sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
941ca7f2e98895ed178bf661b920ed5e7fbf98867001d55eb58e4d586c6086ed | Perl | 797 | 42 | while(<>){
chomp;
$c++;
if($c==1){next}
@tmp=split(/\t/,);
$template=@tmp[0];
$status=@tmp[1];
$leftid=@tmp[3];
$rightid=@tmp[6];
$leftd=@tmp[8];
$rightd=@tmp[9];
$ri{"$leftid - $rightid"}++;
$rit{"$leftid - $rightid"}.="$template\t";
#if("$leftid - ... |
f81f5db9af321877d87bb2920bc54c3785efc6efb70a0914691bfea86c850630 | Perl | 797 | 28 | while(<>){
chomp;
$c++;
@t1=split(/\s+/);
if($c%4==1){
@t2=split(/\./,@t1[0]);
print "@t2[0],";
}
print "@t1[1],@t1[2],";
if($c%4==0){print "\n";}
}
__END__
1266 md5sum IC_??.txt.ru.class.arff.lrclass.txt | awk '{print $1}' | sort | uniq
1267 md5sum IC_??.txt.ru.class.arff.lrclass.txt | awk '{print $... |
334d7606877724df7fc42a38b1b41af2f03a0f3216c0a74bc0c43215c2108f84 | Perl | 801 | 42 | open(F1,"trimfile.txt");
#open(F1,"tf");
$thresh=200;
while(<F1>){
chomp;
$c++;
$name=$_;
$name=~s/\s+/\_/g;
@tmp=split(/\s+/,);
$namesubstr=substr($name,9,5);
$dirstr=uc(substr($name,15,1));
$libstr=substr($name,0,9);
$n1=@tmp[0];
@n2=split(/\_/,$n1);
$n4=@n... |
ec412ffa7282a75bce07ee77caa2641db0cf79b9fd1fe22d78967f34bce73178 | Perl | 802 | 40 | #!/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... |
3e2bc9bd8ec90a8e096428d0c19dbb73b0cdf7de64dbc4835165158f20a961c9 | Perl | 806 | 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;
m... |
1b69327781703c25b447c3b13b9c85aa130a248e0b95ac645b865a18c5d1446b | Perl | 807 | 10 | 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.... |
00f396633ceef61b237f8bc9aab850d4042e7cb1ad0015727ae9978105cc0e0e | Perl | 809 | 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;
m... |
114319dbc0e68342c591cdb30377ad25131b7ffb1832be2c383df8d87482dc04 | Perl | 809 | 38 | use lib 'lib';
use Graph;
use Devel::Size qw(size total_size);
my $N = 16384;
my $fmt = "%5s %8s %9s\n";
my $fmr = "%5d %8d %9.1f\n";
printf $fmt, "V", "S", "S/N";
my $g0 = Graph->new;
my $s0 = total_size($g0);
printf $fmr, 0, $s0, 0;
my $vr;
for (my $n = 1; $n <= $N; $n *= 2) {
my $g0 = Graph->new;
$g0->ad... |
ca92864266ed93009b337ede21fcfd718c2ca3a9c2c384b9a0eb67a87e72cfc3 | Perl | 809 | 34 | #!/usr/bin/perl
use DBI;
$proc_id = $ARGV[0];
$genseq_id = $ARGV[1];
$proc_stat = $ARGV[2];
$seq_aling = $ARGV[3];
@base=('a','t','g','c') ;
$dbh = DBI->connect('DBI:ODBC:mysql_seqdb', 'root','') or die "Unable to Create DB Handler... \n";
my $insh = $dbh->prepare_cached('INSERT INTO seqfile_seqstring... |
4b22c136606ecbf5fcf85f89f314c6e94994091eb650246d5bc7ed568fc73cdf | Perl | 810 | 44 | #! /usr/bin/perl
if ($#ARGV < 0)
{
print "Useage: $0 file1 [file2 ...]\n";
print " Scans each file for NULL characters and prints out\n";
print " the human genome fasta file corresponding to it.\n";
exit(0);
}
$num_files = $#ARGV + 1;
$num_success = 0;
for ($i = 0; $i < $num_files;... |
dd633b273317d21dbbb5514ec52f567c2c75965684af5911df920597aecfe0e1 | Perl | 811 | 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;
m... |
8bedf764ca273332ffb22048af41a3618d419e1947debf95c9320eaabf8c3150 | Perl | 813 | 44 | use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
open(F,$file);
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=1000;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0;
my %hitscore;
my %compname;
my %evalhitscore;
while(<F>){
my @tmp=split(/\s+/,$_);
my $... |
7b5584f79721bcbab1950adb925b11df305faf354b99c6a4aa42d9c751804235 | Perl | 815 | 30 | ##
# C O N F I G . P L
#
# configuration directives for mysqler's archive program
# Please edit this file to reflect your site configuration
##
#
# Your system's URL cgi path
#
$CFG::CgiPrefix = "/cgi-bin/";
#
# and where it actually resides on the system
#
$CFG::CgiDN = "/usr/local/apache/sites/st... |
0c476c824e84cb58c9d324196ee6c5df8a24b4cb5b4ba8b90d5dfe492e01a549 | Perl | 818 | 41 | my $f1 = shift @ARGV;
open (F1, $f1) || die "can't open \"$f1\": $!";
use strict;
use Text::ParseWords;
my %nh;
my %ph;
my $cntt;
my $lc;
my $header;
while (my $line = <F1>) {
$line =~ s/\r//g;
$lc++;
chomp $line;
if($lc==1){$header=$line;}
else{
my @tmp=parse_line('\t',0,$line);
my @tmpp=split(/-/,$tmp[0]);
... |
fa1a05a8cbfa237a50c840c955cbe3c6ee135dbbe830ba6ae4aa24addc78cb08 | Perl | 819 | 35 | #!/usr/bin/perl
if( @ARGV ne 2){die "\nUSAGE\t\"ProgName SeparatedSeqFile\t
AnnotationFile\n\n\n";}
$filess = shift @ARGV;$cp=0;$cnp=0;
$fileas = shift @ARGV;$cp=0;$cnp=0;
open (F1, $filess) || die "can't open \"$filess\": $!";
open (F2, $fileas) || die "can't open \"$fileas\": $!";
while ($line = <F1>) {
... |
cfa33a40fd5bc26e20710f7812cc7cf0291c1b2f40d7de002d1781a3bcccd775 | Perl | 827 | 27 | #!usr/bin/perl
use LWP::UserAgent;
$file=shift@ARGV;
$filetemp=$file;
$oo=$filetemp=~s/http//g;
if(($oo != 1) or ($file eq "")){die "usage linkgrab.pl websiteaddress\n";}
open(S,">$file.success.txt");
open(E,">$file.error.txt");
$input="console";
spidez($file,$input);
sub spidez
{
$f=shift;chomp $f;
... |
58a8344286aaa6c5c91a5bcbfb19c258990e72e61032a1269161d570ea299cc7 | Perl | 833 | 39 | $file=shift @ARGV;
$fileout=$file.".fgp";
open(F,$file);
open(FO,">$fileout");
$lthresh=100;
$profile=$file;
$profile=~s/An$//;
$pro=$profile;
while(<F>){
chomp;
@t=split(/\s+/,$_);
if(@t[3] ne "NA" and @t[4] ne "NA" and @t[3] ne "" and @t[4] ne ""){
$c++;
if(@t[3]<@t[4]){
$mend=@t[3]+@t[2]-1;... |
a51c844194fad9234ad6507d93faf22aa05fca4c8d83cf70f49f0f3cdf5ca347 | Perl | 847 | 43 | #!/usr/bin/perl -w
use ExtUtils::testlib;
use Audio::Ecasound qw(:simple :iam);
use strict;
# :iam is nicer without strict 'subs'
no strict 'subs';
on_error('');
# no strict 'subs' lets you do this:
cs_add play_chainsetup;
c_add chain1;
eci("-i:some_file.wav
-o:/dev/dsp");
cop_add '-efl:... |
7e28775174f8cf5fd024d8988abc199b02440083f30b2ae5822c94eefca31e34 | Perl | 849 | 22 | maxAlignment(Xs, Ys, A):-
findall(N,alignment(Xs,Ys,N),L),
maximum(L,A).
%find common members
alignment(Xs,Ys,N):- member(N, Xs), member(N, Ys).
%remove duplicates from start
maximum([],[]).
maximum([X|Rest], Result) :- member(X,Rest), maximum(Rest,Result), !.
maximum([X|Rest], [X|Res... |
2b4e7b1532c91338eec37a211f22e63d2711997e09b3c5e76dee3b1aa813b185 | Perl | 855 | 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 ... |
4d979b10d59b47a76273e2441253fd42e7654a1d623ddbafc217d1cd3c9ed0f8 | Perl | 855 | 31 | #!/usr/bin/perl -w
use Bio::Seq;
use Bio::Index::Fasta;
$out = Bio::SeqIO->new(-file => ">>seq" , '-format' => 'Fasta');
print "File with list of contig_names? ";
$filename = <STDIN>;
open (FILENAME,$filename) || die " cannot open $filename: $!";
$dir=".";
$db="eh2x";
$dbobj = Bio::Index::Abstract->new("... |
2d0071a02a5aa63733d47ca01168ec35795621514a903631bd6a4c1381267c16 | Perl | 860 | 41 | use strict;
use warnings;
use Text::ParseWords;
my %seqh;
my %sfull;
my $seqc;
my $f1=shift @ARGV;
my %pephsh;
my %pepcnt;
my %peplgt;
open(F1,$f1);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
if($l1=~/^>/){my @st=split(/\|/,$l1);$seqc=$st[1];$sfull{$seqc}=$l1;}
else{$l1=~s/... |
c4d38db99a2f852b54038d3fc98853238f69ff72499c4b27b1cd6d0990d9759a | Perl | 872 | 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 ... |
22042839624c8a74e339fb86dbb9d6f9454c3659e5bd4c521b9e8d887f21fa94 | Perl | 874 | 42 | #!/usr/bin/perl
$f1=shift;
open(F1,$f1);
while(<F1>)
{
if($_=~/^F/){
chomp;
@tmp=split(/\t/);
push(@name1,@tmp[0]);
$n1{@tmp[0]}=$_;
}
}
$f2=shift;
open(F2,$f2);
while(<F2>)
{
if($_=~/^F/){
chomp;
@tmp=split(/\t/);
push(@name1,@tmp[0]);
$n2{@tmp[0]}=$_;
}
}
open(F1O,">$f1.$f2... |
7a36a6ac40d286e05198ed5896cb706b88752769d8c75670cbc4d1a65baf3a0f | Perl | 881 | 15 | #!/usr/bin/perl -w
use strict;
use LWP::Simple;
my $url = "http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl?".
"title=Genew%20output%20data&hgnc_dbtag=on&col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&".
"col=gd_status&col=gd_locus_type&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&".
"col=gd_pub_chrom_map... |
28b043adc34af13e0f1ec51ca5a6ecf2dc7c5517c885e87f9b4bc844020b8d41 | Perl | 884 | 27 | system("export CLASSPATH=/home/animesh/export/weka");
$file=shift @ARGV;
chomp $file;
system("wc $file | awk '{print \$1}' > $file.tmp");
open(TMP,"$file.tmp");
$wc=<TMP>;
$wc+=0;
close TMP;
#for($wcp=2;$wcp<$wc;$wcp++){
for($wcp=3;$wcp<$wc-1;$wcp++){
system("head -n $wcp $file > train.csv");
system("head -n 1 $file > ... |
7fc7389c7c929e581a8df6b5456efbcbd00539cf644637177c4e49d841e7afb5 | Perl | 884 | 30 | use strict;
use warnings;
use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new( -source => 'flatfile',
-directory => 'taxdmp/',
-nodesfile => 'taxdmp/nodes.dmp',
-namesfile => 'taxdmp/names.dmp');
my $name=shift @ARGV;
open(F,$name);
while(<F>) {
my @tmp=split(/\t/);
p... |
4a5be27674f66d7484dafd9771a72a36ff24b5ae74cd65ebc26a0168f58dc712 | Perl | 889 | 28 | #!/usr/local/bin/perl -w
# Generates a list of Bio::EnsEMBL::DBSQL::DBAdaptor objects for all core databases found on two staging servers
# minus databases that contain ancestral sequences.
use strict;
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_multiple_dbs(
{ '-host' => 'ens-stagin... |
2d4569c86388d44e5680475780a8fd5e0d7e57785b43ec4ffed353cb0d199f95 | Perl | 890 | 52 | my @b = qw/A T G C/;
while(){
print $b[int(rand(4))];
}
my %t2o = (
'ALA' => 'A',
'VAL' => 'V',
'LEU' => 'L',
'ILE' => 'I',
'PRO' => 'P',
'TRP' => 'W',
'PHE' => 'F',
'MET' => 'M',
'GLY' => 'G',
'SER' => 'S',
'THR' => 'T',
'TYR' =... |
f1ebd07e0e7b88d62122c2be2e5272c286fa93bb64b51731d495e81552fa2574 | Perl | 894 | 22 | # 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 ... |
b82509c2909412dceb92100fb133f8739ceb628231fbb596df32fa345a5b9748 | Perl | 898 | 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 ... |
8c84b0c57639eccb84b374e7bac962c86edbac2e9814a65583188d7c134aeefa | Perl | 906 | 30 | use strict;
use warnings;
use Bio::SeqIO;
my $f=shift;
my $ftype=shift;
my $i = new Bio::SeqIO(-file => $f, -format => $ftype);
my $o = new Bio::SeqIO(-file => ">$f.cds.fasta");
my $opep = new Bio::SeqIO(-file => ">$f.pep.fasta");
my $seqno=0;
while( my $s = $i->next_seq ) {
my @codingseq = grep { $_->prima... |
028b6d36e82bd7d9bf746a707857402099555c6cacd6c071cfa4651e7c672723 | Perl | 907 | 34 | #! C:/perl/bin/perl
use DBI;
$dbh = DBI->connect('DBI:ODBC:mysql_seqdb', 'root','') or die "Unable to Create DB Handler... \n";
my $insh = $dbh->prepare_cached('INSERT INTO window_analysis VALUES (?,?,?,?,?)') or die "Unable to Prepare... \n";
$process_id =1;
$seqfile_id =1;
$seq_id = 'excluded_4';
$st... |
57a322572b8206e85dbba61d158ec9b2905e0b8b5a4a07a0e08efd773c628677 | Perl | 909 | 38 | #!/usr/bin/perl
#system("ls -1 vol.*.txt | wc > $size");
$size = `ls -1 vol.*.txt | wc`;
split(/\s+/,$size);$size=$_[1];
if($size<1){die"Size NULL\n";}
print "$size\n";
open(FO,">volall.out");
open(FOF,">ftr.out");
for($c=0;$c<$size;$c++){
$cnt=$c+1;
$file="vol.".$cnt.".txt";
print "Processing $c\t$file... |
e96916d1f4df677b88908ea26ce4227e7b3aaea3950cfbb2acadd3bcf9af5e23 | Perl | 909 | 50 | use strict;
use warnings;
use Text::ParseWords;
my $idi = 1;
my $i1 = 0;
my @files=<SL22?????.*hamr_mods.txt>;
my %id;
my %idc;
my %ids;
my %cc;
foreach my $f1 (@files){
my @tmp;
my @name;
my %pg;
my $lcnt;
open (F1, $f1) || die "can't open \"$f1\": $!";
while (my $line = <F1>) {
chomp... |
eb02c3ce966359d96ddef4bce38c0ba4f7fc65febbd3d529d31341635899df27 | Perl | 909 | 17 | @files = <svm_mat_lex.csv.class.arff>;
system("export CLASSPATH=/usit/titan/u1/ash022");
foreach $file (@files) {
$c++;
# print "Processing file # $c $file LR\n";
# system("java weka.classifiers.meta.ClassificationViaRegression -t $file -x 176 > $file.class.arff.176fold.lr.txt ");
# print "Processing file # $c $file... |
8ab0fda7256bd009a90948b2735e8c5d6f9ac08ceb5c743e04029554b8ccc55f | Perl | 910 | 45 | use strict;
use warnings;
use Text::ParseWords;
my $path = shift @ARGV;
my $idi = shift @ARGV;
my $val = shift @ARGV;
my %nc;
my $lcnt;
open (F1, $path) || die "can't open \"$path\": $!";
while (my $line = <F1>) {
chomp $line;
my $cl=$line;
$line =~ s/\r|\`|\"|\'/ /g;
$lcnt++;
my ... |
85fef128c05803c5cb57918f38d5f88f46656e2422b11f0683d2a42e7d3a5e0e | Perl | 911 | 35 | #!/usr/bin/perl -w
#
# Simple test for TrackDb module. Make sure we're able to
# get the list of trackNames for each database of interest and
# for TrackDb's default database.
#
# Figure out path of executable so we can add perllib to the path.
use FindBin qw($Bin);
use lib "$Bin/perllib";
use TrackDb;
... |
c7e1d65666952401a64aa881be3ce5e7b9aa2326bc9e2729e9e45812825f12cc | Perl | 927 | 32 | use strict;
use warnings;
use Text::ParseWords;
my $f = shift @ARGV;
unless(-e $f){die "USAGE:perl findProtein.pl proteinGroups.txt";}
my $id = "Protein IDs"; #column name of IDs
my $pattern = qr/\./; #none of the IDs in above column should NOT contain this
my $idi;
my $lcnt = 0;
print "Uniprot ID(s)";
open (F1, $f)... |
184ee625bfc45c414213649d5ee9b254478ed9efe7066c175f9dad7763e85972 | Perl | 928 | 39 | #!/usr/bin/perl
# Reads a list of numbers on stdin, computes a (blocked) histogram.
#
# If there are two numbers per line, they are assumed to be
# a begin-end pair.
# grep "M u " ATAC/atac.shift.atac | cut -d' ' -f 7 | perl run-length-histogram.pl > atac.histogram
# grep "M u " ATAC/box2.shift.atac | cut -d' ' ... |
f0fc78608ad49c508e299084beba09d6edeab0f2e0d7501572284e424a982b23 | Perl | 934 | 28 | # perl -w
use strict; use lib '.';
use GraphViz;
my $g = GraphViz->new();
my @default_attrs = (
fontsize => '8',
fontname => 'arial',
... |
30ee465b21f766b223a0d609619c8cddc8100eef33208b344c009632bf1dd2b1 | Perl | 935 | 29 | #!/usr/bin/perl
$fs = shift @ARGV;
open F,$fs;
while($l = <F>){
chomp $l;
if($l ne ""){
$l=~s/\-//g;
push(@list,$l);}
}
close F;
#print @list;
foreach (@list){
use LWP::UserAgent;#$a=$ENV{'env_pro'}."\:".$ENV{'env_pas'};
$gif="http://webbook.nist.gov/cgi/cbook.cgi?Struct=C".$_;
$fff=$_.".gif";... |
d2d1e31f44bf25e7f1a3e3d12bbf12e8cfba45adaf62e786729348ca94bd31d6 | Perl | 937 | 32 | use Bio::Tools::BPlite;
my $report = new Bio::Tools::BPlite(-fh=>\*STDIN);
{
$report->query;
$report->database;
while(my $sbjct = $report->nextSbjct) {
$name = $sbjct->name;
while (my $hsp = $sbjct->nextHSP) {
# $hsp->score;
# $hsp->bits;
$percent=$hsp->percent;
# $hsp->... |
06846e1413d6a90d045b4dd473076071562506e205bdbd51e07289483ac5b498 | Perl | 948 | 50 | use strict;
use Text::ParseWords;
my $f1 = shift @ARGV;
my $fa = shift @ARGV;
my @tmp;
my @name;
my @names;
my %pg1;
my %pgfa;
my %nc;
my $lc;
my $hdr;
open (F1, $f1) || die "can't open \"$f1\": $!";
while (my $line = <F1>) {
$lc++;
chomp $line;
$line =~ s/\r//g;
@tmp=parse_line(',',0,$line);
my @slc=@tmp[1..$#... |
d21794f34e617bb99aac760cebba3d2b6501982f6b59e0ea2c118cf32a4f134b | Perl | 955 | 16 | @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... |
bec995baf6c176eaf31028b8818592ffe1b55d59d9e8c8d4c8c1f8209824119c | Perl | 956 | 30 | #!/usr/bin/perl
use strict;
use warnings;
my $f=shift @ARGV;
open (F,$f);
print $f;
my $mot=9;
my $seq=5;
my $pg=8;
my $lenmot=5;
print "Protein\tSequence\tMotif\tAminoAcid\tPosition\tMseq\tLength\n";
while (my $line = <F>) {
chomp ($line);
$line=~s/\r//g;
my @se=split(/\t/,$line);
my @motname=split(... |
521b7875127abbc92329ba39c4cc7ceba7b2cc3d098f087ede54867e19e504ce | Perl | 959 | 44 | mesh@astrakan ecoli]$ cat gs.pl
$f1=shift @ARGV;
chomp $f1;
$f2=shift @ARGV;
chomp $f2;
$break=shift @ARGV;
chomp $break;
print "Sorting $f1\n";
system("sort $f1 > $f1.s");
print "Sorting $f2\n";
system("sort $f2 > $f2.s");
open(F1,"$f1.s");
open(F2,"$f2.s");
open(F,">$f1.$f2.out");
while(<F1>){
chomp $_;
... |
aae4339c4c688e6b92d8b539b0299a5425d1bcc46fd3ea148ea224b9eb8a0aec | Perl | 959 | 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 ... |
050bf884d60ff95d6f681a821ae052cbe19401e7be2a56dff5dbf26a46ed021f | Perl | 965 | 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 ... |
dbfc4122ac4c34c21c29900ac286989c64c6cd12b7fee482a966408fcbe59b65 | Perl | 968 | 26 | #!/usr/bin/perl
use WWW::Mechanize;
use LWP::UserAgent;
my $agent = WWW::Mechanize->new();
$agent->proxy(['http', 'ftp'] => 'http://animesh_sharma:Infosys123@192.168.100.25');
$agent->get($url);
$agent->follow_link( 'n' => 3 );
$agent->follow_link( 'link_... |
8f6e8e5e3ff856d6d7b01948980f17f3baecfe6acf7f2a06769160bceb5cc808 | Perl | 969 | 40 | #!/usr/bin/perl
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName MultSeqFile\t\n\n\n";}
$file = shift @ARGV;
open (F, $file) || die "can't open \"$file\": $!";
$seq="";
while ($line = <F>) {
chomp $line;
if ($line =~ /^>/){
$c++;
#$line=~s/\|/\-/g; $line=~s/\s+//g;#$line=substr($line,1,30);
push(@seqname,$l... |
3a6bafcd1f0fcc6672a473a3f9e87f1d0c6c28cfbdefc278e89f523ecca7f82b | Perl | 970 | 62 | use strict;
use warnings;
#if any parameter is passed then dump out accumulated data
# else just the nu,berof hits at each cutoff
my $acc;
my $temp = shift;
if(defined($temp)){
if($temp eq "acc"){
$acc = $temp
}
else{
die "only acc allowed to set to dump acummulated passes\n";
}
}
... |
dce81bb0936a49c0ee86ea0d6e67e4cd0b2c8896a8d6aba3583bf2c5a1cca58c | Perl | 971 | 43 | use lib '/Home/siv11/ash022/bioperl/';
use Bio::SearchIO;
my $blast_report = new Bio::SearchIO ('-format' => 'blast',
'-file' => $ARGV[0]);
my $result = $blast_report->next_result;
while( my $hit = $result->next_hit()) {
print "\thit name: ", $hit->name(),"\t";
while( my $hsp... |
5dd6b231a2433dbbb512c05209a8b2ba836e98abf0c28d4a8dc1f06ad44f98af | Perl | 974 | 54 | #!/usr/bin/perl
use strict;
my $file=shift @ARGV;
open(F,$file);
my $file0o=$file.".0.out";
open(F0O,">$file0o");
my $fileo=$file.".out";
open(FO,">$fileo");
my $l;
my $c;
my $k;
my $c1;
my %elem;
my $min=1000000000000000000000000000000000;
my $max=0;
my $genomesize=2045775;
while($l=<F>){
$c++;
c... |
8612256999c15128c9f483572335c2364f1813a8ca9eb9c018446e69a9b64f50 | Perl | 976 | 44 | @files=<IC_1*.csv>;
foreach (@files){
$file2=$_;
open(F2,$file2);
$fout="$file2.class.csv";
open(FO,">$fout");
$file1="label.txt";
open(F1,$file1);
while($l1=<F1>){
$l1line++;
chomp $l1;
@t=split(//,$l1);
$len=$#t;
print "$len\t@t[0]\n";
if($len!=0||$l1line>66){die"label file incorrect or more labels"}
el... |
1f06960e0230fa5da532b309b066715f9269bc4ffaa4a76a48bc5a4a0f1dc9e1 | Perl | 977 | 37 | $file=shift @ARGV; chomp $file; open(FC,$file);
while($l=<FC>){
if($l=~/^>/){
chomp $l;
$l=~s/>//;
@tmp=split(/,/,$l);
@tmp2=split(/\.\./,@tmp[1]);
@tmp4=split(/\s+/,@tmp2[1]);
@tmp6=split(/\.\./,@tmp[2]);
@tmp8=split(/\s+/,@tmp6[1]);
#print "@tmp[0] @tmp2[0] @tmp4[0] @tmp6[0] @tmp8[0] @tmp4[4]\n";
#@tmp[0]=~s/^>|\s+$/... |
690d4e70164632e6a1eebf473bbe63997de44318939838527798cf030265da43 | Perl | 978 | 31 | #!/usr/bin/perl -w
use strict;
my $USAGE = "perl filterFasta.pl fasta-file seq-length\n";
my $f1 = shift @ARGV or die $USAGE;
my $slen = shift @ARGV or die $USAGE;
my $seqc;
my %seqm;
open(F1,$f1);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
$l1=~s/\s+//g;
if($l1=~/^>/){$l1=~s/>//g;$l1=~s/[^[:ascii:]]//g;$seqc=$... |
2bbe589e7726ad9bee4975edced4a3a69a090cef9c7d3dc8cd2bda6aac80e711 | Perl | 986 | 29 | # 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 ... |
4252a764ee708825d815ec644e384541c33261b8f0d117cdb00ad81621adfa7a | Perl | 990 | 26 | #!/usr/bin/perl
#>codbac29j5-2o21.rp2_b1.SCF 883 0 883 SCF
# bac2pair.pl sharma.animesh@gmail.com 2009/03/22 01:04:42
#>codbac181n17-1a01.rp2_b1.SCF CHROMAT_FILE: codbac181n17-1a01.rp2_b1.SCF PHD_FILE: codbac181n17-1a01.rp2_b1.SCF.phd.1 CHEM: term DYE: big TIME: Wed Mar 17 10:36:37 2010
#Converts fo... |
34331cf45796668c2d926981662c8d533c94055ebb32f5c1c9a32debe2a7412b | Perl | 993 | 37 | #!/usr/bin/perl
if( @ARGV ne 2){die "\nUSAGE\t\"ProgName SeparatedSeqFile\t Annotated\n\n\n";}
$filess = shift @ARGV;$cp=0;$cnp=0;
$fileas = shift @ARGV;$cp=0;$cnp=0;
open (F1, $filess) || die "can't open \"$filess\": $!";
open (F2, $fileas) || die "can't open \"$fileas\": $!";
while ( $line = <F1> ) {
chomp... |
7f63ae599b9d91fca04d87698facd4e54d0774a6744df0f0d56a3586366ff0fa | Perl | 1,000 | 61 | #!/usr/local/bin/perl
use Math::Complex;
$pi=pi;
$i=sqrt(-1);
$file=shift @ARGV;
chomp $file;
@base=qw/G T A C/;
$base{""}= "0\t0\t\t0\t0";
$base{"G"}="0\t0\t\t0\t1";
$base{"T"}="0\t0\t\t1\t0";
$base{"A"}="0\t1\t\t0\t0";
$base{"C"}="1\t0\t\t0\t0";
$base{"N"}="1\t1\t\t1\t1";
OPENFAS($file);
WRI... |
ae407e310cf6d6df593e2cb242c9968d352dc3e760a9f55a51d36bd0bc680519 | Perl | 1,000 | 52 | if( @ARGV ne 2){die "\nUSAGE\t\"ProgName MultSeqFile1 MultSeqFile2\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);
... |
666855a12b80546bf05b8e04c0d300fe3350f4a72d97e9276b773ee43a1ed906 | Perl | 1,013 | 46 | $min=Inf;
$max=-Inf;
while(<>){
chomp;
@tmp=split(/\s+/);
@name=split(/\-/,@tmp[1]);
push(@nam1,@name[0]);
push(@nam2,@name[1]);
$heat{"@tmp[1]"}=@tmp[2];
if(@tmp[2]>$max){$max=@tmp[2]};
if(@tmp[2]<$min){$min=@tmp[2]};
}
%seen = (); @name1 = grep { ! $seen{ $_ }++ } @nam1;
%seen = (); @name2 = grep { ! $seen{ $_ }++ } ... |
23ab90615646adc6b9dd82a5445c7993390799382e131c495e1ac4ade6b54d12 | Perl | 1,029 | 25 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
b130b7d17f4c79d78a2a76a24ded7aaf50c33424839728100359fd2c1fdf213f | Perl | 1,039 | 55 | #! /usr/bin/perl
if ($#ARGV < 0)
{
print "Useage: $0 file1.bzh [file2.bzh ...]\n";
print " Scans each bzh file and prints out the human genome fasta file\n";
print " corresponding to those runs which failed.\n";
exit(0);
}
$num_files = $#ARGV + 1;
$num_success = 0;
for ($i = 0; $i ... |
43c4b264efbfe02d2328c0e76e4e4d703440891ab0b180e52fa59fff2057584f | Perl | 1,040 | 37 | use strict;
my $file=shift;chomp $file;
my $pep=shift;chomp $pep;$pep=uc($pep);
my $id=0;
my $s=3;
my $e=10;
open(F,$file);
print "MeropsID\tEnzyme\tPattern\tPosition\tAmbiguity\n";
while(my $line=<F>){
my @tmp=split(/\t/,$line);
#my $mat = join('', @tmp[$s..$e]);
my $mat;
fo... |
475040a0cd378b15ef9e8c4be3508d90c2d526861fb538e1e26ce597c1fde03e | Perl | 1,042 | 51 | $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])... |
0f2888debcdb38306b5f7a794dd91050ee97ca0c86a168921640d8e81315e5c6 | Perl | 1,044 | 39 | % Author:
% Date: 17.11.2008
% Program made with inspiration and help from the Prolog Tutorial website linked
% to in course resources for Compulsory Exercise 3. Adaptions have been made to
% suit a userselected number of queens, instead of a set number.
% Creates a list to hold numbers rising from 1 to the selected ... |
278a0595ab0573cbea2d770d6a9f2d6820c547c33c607ef22cd42199d3c389ab | Perl | 1,044 | 40 | $file=shift @ARGV;
open(F,$file);
while ($line = <F>) {
chomp ($line);
if ($line =~ /^>/){
@seqn=split(/\t/,$line);
#$snames=@seqn[0];
$snames=$line;
chomp $snames;
push(@seqname,$snames);
if ($seq ne ""){
... |
5b41165d813d1541c5c8afd445db0bc81676db6ad1607bb802485e1029ef39c9 | Perl | 1,044 | 31 | # 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 ... |
5d3e5fecc05aaf1a97948a6a72cee387ce0fb748cf68d9e49586974bd2cb8789 | Perl | 1,044 | 35 | $filetemplr = shift @ARGV;
chomp $filetemplr;
system("grep -E \"a = C0\|b = C1\" IC_*_toML.txt.class.arff.72fold.lr.txt > $filetemplr ");
open(F,$filetemplr);
$filetemplrout=$filetemplr.".72.out";
open(FO,">$filetemplrout");
while(<F>){
chomp;
$c++;
print "$c\n";
@t1=split(/\s+/);
if($c%4==1){
@t2=split(/\./,@t1... |
376b8d4b7fece097a5ef0c54c7e07f310dec477d7fc8fa78dcf1ce64f04eb5b6 | Perl | 1,046 | 33 | use strict;
sub createOverlapStore {
goto alldone if (-d "$wrk/$asm.ovlStore");
if (! -e "$wrk/1-overlapper/$asm.ovllist") {
if (runCommand("$wrk/1-overlapper",
"find $wrk/1-overlapper/ \\( -name \\*ovb -o -name \\*ovb.bz2 \\) -print > $wrk/1-overlapper/$asm.ovllist")) ... |
a45fbac3ee31240daa19c083be9b571c24f7124cc32722f25da4bde3300cd39d | Perl | 1,046 | 33 | # 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 ... |
b11902cc74b7079be19c99c296a82ee332233ddb69deb7ed9236e6e2d018e6f2 | Perl | 1,052 | 53 | $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=@seqn[0];
$snamessplit=~s/\>//g;
$snames=$line;
chom... |
b4b03a5d9735be577163b52a1810aa5d19238b81a7bc533469da44eb8662d25d | Perl | 1,057 | 42 | my $main_file_pattern=shift @ARGV;chomp $main_file_pattern;
open(F,$main_file_pattern)||die "can't open";
my ($line,$snames,@seqname,@seq,$fresall,$seq,$seqname);
$gl=600000000;
while ($line = <F>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
... |
09424c4470f6abe1f945aa145b9c3da2bbfbeccee658d0bcbd2d75e3578f87f2 | Perl | 1,065 | 46 | #!/usr/bin/perl
$file1=shift @ARGV;
chomp $file1;
open F2,$file1;
$ftr=5;
$rown=0;
while($l=<F2>){
$rule=0;$rulc=0;$rown++;
@t=split(/\s+/,$l);#$len=(@t);
for($c=2;$c<=($ftr*3+1);$c=$c+3){
#print "$c\t@t[$c]\t";
if($l=~/^Rule/ and @t[$c]!~/-/){
if($rulc%1==0){$rule++;}
if($rown%2==0){
... |
27de19bdb68d33a28902bbe5e73a5454513210e139f330cfba6ca71257520635 | Perl | 1,066 | 39 | use blib; # when using inside the dist tree
use PDL; # this must be called before (!) 'use Inline Pdlpp' calls
# for this example you need the numerical recipes library
# edit the INC and LIBS info below to point
# Inline towards the location of include and library files
use Inline Pdlpp => Config =>
INC =... |
b4d24eebde4691e779fc34a993fb0ace841661a35957090cf380bcce78b90782 | Perl | 1,068 | 32 | #!/usr/local/bin/perl
# Rong Chen 6/24/2002
if ($#ARGV != 0)
{
print "This program creates all predicted complex structures ";
print "according to a zdock output. ";
print "create_lig, receptor.pdb, and ligand.pdb must be in your current directory.\n";
print "\nUsage:\n";
print "$0 [dock... |
73f28ec1153c64afa0ca35203c3efce22f82d77a449922f871aa60c7ba7647ae | Perl | 1,080 | 36 | # 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 ... |
a5d846a1e147de53a22e614ec745bffe8fa59da5e08d5e995b17028248c9b5b7 | Perl | 1,081 | 30 | use Bio::Graphics::Panel;
# Create a series of Bio::SeqFeature objects. In this example, we use AcePerl
use Ace::Sequence; # or any Bio::Seq factory
my $db = Ace->connect(-host=>'brie2.cshl.org',-port=>2005) or die;
my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
... |
16a05bb3a902d90cd034821aea78b733106dddc45ec2ae9a3abfbd0a271a673d | Perl | 1,083 | 52 | $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 $snames;
@ty=split(/\s+/,$snames);
push(@seqname,@ty[0]);
if ($seq ne ""){
... |
5ec641ad862dee6c214d6a421293eb190affbafd6ffb1e781e9700aff9ef2a5b | Perl | 1,086 | 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 ... |
f75b7255d366e318998d22759f7d7cecd58d3599576b6bb2b57fedcdbedf3bef | Perl | 1,092 | 57 | use strict;
use warnings;
my $seq;
my $seqc;
my $seql;
my %seqn;
my %pep;
open(F1,$ARGV[0]);
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
my @tmp=split(/\t/,$l1);
my $p=$tmp[34]=~s/\:p\./\:p\./g;
my @tmp2=split(/\;/,$tmp[34]);
if($p>$#tmp2){
#print $tmp2[0],"\t",$#tmp2,"\t",$p,"\n";
for(my $c=0;$c<=$#tmp2;$... |
8739b95ecf4e185cb7251918ab1a0fc138a12c66b08300e2febf6210a457480e | Perl | 1,098 | 17 | # 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 ... |
826965146910e20f4fe6faf95e503b1a5081c7405dcd70c31c085b0671a6d567 | Perl | 1,108 | 53 | #!/usr/bin/perl
print "enter the name of the swissprot file\n";
$file=<>;
chomp $file;
open F1,$file;
$file=~s/\.txt//;
open F2,">$file\.csv";
while($line=<F1>)
{
if($line =~ /^RN/)
{$line=~s/RN//;
#print $line;
@ID=split(/\s+/,$line);
print F2"@ID[1]";
}
if($line =~ /^RA/)
{$line=~s/RA//;$line=... |
826a6d37176ae33b94e2a77af517562e3ddf074af3cdae54bc2c76352ca41517 | Perl | 1,108 | 69 | #!/usr/bin/perl
# ofs2svm.pl sharma.animesh@gmail.com
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift;
my $ftr=shift;
my $fo=$file.".svm.out";
open(F,$file);
open(FO,">$fo");
while(my $l=<F>){
my @t=split(/\s+/,$l);
for(my $c=1;$c<=$ftr;$c++){
print @t[-$c]," ";
... |
def29d375bbde23a5a2d2e42d23d52f9ff8315790556a7dacee3ce1123179b1b | Perl | 1,116 | 51 | use GraphViz;
$g = GraphViz->new();
$graph_file_pattern=shift @ARGV;
open(F,$graph_file_pattern)||die "can't open";
while(<F>){
@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}++;
$label="$e1->$e2($r... |
8ec5bb8d71c9d86541a2e83a0e108d1fdbf153a07f2cc4398ab087404d8da2c1 | Perl | 1,119 | 26 | % Obligatorisk øvelse 3
% Bjørnar Vister Hansen (Stud.nr. 185856)
% bha100@student.uib.no
% Oppgave A
alignment(Xs,Ys,[]).
alignment(Xs,Ys,[A|T]) :- append(U,[A|T1],Xs), append(I,[A|T2],Ys), alignment(T1,T2,T).
maximum([],M).
maximum([X|T],M) :- length(X,Y), length(M,Z), Z >= Y, maximum(T,M).
maxAlignment(Xs,Ys,Alig... |
74141d0951f5933cb58c15b5ce917aa6551d0087eff5cf972747cfaf4de8f0b9 | Perl | 1,120 | 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 ... |
cd79654c75037230cc3b432c0ee38e674b105666e295b3cd5a128d39c3baee47 | Perl | 1,123 | 19 | @files = <svm_mat_lex.csv.study.csv.arff>;
system("export CLASSPATH=/usit/titan/u1/ash022");
foreach $file (@files) {
$c++;
print "Processing file # $c $file LR\n";
system("java weka.classifiers.meta.ClassificationViaRegression -t $file -x 176 > $file.class.arff.176fold.lr.txt ");
system("java weka.classifiers.m... |
af8387e54bb3edb14c0b199e7f235beeb0f8f7ef62d6d0b02408a7b1ffebc26b | Perl | 1,130 | 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 ... |
c7e343f588d4c808a71196c52752c4a992a9f86248eef4508a00ddb45e17057a | Perl | 1,131 | 26 | % Obligatorisk øvelse 3
% Bjørnar Vister Hansen (Stud.nr. 185856)
% bha100@student.uib.no
% Oppgave A
alignment(Xs,Ys,[]).
alignment(Xs,Ys,[A|T]) :- append(U,[A|T1],Xs), append(I,[A|T2],Ys), alignment(T1,T2,T).
maximum([],M).
maximum([X|T],M) :- length(X,Y), length(M,Z), Z >= Y, maximum(T,M).
maxAlignment(Xs,Ys,Alig... |
d33783e59e57bf13d0c28c79ea5b124eba7e16874cbc9005dd15b3d8e294e198 | Perl | 1,131 | 52 | #!/usr/bin/perl
# Reads a list of numbers on stdin, computes the n50.
#
# If there are two numbers per line, they are assumed to be
# a begin-end pair.
# grep "M u " ATAC/atac.shift.atac | cut -d' ' -f 7 | perl n50.pl 3076782067
# grep "M u " ATAC/box2.shift.atac | cut -d' ' -f 7 | perl n50.pl 3076782067
my @va... |
da16a1364708ed6d873f0b00f7e9be80cb7c3e0ad108a3dfca711811b2415ebc | Perl | 1,132 | 39 | my $main_file_pattern=shift @ARGV;chomp $main_file_pattern;
open(F,$main_file_pattern)||die "can't open";
my ($line,$snames,@seqname,@seq,$fresall,$seq,$seqname);
while ($line = <F>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
push(@seq... |
9f033cec4974a4da059eb2b33408ef3ca17fc5e1f93e6a345070f38b5be38945 | Perl | 1,137 | 41 | #!/usr/bin/perl
if( @ARGV ne 2){die "\nUSAGE\t\"ProgName SeparatedSeqFile\t Annotated\n\n\n";}
$filess = shift @ARGV;$cp=0;$cnp=0;
$fileas = shift @ARGV;$cp=0;$cnp=0;
open (F1, $filess) || die "can't open \"$filess\": $!";
open (F2, $fileas) || die "can't open \"$fileas\": $!";
while ( $line = <F1> ) {
chomp... |
a2568018428587a51c6f49fa1ed2805be449816b3604065a808127ba4f476f5c | Perl | 1,143 | 40 | use strict;
use warnings;
use LWP::Simple;
use WWW::Mechanize;
my $query=shift @ARGV;
chomp $query;
print $query;
my @collurl;
my $purl = 'http://www.ensembl.org/Multi/Search/Results?species=all;idx=;q='.$query.'%201';
#my $url= 'http://www.ensembl.org/Bos_taurus/Search/Details?species=Bos_taurus;idx=Gene;end=14;q=hi... |
04d0819a0b975b17efb3b1d1024ffe71db44694f2c2041e49a63d9218006c3d8 | Perl | 1,144 | 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 ... |
746a0b34bdc0ae69f39334c2eceb16b0d7f449bbf671c00b9222e0f3d99b0159 | Perl | 1,144 | 35 | # 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 ... |
20e9300fe730b0825d54a6c300fb343ce21f0850aebb62180657bd4f399d2d7b | Perl | 1,151 | 47 | #!/usr/bin/perl -w
#
# This small example program walks the directory tree and draws a
# directory of the files and directories in the GraphViz distribution.
#
# It also shows the use of the GraphViz::No subclass.
use strict;
use lib '../lib';
use IO::Dir;
use GraphViz;
use GraphViz::Small;
use GraphViz::No;
my $dire... |
773d7766ddf0e83189527d7d82de3837f4a16a42e87a299638243518db3f1d28 | Perl | 1,153 | 39 | #!/usr/bin/perl
use strict;
my $main_file_pattern=shift @ARGV;chomp $main_file_pattern;
my $start=shift @ARGV;
my $end=shift @ARGV;
open(F,$main_file_pattern)||die "can't open";
my $fo=$main_file_pattern.".$start.$end.fasta";
open(FO,">$fo")||die "can't open";
my $seq;
my $seqn;
while (my $line = <F>) {
chomp $li... |
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