresh;
if($ARGV[0]){$thresh=$ARGV[0];}
else{$thresh=10000;}
my $vop=abs(sqrt(6/(est_pi($thresh))));
print $vop;
sub est_pi{
my $trial=0;
my $threshold=shift;
... |
b0153bf08acf9cde2349f5175653aeeb70c780af7da372479f66ed95e8827b9c | Perl | 1,600 | 56 | #!/usr/bin/perl
# source http://www.farhadsaberi.com/perl/2010/10/perl-file-find-breath-depth-first-search-algorithms.html
use strict;
use warnings;
sub BFS{
my $start_dir = shift;
my @queue = ($start_dir);
while(scalar(@queue) > 0){
my @tmp_queue;
... |
26b828d3ccaeb90bffae2f8c9a78e2657559c8c10d141f5199d5a24ff18d23f7 | Perl | 1,613 | 69 | use strict;
use Text::ParseWords;
use Scalar::Util qw(looks_like_number);
my %vh;
my %nh;
my %ch;
my $cnt;
my $cntt;
my $f1 = shift @ARGV;
open (F1, $f1) || die "can't open \"$f1\": $!";
my $gn=shift;
#if(!looks_like_number($gn)){$gn=16;}
my $lc;
while (my $line = <F1>) {
$lc++;
$line =~ s/\r//g;
chomp $line;
if(... |
0faa4ea8006af20e07865c61b697c34f5dac93044f9ac09caa3310b9b36a2ec9 | Perl | 1,616 | 48 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
e6a29ed75ff55fbf1eb0b89a8ac8bc4f6ffd925784f00435b568b145d7fe495e | Perl | 1,622 | 82 | use warnings;
use strict;
$|=1;
use Data::Dumper;
my $fileflow=shift @ARGV;
open(F,$fileflow);
my $fo1=$fileflow.".actual.val";
open(FO1,">$fo1");
my $fo2=$fileflow.".mod.val";
open(FO2,">$fo2");
my $fo4=$fileflow.".csv";
open(FO4,">$fo4");
my $l;
my $c;
my @temp;
my @temp2;
my $length;
my $c2;
my $p0;
my $p1;
my... |
64ac93ea044c379bbf7249684b4b4c2d7b512de85bd100e4e38328540078556d | Perl | 1,634 | 81 | #!/usr/bin/perl -p -i.bak
# vim: ts=16
# A small script that replaces all old style labels with new ones
#
s/CYR_A/CYRA/g;
s/CYR_BE/CYRB/g;
s/CYR_VE/CYRV/g;
s/CYR_GHE/CYRG/g;
s/CYR_DE/CYRD/g;
s/CYR_IE/CYRE/g;
s/CYR_YERU/CYRERY/g;
s/CYR_YE/CYRYO/g;
s/CYR_ZHE/CYRZH/g;
s/CYR_ZE/CYRZ/g;
s/CYR_I/CYRI/g;
s/CYR_SH... |
002c5d38ab90a53dfc70c028b8e83c63616d7b5b81d991a225f0638f1ab4ad6e | Perl | 1,648 | 71 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
9c80199f38bef74f2bee561b3263cafea5775c688435357b117274faaf62e53a | Perl | 1,648 | 67 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
77202aa83623d58c95ffd3836272ad58f5e88029fd984dd995ccbd38001d5e36 | Perl | 1,652 | 48 | #!/usr/bin/perl
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... |
82e78fff6da380e4762edaed53a2bf027150384d6fec21e213323d1b7bc65b19 | Perl | 1,652 | 54 | #!/usr/bin/perl
use strict;
use warnings;
my $f=shift @ARGV;
unless(-e $f){die "USAGE:perl motif.pl <fasta file> <motif as regular expression>";}
my $motif=shift;
my $rev=shift;
if($rev){$motif=reverse($motif);$motif=~tr/][/[]/;}
my $seqn="";
my $seq="";
my $cnt=0;
sub motifind {
my $flag=0;
my $seql... |
bd52e271240a6c536bbf6fc51c781eeea947b2cffd5d79b12b112e4614d93711 | Perl | 1,652 | 53 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6f0b4c22e9f59eb5fd98cb131eca3079b39abad97d911d01f476456c71db2fd9 | Perl | 1,657 | 67 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
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