sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fe94a486b2dfa0dcb9e504e2a1aaf334b2209274aecf84fad1e0221d28a49c93 | Perl | 306 | 23 | #!/usr/bin/env perl
use strict;
my $delimeter = ($ARGV[0] eq '-s') ? '\s+' : '\t';
while (<STDIN>) {
unless (/\w/) {
print "0\n\n";
next;
}
chomp;
my $x = 0;
my @x = split (/$delimeter/);
foreach my $word (@x) {
print "$x\t$word\n";
$x++;
}
print "\n";
#last;
}
|
a0579ca13d8727f8c0c187d214b4d6110746cb716293885fe475dab7ecd14d32 | Perl | 318 | 26 | #!/usr/bin/perl -w
#
#Author: Jue Ruan
#
use strict;
my $rs = [""];
while(<>){
my @ts = split;
if($ts[0] ne $rs->[0]){
if(length $rs->[0]){
print join("\t", @{$rs}), "\n";
}
$rs = \@ts;
} else {
if($ts[9] > $rs->[9]){
$rs = \@ts;
}
}
}
if(length $rs->[0]){
print join("\t", @{$rs}), "\n";
}
1;
|
50157ba205ef7e805e399543546951f0a85f35f00574941512d0adebeb85b894 | Perl | 342 | 26 | #!/usr/bin/perl -w
#
#
use strict;
my $cnt = shift or die("Usage: $0 <parts> <index> <fasta_file>\n");
my $idx = shift or die("Usage: $0 <parts> <index> <fasta_file>\n");
$idx --;
my $ns = 0;
my $print = 0;
while(<>){
if(/^>/){
if($ns % $cnt == $idx){
$print = 1;
} else {
$print = 0;
}
$ns ++;
}
pr... |
a9265106927b1e64c3392ef43e1d6d1cb008b507e28f957f7dda4da1175b7df0 | Perl | 348 | 25 | #!/usr/bin/env perl
use strict;
use warnings;
while (<>) {
my $filename = $_;
chomp $filename;
my $count = 0;
open (my $fh, $filename) or die "Error, cannot open file $filename";
while (<$fh>) {
if (/^>/) {
$count++;
}
}
print "$count\t$filename\n";
cl... |
f02d9b89ddb31b9368097f8f05555ca1c11eb20cd39ea4d44808a6d86c62e8d1 | Perl | 353 | 23 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 bowtie.raw \n\n";
my $bowtie_raw = $ARGV[0] or die $usage;
open (my $fh, $bowtie_raw) or die "Error, cannot open file $bowtie_raw";
my $header = <$fh>;
print $header;
while (<$fh>) {
if (/random/) { next; }
if (/chrUn/) { next; }
s... |
b91a821b25ea4d3a4fd1796695c20265090bd61c9bec72ce3a691dab209f299f | Perl | 358 | 26 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 tmp.MPIiworm.rank.txt\n\n";
my $file = $ARGV[0] or die $usage;
main: {
open (my $fh, $file) or die $!;
my $seq_counter = 0;
while (<$fh>) {
chomp;
$seq_counter++;
print ">s$seq_counter\n$_\n";
... |
dd4f755725ee800e6125e3e00dabb2e2be84a927219ecf0c63182f03424eac68 | Perl | 371 | 34 | #!/usr/bin/perl -w
#
#AUthor: Ruan Jue
#
use strict;
my $seq = shift;
if($seq){
rev_seq($seq);
} else {
$seq = '';
while(<>){
if(/^>/){
&rev_seq($seq);
print; next;
$seq = '';
}
chomp;
$seq .= $_;
}
&rev_seq($seq);
}
1;
sub rev_seq {
my $s = shift;
$s =~tr/ACGTacgt/TGCAtgca/;
$s = reverse $... |
a94ef28f8971e6a9e4132ba68101a2c612d6eb6f6a39d6f0c51aadb36338be2d | Perl | 375 | 25 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
my $usage = "usage: $0 bams.list\n\n";
my $bam_list_file = $ARGV[0] or die $usage;
open (my $fh, $bam_list_file) or die $!;
while (<$fh>) {
chomp;
my $bam_file = $_;
my $base_dir = dirname($bam_file);
my $cmd = "cufflinks -o $ba... |
fc695789d83ed00210b4f599023b207c01dc2c6c2ae5007efc75227ae8e6352a | Perl | 391 | 20 | #!/usr/bin/env perl
use strict;
use warnings;
while (<>) {
if (/Welding: >(a\d+;\d+).*to >(a\d+;\d+)/) {
my $from = $1;
my $to = $2;
print join("\t", sort($from, $to)) . "\n";
}
elsif (/SCAFFOLD_ACCEPT:\s+(a\d+;\d+)\s+\d+\s+(a\d+;\d+)/) {
my $from = $1;
my $to = $2;... |
20d348d1a27ccaa1f4c1a6e0045636c2943adcef3f92a1e90e84254aaa3f5b7d | Perl | 392 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 gene_gff3.list\n\n";
my $gene_gff3_files = $ARGV[0] or die $usage;
main: {
open (my $fh, $gene_gff3_files) or die $!;
while (<$fh>) {
chomp;
my $filename = $_;
my $cmd = "gene_gff3_to_bed.pl $filename > $filename... |
309a17bccd74d05eaf23d2e33a47bfab67096aeafea6465cdd7a34573f551192 | Perl | 407 | 36 | #!/usr/bin/perl -w
#
#
#
use strict;
my $Q = '!';
my $tag = '';
my $seq = '';
while(<>){
if(/^>(.+?)$/){
if(length $seq){
print "\@$tag\n";
print "$seq\n";
print "+\n";
print $Q x length($seq);
print "\n";
}
$tag = $1;
$seq = '';
} else {
chomp;
$seq .= $_;
}
}
if(length $seq){
print "... |
aee3f132233ae9d7d0464f26d05fb29277a7f0d20e20e390cee6426c0bffa20f | Perl | 407 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 cuff_gtf.list\n\n";
my $trans_gtf_files = $ARGV[0] or die $usage;
main: {
open (my $fh, $trans_gtf_files) or die $!;
while (<$fh>) {
chomp;
my $filename = $_;
my $cmd = "cufflinks_gtf_to_bed.pl $filename > $filen... |
31498479eb9a39d362f3dcafd923999f8f86484024aeedcef0ad076c1e7f7778 | Perl | 409 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 trans_gff3.list\n\n";
my $trans_gff3_files = $ARGV[0] or die $usage;
main: {
open (my $fh, $trans_gff3_files) or die $!;
while (<$fh>) {
chomp;
my $filename = $_;
my $cmd = "transcript_gff3_to_bed.pl $filename > ... |
23991ea4a7738f6c5ae52e3518a381746cfd696845870e4a9779fbe80b9b72e9 | Perl | 424 | 20 | #!/usr/bin/env perl
while(<>){
$_=~ tr/\n//d;
@arr=split("\t",$_);
$col=$#arr;
for($i=0;$i<=$#arr;$i++){
$index=sprintf("%s%s",$.,$i);
$hash{$index}=$arr[$i];
}
$row=$.;
}
for($a=0;$a<=$col;$a++){
for($b=1;$b<=$row;$b++){
... |
15c6ea9401b15b78d3c344b6cd9c54c64da40568cef59296bde8e51e4b56690a | Perl | 439 | 32 | #!/usr/bin/env perl
use strict;
use warnings;
my %data;
while (<>) {
if (/^\#/) {
print;
next;
}
unless (/\w/) { next; }
my $line = $_;
if (/^(comp\d+_c\d+)/) {
my $comp = $1;
$data{$comp} .= $line;
}
else {
die "Error, cannot decode component iden... |
a0c0ac3a5f4e495e4cf61d7e8729c3b5704aaf6569f8d57e2cbd7390445fe71b | Perl | 442 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fasta\n\n";
my $fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_re... |
50ed98ec03b3fb504afa3442f3cb3aa9ded9deb54d857b9c4b9aec3ca326a1f7 | Perl | 464 | 29 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fasta\n";
my $fasta_file = $ARGV[0] or die $usage;
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $header = $seq_o... |
51322928129cfa5016f052d9ef252f57fc70352875b8edad340cc7af02f07458 | Perl | 483 | 32 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$ENV{EUK_MODULES}");
use Gene_obj;
while (<>) {
chomp;
my ($scaff, $read_acc, $lend, $rend) = split(/\t/);
my $gene_obj = new Gene_obj();
$gene_obj->populate_gene_object({}, {$lend => $rend});
$gene_obj->{asmbl_id} = $scaf... |
e2deec54212562e6cf2bde49767ebd32042376857aacc5b6f22884bfa5fe8a8d | Perl | 489 | 43 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Std;
my $usage =
"$0 file_fasta
Parses RNA sequences to DNA by substituting 'U's with 'T'.
";
my $file_fasta=shift or die $usage;
parse_fasta($file_fasta);
exit;
sub parse_fasta{
my ($file) = @_;
open (FASTA, "<$file") or die "can not open $file... |
80b190cee4e02595bc205110e1c10d220029c4cd8006490e2b561e46615debba | Perl | 491 | 30 | #!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
my $curr_dir = cwd();
foreach my $file (<*_1.*fastq*>, <*_1*.fq*>) {
$file =~ /^(\S+)_1\.*/ or die "Error, cannot decipher filename $file";
my $core = $1;
my $right_fq = $file;
$right_fq =~ s/_1\./_2\./;
unless (-s $right_fq) {
... |
a9959e4578441d1bcbba3422e50f128c984f2068806fad256199d347e63caebf | Perl | 492 | 29 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 comp.raw.graph\n\n";
my $chrys_graph = $ARGV[0] or die $usage;
main: {
open (my $fh, $chrys_graph) or die "Error, cannot open file $chrys_graph";
print "digraph G {\n";
while (<$fh>) {
chomp;
my ($id, $prev_id, @... |
33a7a266c0158d291ece0b38f8fc5940e5c106aa7e62d1e39afa32c377047afa | Perl | 494 | 30 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 subcluster_A subcluster_B ... > merged.subclusters\n\n";
my @files = @ARGV;
unless (@files) {
die $usage;
}
my $printed_header_flag = 0;
foreach my $file (@files) {
open (my $fh, $file) or die "Error, cannot open file $file";
... |
dd567a0fefbc004ecd136824764d8148cb533b6964a7cc890a09ec30314ae8aa | Perl | 505 | 39 | #!/usr/bin/perl -w
#
# Author: Ruan Jue
#
use strict;
my $total = 0;
my @nums = ();
my $len = 0;
while(<>){
next unless(/(\d+)/);
push(@nums, $1),$total+=$1 if($1);
}
print "Total: $total\n";
my @nxxs = ();
for(my $i=0;$i<=10;$i++){
push(@nxxs, int($total*$i*0.1));
}
push(@nxxs, $total + 1);
my $i = 0;
my $j = ... |
bd0dbe6966b5ce2ba2a8f7c1e92fd4ee2a108f1521e0d4bad7d37c52511b5ff4 | Perl | 509 | 25 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fastaFile\n\n";
my $file = $ARGV[0] or die $usage;
my $fasta_reader = new Fasta_reader($file);
print join("\t", "#fasta_entry", "length") . "\n";
while (my $seq_obj = $fasta... |
7be89ea461b0da4886918acd9bac7a6a10bd72b81c3ae9edb20e4a6ae97d0c7b | Perl | 518 | 33 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 matrix.fpkm min_sum_counts\n\n";
my $fpkm_matrix = $ARGV[0] or die $usage;
my $min_sum = $ARGV[1] or die $usage;
open (my $fh, $fpkm_matrix) or die $!;
my $header = <$fh>;
print $header;
while (<$fh>) {
my $line = $_;
chomp;
my @x = s... |
a1a5805b87317519a0588febb7ec44c00954a16df2a5bcaee9e32c9da75f7588 | Perl | 519 | 33 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 transcripts.fasta\n\n";
my $trans_fasta = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($trans_fasta);
while (my $seq_obj = $fasta... |
c4cbb9f16185e33369a0eddaf18cb18dfebf77883917e7089573789dd8644122 | Perl | 523 | 27 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin");
use HTC::GridRunner;
my $config_file = "$FindBin::RealBin/../htc_conf/BroadInst_LSF.test.conf";
main: {
my @cmds;
for my $num (1..10) {
my $cmd = "echo hello $num";
push (@cmds, $cmd);
}
push (... |
f4366ed916e93d1b86a6bf35536691060ece42615bbccc2e77cb5fa01c0dc7b8 | Perl | 523 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
while (<>) {
if (/>(\S+)/) {
my $acc = $1;
if ($acc =~ /^(.*c\d+_g\d+)(_i\d+)/) {
my $gene = $1;
my $trans = $1 . $2;
print "$gene\t$trans\n";
}
elsif ($acc =~ /^(.*comp\d+_c\d+)/) {
my ... |
cf60f440260eda7e623f6adfbbb65ffd9d955bbde7f5bd5ceb1f092ef8e95e28 | Perl | 537 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use Cwd;
my $cgi = new CGI();
print $cgi->start_html(-title => cwd());
my @entries = `wc -l *.matrix`;
chomp @entries;
print "<table>\n";
print "<tr><th>Num entries</th><th>file</th></tr>\n";
foreach my $entry (@entries) {
$entry =~ s/^\s+//;
my ($coun... |
4a9ef51b7588c65b187617d0ca30aa1f5304f43966714451df92c55e20bbeacd | Perl | 538 | 30 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 reads.fasta ref_transcripts.fasta [SS]\n\n";
my $reads_file = $ARGV[0] or die $usage;
my $ref_transcripts_fasta = $ARGV[1] or die $usage;
my $SS_flag = $ARGV[2] || 0;
my $cmd = "$FindBin::RealBin/../../Inchworm/bin/inchworm "
. ... |
eb934b220d303e6b63cdb860d0db24e81dbc3f0a94f0eb4aa90dc40018531f2d | Perl | 545 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Process_cmd;
use File::Basename;
my $usage = "usage: $0 collectl_dir/ \n\n";
my $collectl_dir = $ARGV[0] or die $usage;
main: {
my $cmd = "$FindBin::Bin/util/collectl_dat_to_time_matrix.py --dat $collectl_... |
984331e69733da002e111069a28ae2efd3fc3efc084db4d70a49da74aae66b7b | Perl | 547 | 28 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
my $usage = "\n\n\tusage: $0 target_trans_files.list [opts ex. --wgsim ...]\n\n";
my $target_trans_files_file = $ARGV[0] or die $usage;
shift @ARGV;
main: {
my @ref_files = `cat $target_trans_files_file`;
chomp @ref_files;
... |
0fc2c97132685aef88c1fba71b3690f1ac249a0cb1c26955bd616ce743caa2a5 | Perl | 556 | 35 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 tmp.iworm.thread.txt\n\n";
my $file = $ARGV[0] or die $usage;
main: {
open (my $fh, $file) or die $!;
my $seq_counter = 0;
reader:
while (1) {
my @vals;
for (1..4) {
my $line = <$fh>;
... |
238949babad141e1d374e9abfc2646d1bae0e5e7e22d88adad9da48cc73ff5c6 | Perl | 558 | 30 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fastaFile min_length\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $min_length = $ARGV[1] or die $usage;
my $fasta_reader = new Fasta_reader($fasta_file);
while (my... |
09fbc979bc207e6b0265963757364e15205ca5333a0db522f978568ab7851f36 | Perl | 562 | 29 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin");
use HTC::GridRunner;
my $config_file = "$FindBin::RealBin/../htc_conf/BroadInst_SGE.test.conf";
main: {
my $cache_file = "cache_completed_SGE_cmds";
my @cmds;
for my $num (1..10) {
my $cmd = "echo hello $... |
946ebf7bbedf866af0403fcab4a95ef5c6770fcad6bc571b0150bad6d260c10a | Perl | 571 | 21 | #!/usr/bin/env perl
use strict;
use warnings;
local $/ = ">";
while(<>){
chomp;
my $lineSepPos = index($_, "\n");
my $header = substr($_,0,$lineSepPos);
if($header){
print(">", $header, "\n");
my $sequence = reverse(substr($_,$lineSepPos));
# see http://shootout.alioth.debian.org/u32/performance.php?test=re... |
6683c7bbe2c108206fbc4ba6d7740f1bfc815b2ac6bb9d0b04cb5106cb3e76dd | Perl | 575 | 32 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 iworm_cluster_welds_graph.txt.sorted.wIwormNames\n\n";
my $iworm_welds = $ARGV[0] or die $usage;
main: {
open (my $fh, $iworm_welds) or die "Error, cannot open file $iworm_welds";
print "digraph G {\n";
while (<$fh>) {
c... |
ce8a0205da32d10860d287a0b3fe4e2cf1d3888c044dacb2381c76331ec64f76 | Perl | 584 | 32 | #!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
my $curr_dir = cwd();
foreach my $file (<*.Left.fq*>, <*.left.fq*>, <*_Left.fq*>, <*_left.fq*>) {
$file =~ /^(\S+)[\._]Left.fq/i or die "Error, cannot decipher filename $file";
my $core = $1;
my $right_fq = $file;
$right_fq =~ s/([\._])Left/${... |
a60ad6b218f766278d445160c7414731f1ada7bd33f48c8432506d2146397ac5 | Perl | 597 | 39 | #!/usr/bin/env perl
use strict;
use warnings;
use Fasta_retriever;
use List::Util qw(shuffle);
my $usage = "usage: $0 file.fasta\n\n";
my $file = $ARGV[0] or die $usage;
main: {
my @accs;
open (my $fh, $file) or die $!;
while (<$fh>) {
if (/^>(\S+)/) {
my $acc = $1;
pus... |
41dd196d295dd7c5b4bfc965ac125f63edfd75d3466223f2304c1f13b2a7db5e | Perl | 606 | 30 | #!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
my $curr_dir = cwd();
foreach my $file (<*_R1*.fastq*>, <*_R1*.fq*>, <*.R1*.fastq*>, <*.R1*.fq*>) {
$file =~ /^(\S+)[\._]R1[\._].*f(ast)?q/ or die "Error, cannot decipher filename $file";
my $core = $1;
my $right_fq = $file;
$right_fq =~ s/([\... |
9da049dc52ec87c8ea0347bba91b47bd3021fffdcc79fbc25885523927957458 | Perl | 626 | 37 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 [multiFastaFile]\n\n";
if (defined($ARGV[0]) && ($ARGV[0] eq "-h" || $ARGV[0] eq "--help")) {
die $usage;
}
my $input = $ARGV[0] || *STDIN{IO};
unless (-f $input || ref ... |
5a14d8fd61854714995963d37d0888d3aa9dafdf215982489cc974847d54ab2f | Perl | 627 | 41 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 db query [opts]\n\n";
unless (@ARGV) {
die $usage;
}
my $db = $ARGV[0] or die $usage;
my $query = $ARGV[1] or die $usage;
shift @ARGV;
shift @ARGV;
main: {
my $cmd = "makeblastdb -in $db -dbtype nucl";
&process_cmd($cmd) unless (-s "... |
9719f0661531ff90d430293d6d39763c492e82dceec9cc0b2fdcbe89b65b2fec | Perl | 628 | 41 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 db query [opts]\n\n";
unless (@ARGV) {
die $usage;
}
my $db = $ARGV[0] or die $usage;
my $query = $ARGV[1] or die $usage;
shift @ARGV;
shift @ARGV;
main: {
my $cmd = "makeblastdb -in $db -dbtype nucl";
&process_cmd($cmd) unless (-s "... |
0d6959b1f973be15fec9f5ac49a65b59831afd6413ab2ff22ab9c1849113fd38 | Perl | 632 | 37 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
my $usage = "\n\nusage: $0 transcripts.fa\n\n";
my $transcripts_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($transcripts_file);
whi... |
db8a30b2c2dd56b8c7d57f0a8029c3e581efa236c80db0c572c612706a50e88e | Perl | 636 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 token < trinity_fasta_files_listing\n\n";
my $token = $ARGV[0] or die $usage;
my $counter = 0;
while (<STDIN>) {
my $filename = $_;
chomp $filename;
unless (-e $filename) {
print STDERR "ERROR, filename: $filename is indicat... |
77dc1dd42d75375478e9777a77a2b5156522204acb03d0a1b2c67dfab438fe48 | Perl | 640 | 31 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fa [kmer_length=25]\n\n";
my $fa_file = $ARGV[0] or die $usage;
my $kmer_length = $ARGV[1] || 25;
main: {
my $fasta_reader = new Fasta_reader($fa_file);
whi... |
13cc56ea4f77b1836525c465f4d45f7746178c76d10c0a3ffd18f10f3ce81e45 | Perl | 644 | 35 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.fq TopEntriesCount [append]\n\n";
my $fq_file = $ARGV[0] or die $usage;
my $top_entries_count = $ARGV[1] or die $usage;
my $append = $ARGV[2];
my $count = 0;
open (my $fh, $fq_file) or die "Error, cannot open file $fq_file";
while (my $line1 ... |
17b232ea8f3b48a386a1e7fdab7b1c186d4e5bc45f38c8a8e9f07629533d42b5 | Perl | 647 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
my @entries;
while (<>) {
if (/>(\w+).*path=\[(.*)\]/) {
my $acc = $1;
my $path = $2;
my @node_descr = split(/\s+/, $path);
my @nodes;
foreach my $node (@node_descr) {
$node =~ s/:.*$//;
... |
2b62d7f5b127a2bf5bf5b3000bdc5bf7bc22886854bc7ba7f027b1d9791863b9 | Perl | 650 | 40 | #!/usr/bin/perl -w
#
#
use strict;
my $cnt = shift or die("Usage: $0 <n_files> <fasta_file> [gzip:0]\n");
my $inf = shift or die("Usage: $0 <n_files> <fasta_file> [gzip:0]\n");
my $zip = shift || 0;
$zip = 0 unless($zip eq '1' or $zip eq 'y');
my $ouf = $inf;
if($ouf eq '-'){
$ouf = 'unnamed';
} else {
unshift @ARGV... |
9c108bfda0225deb3fbd3e9f33238afbcf09d8e67012c4b87a318440a9785664 | Perl | 653 | 35 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.maps (G|T)\n\n";
my $maps_file = $ARGV[0] or die $usage;
my $GorT = $ARGV[1] or die $usage;
main: {
open (my $fh, $maps_file) or die $!;
while (<$fh>) {
chomp;
my ($genes_info, $asms) = split(/\t/);
my @gene... |
a7856ea9846a2418e5a307fbfa8f4235a9ce0a3788657e2a269aa135699c3577 | Perl | 668 | 38 | #!/usr/bin/env perl
use strict;
use warnings;
my %counter;
while (<>) {
if (/^>/) {
if (/^>(.*c\d+_g\d+)/) {
$counter{$1}++;
}
elsif (/^>(.*comp\d+_c\d+)/) {
# older format
$counter{$1}++;
}
else {
die "Error, dont recognize... |
10f891b17608f44a4824bf161df34ca562956ad16b097fed19208a2be82f125b | Perl | 677 | 40 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
my $usage = "usage: $0 bfly_fasta_files.list.file\n\n";
my $bfly_list_file = $ARGV[0] or die $usage;
main: {
open (my $fh, $bfly_list_file) or die $!;
while (<$fh>) {
chomp;
my $file = $_;
my $base = basena... |
5b2d92d0d9b45642c15f58e83dd34e58ce31190fcb864c6089df6e66a67bea7d | Perl | 678 | 35 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::RealBin or die "error, cannot cd to $FindBin::RealBin";
my @files_to_keep = qw (cleanme.pl
... |
da3d1ce757c31f6a31b994f5cf8566777c9153826c38ab27f985769c490176b3 | Perl | 679 | 37 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 seqs.fasta\n\n";
my $file = $ARGV[0] or die $usage;
my %seq_to_header;
my $fasta_reader = new Fasta_reader($file);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_seq... |
173b99abfd51b9933cf9ef9c85b9a98a4602b8fed0d7c5e66b415cb48d18fbaa | Perl | 680 | 43 | #!/usr/bin/perl -w
#
#Author: Ruan Jue
#
use strict;
use DB_File;
my $fasta_file = shift or die("Usage: $0 <fasta_file>\n");
die("$fasta_file.dbm already exists!!!") if(-e "$fasta_file.dbm");
open(IN, "<", $fasta_file) or die;
my %seqs;
tie %seqs, 'DB_File', "$fasta_file.dbm", O_RDWR | O_CREAT, 0644, $DB_HASH or di... |
6cb562bbab711f916cb43a8df2c341c61746207c6232d482b5320d65068a24d7 | Perl | 683 | 33 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.fc\n";
my $fc_file = $ARGV[0] or die $usage;
open(my $fh, $fc_file) or die "Error, cannot open file $fc_file";
my $header_1 = <$fh>;
if ($header_1 !~ /^\#/) { die "Error, unexpected formatting of file: $fc_file";}
my $header_2 = <$fh>;
if ($h... |
acdb192f741865212af05f16e45a7381206640b741656ae960d30d54990fdc7f | Perl | 685 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 file.fasta\n\n";
my $fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
my %seen;
while (my $seq_obj = $fasta_reader->next()) {
... |
409b7c2d301e69324717db1077f86b26627c3433c4c6d9554dd39ec632ee66d3 | Perl | 700 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Nuc_translator;
my $usage = "usage: $0 file.sam\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
while (my $sam_entry =... |
d0ad2bd76eca207eb44c22bdf47c0555a66e4879e59cea85835a815d7a22b456 | Perl | 704 | 42 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 partitions.gff join_within_dist\n";
my $partitions_gff = $ARGV[0] or die $usage;
my $join_within_dist = $ARGV[1] or die $usage;
my @prev_line;
open (my $fh, $partitions_gff) or die "Error, cannot open file $partitions_gff";
while (<$fh>) {
chomp... |
587a0372b8141384561144bc27684b19223996450e9670bb5cea6bf95512dc03 | Perl | 712 | 37 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 [multiFastaFile] [NO_FULL_HEADER_FLAG=0]\n\n";
my $input = $ARGV[0] || *STDIN{IO};
my $NO_FULL_HEADER_FLAG = $ARGV[1] || 0;
unless (-f $input || ref $input eq 'IO::Handle'... |
fee7a15b50fa9ed3ade25dae398f3fd1c61ab36c6c950513bef994362d41f0dc | Perl | 716 | 45 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Cwd;
my $usage = "usage: $0 trin_fa.list\n\n";
my $trin_fa_files = $ARGV[0] or die $usage;
my $workdir = cwd();
open (my $fh, $trin_fa_files) or die "Error, cannot open file $trin_fa_files";
while (<$fh>) {
chomp;
my $trin_fa_file = $_;... |
378377571dc15a4b1b01580aed8bd23fed6c362cfdef14924a6c4a7466e55acb | Perl | 735 | 39 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 results.oracle\n\n";
my $oracle_results = $ARGV[0] or die $usage;
main: {
my %genes;
my %isoforms;
open (my $fh, $oracle_results) or die "Error, cannot open file $oracle_results";
while (<$fh>) {
chomp;
my @x ... |
23b959f20f8ee8112688628680fbedce0ff923e7757c2d0799b73f860af728ca | Perl | 739 | 37 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.fastq append_no\n\n";
my $fastq_file = $ARGV[0] or die $usage;
my $append_no = $ARGV[1] or die $usage;
my @lines;
my $counter = 0;
open (my $fh, $fastq_file) or die "Error, cannot open file $fastq_file\n";
while (<$fh>) {
chomp;
$co... |
6ff571839b405c28ac9c1656b26c1aece1352a1b79fb4e2e407eba049ca6d9f3 | Perl | 739 | 36 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 genome_db transcript_db maxIntron outFile\n\n";
my $genome_db = $ARGV[0] or die $usage;
my $transcript_db = $ARGV[1] or die $usage;
my $max_intron = $ARGV[2] or die $usage;
my $outFile = $ARGV[3] or die $usage;
main: {
my $ooc_cmd = "blat -t=dna... |
9a10f1a5359187dc7490cfdd327fc761f4be50b0070f2ea0a72c98d43b234722 | Perl | 743 | 45 | #!/usr/bin/perl -w
#
# Author: Jue Ruan
#
use strict;
my $tag = '';
my @seqs = (['', '']);
while(<>){
chomp;
if(/^>(\S+)/){
my $name = $1;
my $comm = substr($_, length($name) + 1);
my $subr = '';
if($name=~/^(.+?)(\/\d+_\d+)$/){
$name = $1;
$subr = $2;
}
if($name eq $tag){
push(@seqs, [$subr, '... |
d829805c1a832f53ab5a9a1dc40fab107d6b5f95bef8ba8b5c97da3fc2166cdb | Perl | 756 | 35 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 IwormFastaFile min_length min_cov\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $min_length = $ARGV[1] or die $usage;
my $min_cov = $ARGV[2] or die $usage;
my $fasta... |
173bde73889ad956fc51444336db3736ce6be89b146aedc8b4fb2896a057d6ef | Perl | 768 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fasta_file\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = ... |
de09fe5be43823551f86e5b97ee733dd08ed48f979c723f1d54ca57d1cbd9d70 | Perl | 769 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 expr.RSEM\n\n";
my $expr_file = $ARGV[0] or die $usage;
open (my $fh, $expr_file) or die $!;
my $header = <$fh>;
my @fpkms;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $fpkm = $x[6];
push (@fpkms, $fpkm);
}
@fpkms = reverse so... |
a370fe028a80d3ac9dba5ffa31ea80f7bf2e2321643153a8242d98ca900ee67b | Perl | 780 | 38 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
my $usage = "\nn\\tusage: $0 nucFasta \n\n";
my $fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
while (my $seq_obj = $fas... |
a0993c2814b64eb9194dff4e9d546d01042162473d46a2ff5cfc6b76b556da7d | Perl | 794 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 bfly_graph_out_list.file bfly_jar\n\n";
my $bfly_graph_list_file = $ARGV[0] or die $usage;
my $bfly_jar = $ARGV[1] or die $usage;
main: {
open (my $fh, $bfly_graph_list_file) or die $!;
while (<$fh>) {
chomp;
my $graph_ou... |
63d7d7babe7ef07383d003a1f532d927486b481ef7eec685aa30a07391377af9 | Perl | 798 | 40 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 targets.fasta\n\n";
my $target_fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($target_fasta_file);
my %seqs = $fasta_reader->retrieve_all_seqs_hash();... |
91ffcde3bea3e239938afafd63097384bfc6cf2b755edf9e427d821ac852cdd8 | Perl | 799 | 40 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
my $usage = "usage: $0 genome_fa_files.list\n\n";
my $genome_fa_files = $ARGV[0] or die $usage;
open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
while (<$fh>) {
chomp;
my $genome_file = $_;
my $outdi... |
13510bf60065ce247039601158af35489f71e8afc6e994e99522b4307694de46 | Perl | 804 | 39 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use BHStats;
my $count = 0;
my $sum = 0;
my @values;
while (<STDIN>) {
chomp;
$sum += $_;
$count++;
push (@values, $_);
}
@values = sort {$a<=>$b} @values;
if ($count) {
my $average = ($sum/$... |
9b7dafcafcfdd6ef0e78237a0f94d0b3c23edd0d4b0863b86f00ef11f52d1a4e | Perl | 817 | 41 | #!/usr/bin/env perl
use strict;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 file.sam\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
my $filtered_count = 0;
my $total_count = 0;... |
f53b9451c7197b64c313ba10d2845b63818e70c60708fb96f6e8793d143e5023 | Perl | 823 | 40 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 DE_counts.pairs\n\n";
my $pairs_info = $ARGV[0] or die $usage;
main: {
my %sample_pair_to_counts;
open (my $fh, $pairs_info) or die $!;
while (<$fh>) {
chomp;
my ($sampleA, $sampleB, $count) = split(/\t/);
$sa... |
44299e05a87f4247e453fb9a3aa565463450f73f65897a301c737354ce1a3f53 | Perl | 827 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 fileA fileB ...\n\n";
my @files = @ARGV;
unless (@files) {
die $usage;
}
main: {
my %data;
foreach my $file (@files) {
open (my $fh, $file) or die $!;
while (<$fh>) {
chomp;
unless (/\w/) { next... |
a5b39d93a323adda4f3dd7c85ca2bb19301d105ac1afa5d2860583e2b0587ae1 | Perl | 828 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\nusage: $0 token_list_file file_to_join [-v]\n\n";
my $token_list_file = $ARGV[0] or die $usage;
my $file_to_join = $ARGV[1] or die $usage;
my $invert_selection = $ARGV[2] || 0;
my %tokens;
{
open (my $fh, $token_list_file) or die "Error, cannot open fi... |
9dbf1101009001c38f8dbf1ef8b9b82b063f8d594b47f4202e4a44f3fb74e68d | Perl | 838 | 48 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "\n\nusage: $0 edgeR_dir\n\n";
my $edgeR_dir = $ARGV[0] or die $usage;
unless (-d $edgeR_dir) {
die "Error, require a directory name for the parameter.\n\n$usage\n";
}
my ($fpkm_matrix_file) = <$edgeR_dir/*FPKM>;
unless ($fpkm_matrix_file) ... |
fb079b7266c396fa3f49b40a11dcfe8e3b5bb861037d2252392eae8271166cc2 | Perl | 857 | 38 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 RSEM.isoforms.fpkm\n\n";
my $fpkm_file = $ARGV[0] or die $usage;
my $Rscript = "$fpkm_file.R";
open (my $ofh, ">$Rscript");
print $ofh "source(\"$FindBin::RealBin/R/expression_analysis_lib.R\")\n";
print $ofh "pdf(\"$fpkm_file.genes_... |
9a7ff40b52fecd0688e86a0efd7b02471643079e94300b5b028944e33ad003b6 | Perl | 871 | 43 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
my $usage = "usage: $0 genome_fa_files.list\n\n";
my $genome_fa_files = $ARGV[0] or die $usage;
open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
while (<$fh>) {
chomp;
my $genome_file = $_;
my $gff3_... |
a05d5933a4c2307d916d548bdab8d828612b870b37db2a526c50da23b5e72584 | Perl | 875 | 50 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use BHStats;
my $usage = "usage: $0 fpkm.matrix\n\n";
my $matrix = $ARGV[0] or die $usage;
my $pseudocount = 0.1;
main: {
open (my $fh, $matrix) or die $!;
my $header = <$fh>;
while (<$fh>) {
... |
43afeb85a5a0a51c6576de1974b2264b9ad52b95e64de1c6a1ab7b332f8eaa44 | Perl | 877 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 tpm.matrix\n\n";
my $matrix_file = $ARGV[0] or die $usage;
open (my $fh, $matrix_file) or die $!;
my $header = <$fh>;
my @tpms;
while (<$fh>) {
chomp;
my @x = split(/\t/);
shift @x; # gene accession
my $max_tpm = shift @x;
wh... |
b5ae0a8e49ea4771b12860f89f675de819deaad32acb5b17185e3aa3a15b004d | Perl | 887 | 40 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 samples_file dir/containing/bams\n\n";
my $samples_file = $ARGV[0] or die $usage;
my $bam_dir_path = $ARGV[1] or die $usage;
my %tissue_id_to_bams;
open(my $fh, $samples_file) or die $!;
while(<$fh>) {
chomp;
my ($tissue_type, $sam... |
67cc7010eff0b1e286e483bb0a7ce29f6814c6bee559184036ecfd1d106eb27b | Perl | 888 | 39 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 venn.class\n\n";
my $venn_class = $ARGV[0] or die $usage;
main: {
print join("\t", "#acc", "up", "down", "up+down", "both", "UP_list", "Down_list") . "\n";
open (my $fh, $venn_class) or die $!;
while (<$fh>) {
chomp;
... |
91ba02271a4d6b284018ccb9abad6b5af6c4b9a113b8491b3dc86228ea6d9ed2 | Perl | 891 | 42 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 file.kmers bfly.log\n\n";
my $file_kmers = $ARGV[0] or die $usage;
my $bfly_log = $ARGV[1] or die $usage;
my %kmers;
{
open (my $fh, $file_kmers) or die $!;
while (<$fh>) {
chomp;
$kmers{$_} = 1;
}
close $fh;
... |
3e513fc42c228549843677fb33a8ae4565225d1dd284366c3fd3c7a6ea7b1ab5 | Perl | 895 | 48 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "\n\nusage: $0 transcripts.fasta\n\n";
my $fasta_file = $ARGV[0] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);
my @seq_lengths;
my $cum... |
992bc83ad4600467a090aa91d15b6b07156864a4abb91a728414790add5cbdff | Perl | 896 | 36 | #!/usr/bin/env perl
use strict;
use warnings;
my $me = $ENV{'USER'};
my @jobs_running_ln = `qstat -u $ENV{'USER'}`;
if (!@jobs_running_ln || scalar(@jobs_running_ln)<1){
print "No running jobs for user $me\n";
exit();
}
my %jobs_running;
foreach my $job_ln (@jobs_running_ln){
$job_ln=~/^(\S+)/;
$jobs_running{$1}... |
b7ed9f02db0034fbc301c6346baedf3826697f32525b873d08c7dd4f1194e7c9 | Perl | 905 | 46 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 seqs.fasta\n\n";
my $file = $ARGV[0] or die $usage;
my %seq_to_header;
my $fasta_reader = new Fasta_reader($file);
while (my $seq_obj = $fasta_reader->next()) {
my ... |
07883e1592f3e2f15e5db6204bb4bdb20eed10b7c28186b97656d1ee0f0a8163 | Perl | 929 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 (FPKM|RAW) fileA fileB ...\n\n";
unless (@ARGV && scalar(@ARGV) > 2 && $ARGV[0] =~ /^(FPKM|RAW)$/) {
die $usage;
}
my $dat_type = shift @ARGV;
my @files = @ARGV;
my %data;
foreach my $file (@files) {
open (my $fh, $file) or die "Error,... |
3d1e3a1427924632236446c9aa738545611d2ecc16d4caaf1468dad29376d3d2 | Perl | 929 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 up_cats.counts\n\n";
my $counts_file = $ARGV[0] or die $usage;
main: {
my %data;
open (my $fh, "$counts_file") or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $trans = $x[0];
my $category = ... |
00afe91cc1b7081f90a86067722ea6aecb1387638235267677f8ca3ceaba6cbb | Perl | 932 | 63 | #!/usr/bin/perl -w
#
# Author: Ruan Jue
#
use strict;
use Getopt::Std;
our ($opt_h, $opt_s);
getopts("hs");
my $total = 0;
my @nums = ();
my $len = 0;
while(<>){
if(/^>(\S+)/){
if($opt_s){
print "\t$len\n" if($len);
print $1;
}
push(@nums, $len),$total+=$len if($len);
$len = 0;
} else {
$len += le... |
bdbedc3b1067ac3b242ef079f0ffaf9dcd794b171cdf6426b94596bc6a0ba34d | Perl | 933 | 51 | #!/usr/bin/perl -w
#
# Author: Ruan Jue
#
use strict;
use Getopt::Std;
my $prefix = $ENV{'PARAM_RENAME_FA_PREFIX'} || 'S';
my $suffix = $ENV{'PARAM_RENAME_FA_SUFFIX'} || '';
our ($opt_p, $opt_s, $opt_h, $opt_f);
getopts("hp:s:f:");
die("Usage: $0 [-p name_prefix] [-s name_suffix] [-f trans_file] <fastq_file>\n") if(... |
327c4312a658f6c91916cb8dfd86f706826994eab4f9261c809f4bd8b17f0aff | Perl | 936 | 47 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Carp;
use Data::Dumper;
my $usage = "usage: $0 file.sam number_records_to_check=10\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $num_records_to_check = $ARGV[1] || 10;
ma... |
72f57bbdc4aa53af61252b4971c6a8520d6dfaa70a5dd6c60a99ebf4fe2d163d | Perl | 952 | 41 | #!/usr/bin/env perl
use strict;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 file.sam\n\n";
my $sam_file = $ARGV[0] or die $usage;
main: {
my $sam_reader = new SAM_reader($sam_file);
my $filtered_count = 0;
my $total_count = 0;... |
f2cc57682e940947b086272bcff3dcc2e0ab2bb7954f0425fe3cb64adcbb8ae2 | Perl | 955 | 44 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 genes.fasta transcripts.fasta max_intron BLAT_CPU [STRAND-SPECIFIC_FLAG=0]\n\n";
my $genes_fasta = $ARGV[0] or die $usage;
my $trans_fasta = $ARGV[1] or die $usage;
my $max_intron = $ARGV[2] or die $usage;
my $blat_cpu = $ARGV[3] or di... |
759228397e2ad389b99a93bb27f2d1c01ceb080368402b8300a247a7d747f139 | Perl | 957 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 matrix.fpkm\n\n";
my $matrix = $ARGV[0] or die $usage;
main: {
open (my $fh, $matrix) or die "Error, cannot open file $matrix";
my $header = <$fh>;
print $header;
while (<$fh>) {
chomp;
my ($acc, @vals) = spl... |
6827483680c36df4d25141cde9eca84657dc24cdf321c63f7706588e7bb51b07 | Perl | 958 | 49 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Cwd;
my $usage = "usage: $0 genome_fa_files.list\n\n";
my $genome_fa_files = $ARGV[0] or die $usage;
my $workdir = cwd();
open (my $fh, $genome_fa_files) or die "Error, cannot open file $genome_fa_files";
while (<$fh>) {
chomp;
my $geno... |
1f13e33fe2e52442059a91b14a72a71b73f94d2cdcaec83a9c9ad4b38887071d | Perl | 961 | 46 | #!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
use FindBin;
my $usage = "usage: $0 info_files.list.txt output_basedir [eval cmds]\n\n";
my $files_listing_file = $ARGV[0] or die $usage;
my $output_basedir = $ARGV[1] or die $usage;
shift @ARGV;
shift @ARGV;
main: {
my @files = `cat $files_listing_file`... |
5543bf18fcaa89b14acfe1d79701ce1fcf500baa366ad4ec5447a2cdb363b0fa | Perl | 975 | 46 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 min_len min_per_len min_per_id file.per_len_and_id ...\n";
my $min_len = shift @ARGV;
my $min_per_len = shift @ARGV;
my $min_per_id = shift @ARGV;
my @files = @ARGV;
unless ($min_len && $min_per_len && $min_per_id && @files) {
die $usage;
}
... |
960e356a7c36b93d806a0f3575961f08f8eceaf1f02d10505bbcb6648e4e1842 | Perl | 981 | 47 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Ktree;
use Nuc_translator;
my $usage = "usage: $0 fasta_file KmerSize [DSmode]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $kmer_length = $ARGV[1] or die $usage;
my $DS_mode =... |
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