sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1bf73e8c685171db2e1c38a56c3c822f49e8a26bb4c996cc2f7b7153baa0aaea | Perl | 3,526 | 124 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
use FindBin;
use File::Basename;
use POSIX;
$|++;
#my $BASE_URL = "ftp://ftp.broad.mit.edu/pub/users/bhaas/trinity_sample";
my $BASE_URL = "http://www.broadinstitute.org/~bhaas";
main: {
my $cgi = new CGI();
... |
fbebbc7a7a3585f53608529f99dcee875664cb7f52d7a57036da8bf113d0032d | Perl | 3,550 | 159 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "\n\n\tusage: $0 < list of audit.txt files from stdin \n\n\n";
my $MIN_SEQ_LEN = 1000;
my $total_genes = 0;
my $total_genes_reco = 0;
my $total_refseq_trans = 0;
my $total_iso_reco_count ... |
6185cd436a1ad9fac32698b191216ca7ca0d77db2a1a82a92413385ee5b6c223 | Perl | 3,584 | 130 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Fasta_reader;
my $usage = "usage: $0 coord_sorted.sam genome.fa [SS_lib_type]\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $genome_fa = $ARGV[1] or die $usage;
my $SS_lib_ty... |
d413d0b6c96d71470b5ab91e267e5997bc741c5c971d9f4cf7fef45db2b3daff | Perl | 3,623 | 160 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 splicePaths_A splicePaths_B\n\n";
my $fileA = $ARGV[0] or die $usage;
my $fileB = $ARGV[1] or die $usage;
main: {
my %combosA = &get_combos($fileA);
my %combosB = &get_combos($fileB);
my %introns_to_combos;
&index_combos_by_int... |
3578a7520db90a79f076d82c0d8fb6692b21c85a88f946f1f1ccf58f61259c42 | Perl | 3,647 | 161 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::RealBin/../TrinityWeb/cgi-bin/PerlLib/");
use CanvasXpress::Heatmap;
use CanvasXpress::PlotOnLoader;
use CanvasXpress::Line;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use CGI;
my $usage = <<__EOUSAGE__;
#########... |
dc28c0c498b2fc15094e59390a46b1fe8f6dc3e0a39c564c106e8370e78f3886 | Perl | 3,773 | 143 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib("$FindBin::Bin/../../PerlLib");
use Fastq_reader;
use Data::Dumper;
my $help_flag;
my $usage = <<__EOUSAGE__;
###############################################... |
0c7eb650691e4bfb24f86f9e314b9f7dcea327c2b4df1eeff40e7376b1bd90d2 | Perl | 3,784 | 151 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use File::Basename;
my $usage = "usage: $0 alignments.sam SS_lib_type=F,R,FR,RF\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $SS_lib_type = $ARGV[1] or die $usage;
unle... |
295519ba736c960742f57a151e395d32eb23d41fd94ee819a55e370428a1dcf0 | Perl | 3,815 | 149 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
my $usage = <<__EOUSAGE__;
###################################################################################
#
# --target <string> 'genes' or 'samples'
#
# -K... |
b3c65ff5c1a47c6f008705414d9d5b328da0219fe4b977ac4a8e26738c7621b7 | Perl | 3,823 | 160 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use SAM_entry;
my $help_flag;
my $usage = <<__EOUSAGE__;
###########################################
#
# Required:
#
# --bam <s... |
b45a6e25ab71d71127e6bc20c4ed2329f9b293de4d4bc01ce9d50ce273bff2f8 | Perl | 3,823 | 116 | #!/usr/bin/perl
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rig... |
d1397385e5303d8261807e96b02fd6d727b22451781407b3fbce8d071b7b2cd5 | Perl | 3,836 | 167 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --genome <string> targe... |
cf76ed68ea00427dbb3dd7c9fe5b9b7908620c2c6f2485cd6fe071b7df3c8f4d | Perl | 3,864 | 167 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
####################################################################
#
# Required:
#
# --GO_annots <string> GO assignment... |
a5153eb58dc616957f1b056a10513e3d2f3a03f385213c74cfd24c7391476247 | Perl | 3,865 | 165 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#####################################################
#
# --DE_results <string> DE_results file
#
# --gene_trans_map <string> gene-trans... |
764d2d794015893b9529719f96759d9c9554c43f60a303efbfd062f0a45c5811 | Perl | 3,866 | 160 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Fasta_reader;
use BHStats;
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 @all_seq_lengths... |
c9b9a73b8267b9898a1fb50b838d6d188e08c7b4d25af9ed61b59c51799277e6 | Perl | 3,884 | 155 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE;
#################################################
#
# usage: $0 [opts] < trinity_fasta_files_listing
#
##################################... |
d7befea7dbdfd61af5d61465fbe5b304f4ede065140f9f2f75f2397d7819685c | Perl | 3,911 | 184 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use File::Basename;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use CanvasXpress::Heatmap;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
my $usage = <<__EOUSAGE__;
###########################... |
fcd5f8434e22b533362f5c56f9418766155fff784984187f1c9d41ebaa5236d3 | Perl | 4,026 | 156 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Process_cmd;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Pipeliner;
use File::Basename;
my $CPU = 2;
my $usage = <<__EOUSAGE;
###########################################################... |
839b1e6cade2f61d8417d810b0ebed829b54c36d6b4c5988b1c0d82549eb9551 | Perl | 4,048 | 145 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Nuc_translator;
use Carp;
use Data::Dumper;
my $DEBUG = 0;
my $usage = "usage: $0 file.sam out_prefix [STRICT]\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $out_prefix =... |
fce9a3f30ab01245568e330590677ec7cd41fa9bf217bd71f3ecb77c77749b6d | Perl | 4,057 | 176 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Cwd;
my $usage = <<__EOUSAGE__;
############################################################... |
b7045af8b400f65e8f1b0125aaba8b088e37a862f8a59c42150dbc78d62a01e0 | Perl | 4,104 | 153 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 chrysalis_dir/ component_no (WELDS|SCAFF|BOTH)\n\n";
my $chrysalis_dir = $ARGV[0] or die $usage;
my $component_no = $ARGV[1];
my $draw_type = $ARGV[2] or die $usage;
unless (defined $component_no) {
die $usage;
}
unless ($draw_type =~ /^(... |
d16d311f990f65849c4c71224de876af807d48e129ac29d95aa7968df654b6da | Perl | 4,142 | 180 | #!/usr/bin/env perl
use strict;
use warnings;
use Statistics::Descriptive;
my $usage = "usage: $0 bwasw.sam.align_stats [longest_contig_only] [no_require_100pct_align]\n\n";
my $align_stats_file = $ARGV[0] or die $usage;
my $longest_contig_only_flag = $ARGV[1] || 0;
my $no_require_100pct_align = $ARGV[2] || 0;
=f... |
05ef30577f5a32e2be3e8482c284340a16a1b76133d750e7b1352a9a0f068ea7 | Perl | 4,160 | 183 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --genome <string> targe... |
e5b00264ba437601706617361dce9ca5e152bf19e3fd79537559dd53b0d25f36 | Perl | 4,185 | 166 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use File::Basename;
$ENV{PATH} .= ":$FindBin::RealBin/../../trinity-plugins/slclust/bin/";
my $help_flag;
my $min_per_id = 99;
my $max_per_gap = 1;
my $min_per_length = 99;
my $usage = <<__E... |
91f2ef5d156e38073baf51fee239f366c819f8d1302ec777ff2853c68bbd632d | Perl | 4,191 | 154 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib");
use Fasta_reader;
use ColorGradient;
use Data::Dumper;
my $usage = "usage: $0 graph.seqinfo refseqs.fa\n\n";
my $graph_seqinfo_file = $ARGV[0] or die $usage;
my $refse... |
d098913b9d94854b4d98fbc80b386f6c7f9aa332737f3d0eeb225a16a3be3682 | Perl | 4,225 | 188 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib "$ENV{TRINITY_HOME}/PerlLib";
use Fasta_reader;
use List::Util qw (shuffle);
#use Math::Random;
my $usage = <<__EOUSAGE__;
################################################... |
58d2d2ab2fa76fe03f336747c7e0e34748edffe3360cf4e6ebece968ff2dbf9d | Perl | 4,293 | 173 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################
#
# Required:
# --genome <string> targe... |
41623d0669ef19b67ca944ee51e041d8c7cbc9ca9a66047662f522851d686c1f | Perl | 4,332 | 152 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use DelimParser;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###############################################################################
#
# Required:
#
# --lef... |
ae65261488476c1dd4d7fdadddcc283b11990bad40dbfd421ea4d0f125b786a6 | Perl | 4,360 | 173 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#######################################################################
#
# Required:
#
# --matrix|m <string> replicates.TMM_normalized.fpkm.matrix
#
# --samples_fi... |
d70949300e9397bc0a7a20b694b8a1b54eab11662756502416ba6cf1fdc25bc7 | Perl | 4,429 | 177 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "\n\nusage: aligned_reads.sam [debug]\n\n"
. "Note: uses the bitflag settings for counting entries. Proper-pairing supercedes other settings.\n\n";
my $sam_file = $A... |
f7e2d60bbfca24a018962809ee688e79ef27180ca4808cf74d4bbb2d8d1dc1be | Perl | 4,446 | 167 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib "$FindBin::RealBin/../../PerlLib";
use Pipeliner;
use File::Basename;
my $usage = <<__EOUSAGE__;
############################################################... |
44b00a3db67a8b587456f01e3116270de02499a11d4ecc6530d74e8addc25f51 | Perl | 4,483 | 173 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use Cwd;
$ENV{LC_ALL} = 'C';
my $util_dir = "$FindBin::RealBin";
my $usage = <<_EOUSAGE_;
#########################################################################################
#
# Required:
#
#... |
3c1e1cfc8215da1a7c74f34b0204a19d267f2b12cacfd1f7ee83176e7ed16557 | Perl | 4,524 | 196 | #!/usr/bin/env perl
use strict;
my $SEE = 0;
###############
# blat format: # Q=cDNA T=genomic
################
# 0: match
# 1: mis-match
# 2: rep. match
# 3: N's
# 4: Q gap count
# 5: Q gap bases
# 6: T gap count
# 7: T gap bases
# 8: strand
# 9: Q name
# 10: Q size
# 11: Q start
# 12: Q end
# 13: T name... |
eaf08f8f9f51fa20fb8863be3416f5ef3292c60e8ecbce91fc35cd87bbe9a642 | Perl | 4,606 | 194 | #!/usr/bin/env perl
use strict;
use warnings;
use threads;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling);
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
use Fasta_reader;
use Statistics::Descriptive;
my $usage = <<_EOUSAGE_;
#########################################################... |
2c82007bc921fbe53dbd2bacebd204226d21ecf981a639899f9500b95ea0388f | Perl | 4,609 | 226 | #!/usr/bin/env perl
# works for trinity transcripts or trinity genes, Sept 28 2016 bhaas
# lightweight fasta reader capabilities:
package Fasta_reader;
use strict;
sub new {
my ($packagename, $fastaFile) = @_;
## note: fastaFile can be a filename or an IO::Handle
my $self = { fastaFile => undef,,
... |
532c7cf398b801a10ae0603c5234486c7f5863a032c8d9dc1a5160ce3025db3f | Perl | 4,613 | 168 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Gene_obj;
use GFF3_utils;
use SAM_reader;
use SAM_entry;
use Fasta_reader;
use Data::Dumper;
use Getopt::Long qw(:config no_ignore_case bundling);
my $usage = <<_EOUSAGE_;
###################################... |
60b554ff8f115441cddf670bc37a771e13025dc89be7f5b33ea32a4e46445f21 | Perl | 4,613 | 155 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "\n\nusage: $0 abundance.tsv gene_to_trans_map_file.txt\n\n\n";
my $abundance_tsv = $ARGV[0] or die $usage;
my $gene_to_trans_map_file = $ARGV[1] or die $usage;
main: {
my %trans_to_gene_info;
{
open (my $fh, $gene_to... |
4873c4ff0b69f263fcb959d585c3fdd95cc11f6c2ac6b6fa8324dd2a2b967de1 | Perl | 4,615 | 171 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Data::Dumper;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###################################################... |
1e4f90fae850edb16da578439c1f64edf7e9a713c2234726585a18374a70168a | Perl | 4,629 | 186 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#######################################################################
#
# Required:
#
# --matrix <string> replicates.TMM_normalized.fpkm.matrix
#
# --samples_file... |
4ef6489c1aab5d6b9b94e0a2a52190c8003a798d212042a5428d4b1cf5733650 | Perl | 4,700 | 163 | #!/usr/bin/env perl
## Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2022, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2022, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is sub... |
49de9f9af4b8fa9ed39a7ebd60a426df4c9cfe5257110102573f2535b8897330 | Perl | 4,724 | 200 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use File::Basename;
my $usage = "usage: $0 isoform.EXPR.matrix Trinity.fasta [by=transcript|gene (default:transcript)]\n\n"
. "\t note, use the isoform.EXPR.matrix file regardiess of wehther... |
9935852c3354441a10bc7f4655266221a7287b39be22964c7c4c226d5d7edc50 | Perl | 4,729 | 206 | #!/usr/bin/perl -w
#
# Author: Jue Ruan <ruanjue@gmail.com>
#
use strict;
use warnings;
use POSIX;
use POSIX ":sys_wait_h";
use Time::HiRes;
my $USER = $ENV{USER};
if(not defined $USER){
$USER = `whoami`;
chomp $USER;
}
my $RUNITALL = $ENV{RUNIT_ALL} || 0;
my $cmd = join(" ", @ARGV);
$cmd=~s/^\s+//;
$cmd=~s/\s+$//;... |
fae206daa107ca76b4e4d3224e065aa1f3a67e244226fcffa7f2e45bdf3c8fba | Perl | 4,741 | 178 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/PerlLib");
use Gene_obj;
use GFF3_utils;
use SegmentGraph;
my $usage = "usage: $0 genes.gff3\n\n";
my $gff3_file = $ARGV[0] or die $usage;
main: {
my $gene_obj_indexer_href = {};
## ... |
9f4e65f38868c3a4b23635ed73000e1c8532d5d2871d691d878bbff0d1965642 | Perl | 4,824 | 161 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "\n\nusage: $0 results.xprs gene_to_trans_map_file.txt\n\n\n";
my $results_xprs = $ARGV[0] or die $usage;
my $gene_to_trans_map_file = $ARGV[1] or die $usage;
main: {
my %trans_to_gene_info;
{
open (my $fh, $gene_to_t... |
2396fbfdc6df284a3b0f129790d1eaa6dfe280eae7044f8151b8f856cbee5f5a | Perl | 4,828 | 179 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use GFF3_alignment_utils;
use WigParser;
use Data::Dumper;
my $usage = "usage: $0 gmap.gff3 jaccard.wig [lowest_in_window_size=300]\n\n";
my $gmap_gff3 = $ARGV[0] or die $usage;
my $jaccard_wig = $ARGV[1] or die ... |
eab6ce6827f31ef801005772310e8ef6d502a8e91eda2cb9a41f9998925d1ce0 | Perl | 4,831 | 189 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib/");
use Ascii_genome_illustrator;
use Cwd;
my $usage = "usage: $0 refseqs.fa target.fa min_per_id [min_pct_aligned]\n\n";
my $REFSEQS_FA = $ARGV[0] or die $usage;
my $TARGET_FA = $ARGV[1] or die $usage;
my $MIN_PER... |
1808f06d50c51d5cbb892f9ab06d4c9c58bd5f26ad530c760e95db4424d05b72 | Perl | 4,897 | 199 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
use Cwd;
my $usage = <<__EOUSAGE__;
###############################################################################
#
# Required:
#
# --target <string> :... |
d9d802eded1a35b09ba4ae4be12c5ff1f8626d5328dc62134db0c3c170af8fb7 | Perl | 4,903 | 221 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::RealBin/../../PerlLib");
use Pipeliner;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
our $HISAT_HOME;
BEGIN {
if ($ENV{HISAT_HOME}) {
$HISAT_HOME = $ENV{HISAT_... |
dd83849ca053b06d649b7fa0d20d628b14454b2a9486ef96a16764bb79883643 | Perl | 4,948 | 189 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib "$FindBin::RealBin/../../PerlLib";
use Fasta_reader;
use List::Util qw(min max);
use Overlap_piler;
use Data::Dumper;
my $usage = "\n\n\tusage: $0 blast.outfmt6 query_fasta target_fasta\n\n\n";
my $blast_file = $ARGV[0] or die $usage;
my $query_fasta... |
ab3230e63d8f76a42a6f31a00a1cc687eb1e58bd9fa25bf15683b3891418b8ca | Perl | 5,009 | 165 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "\n\nusage: $0 quant.sf gene_to_trans_map_file.txt\n\n\n";
my $quant_sf = $ARGV[0] or die $usage;
my $gene_to_trans_map_file = $ARGV[1] or die $usage;
main: {
my %trans_to_gene_info;
{
open (my $fh, $gene_to_trans_map_... |
eddd84ffefa4268d6f40ecd9b0e2e189c48e223e5e88870005770b17cdf180fc | Perl | 5,153 | 160 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "usage: $0 sample_avg_expr.matrix edgeR_directory/ [FDR=0.05]\n\n";
my $sample_expr_matrix = $ARGV[0] or die $usage;
my $DE_dir = $ARGV[1] or die $usage;
my $MAX_FDR = $ARGV[2];
unless (defined $MAX_FDR) {
$MAX_FDR = 0.05;
}
my @DE_resu... |
1fb944dde29c2742c088fbd84d8979e111e4a4b6591cb6f8e7de16dc88db9908 | Perl | 5,171 | 182 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Carp;
use List::Util qw(min max);
my $usage = "usage: $0 file.sam [debug_flag=0]\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $DEBUG = $ARGV[1];
main: {
my %PATH_COUNT... |
ca460d42f90366983cea365403c59f9222847867eb1f8792b48f22ece8f49762 | Perl | 5,190 | 154 | #!/usr/bin/perl
# Author: Glenn J Tattersall
# Date: 2024-03-22
# Version: 2.0
#use strict;
#use warnings;
use Getopt::Std;
our($opt_i, $opt_o, $opt_b, $opt_p, $opt_x, $opt_s, $opt_c, $opt_v);
my $n=0;
my $folder = "temp";
my $infilename = "filename.csq";
my $outfilebase = "frame";
my $outfilename = "";
my $pattype... |
f358929c3f23761c15e95761f26bd8af7ac1395cfeff7afc12eac766c55b1881 | Perl | 5,328 | 204 | #/!/usr/bin/env perl -w
=head1 NAME
gls
=head1 DESCRIPTION
Display the files generated by the current user within the local instance of Galaxy.
Information is grouped by user's Galaxy histories and ordered by date/time
=head1 OPTIONS
- i|info = show more info about file [default = no]
- e|error ... |
31e591797722d1068c1f8d070d596e03ebb4150fa6fdce6a405b3c2d495cd0a0 | Perl | 5,373 | 207 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
use FindBin;
use File::Basename;
use lib ("$FindBin::RealBin/../../PerlLib");
use Data::Dumper;
my $usage = <<__EOUSAGE__;
#########################################################################... |
63fbac7f9b5f85440968dc50abc6bd2ed94fb5aaf202c44be9a7124b4c62a7d2 | Perl | 5,384 | 191 | #!/usr/bin/env perl
use strict;
use lib "/home/devel/talioto/myperlmods";
use lib "/home/devel/talioto/myperlmods/Bio";
use SeqOp;
use Getopt::Long;
use File::Basename qw( fileparse );
my $fname = 0;
my $num_n = 1;
my $species = '';
my $taxid = '';
my $assembly_name = 0;
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday... |
4cb1d09dfdeb5abe63c774a1b94b2c14008ec542e54bd04860bdf8063d2478df | Perl | 5,521 | 199 | #!/usr/bin/perl
# miRDeep2 prepare-signature perl script
# Copyright (C) 2008 - 2012 Marc Friedländer
# Copyright (C) 2009 - 2012 Sebastian Mackowiak
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fou... |
27d0ac19298c47a61d77edfe524ba73468c28e01f27f22f9e18c85b4cb88813f | Perl | 5,607 | 224 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Fastq_reader;
use SAM_reader;
use SAM_entry;
my $usage = <<_EOUSAGE_;
#################################################... |
9f63aa62640cfc659c6073eab07edfaeebede9ce938a1844f616a14c9fae5c95 | Perl | 5,637 | 191 | #!/usr/bin/perl
use strict;
use Getopt::Std ;
our ($opt_h, $opt_f,$opt_q, $opt_v,$opt_c, $opt_t, $opt_w, $opt_H, $opt_m, $opt_a, $opt_c);
getopts("hf:v:qcw:Hmac");
&usage if $opt_h;
sub usage {
die "AddVariantsToDiffFile8Strains.pl -f diff file
-v <variants file> (must have a header with strain names)
-w win... |
cdb517c5a73be10a2459efa04607bd4a091ff7e98717d878fed7929566d26d25 | Perl | 5,809 | 226 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use threads;
use File::Basename;
use File::Spec;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling);
use lib("$FindBin::Bin/../../PerlLib");
use Thread_helper;
use Cwd;
my $CPU = 2;
my $usage = <<_EOUSAGE_;
####################################... |
573fbaae99a4aff5dc2d0e9fc12e3334667b794b08f75607b1c38a66024e817a | Perl | 5,825 | 171 | #!/usr/bin/env perl
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use strict;
use warnings;
use Getopt::Std;
use Fasta_reader;
use Longest_orf;
use List::Util qw (min max);
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $usage = "\n\nusage: $0 transcripts.fasta\n\n";
my $transcripts_fasta_file = $... |
6561999b4c67eaf341849363f22df14aac6219f149abf0962ac812861a4f5780 | Perl | 5,925 | 249 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
#############################################################################################
#
# --genes|G <string> gene DE_results file
# -... |
0d57bbd1ec1a353627c58be5f3f98d762b5f3429c73752329f59686578bd9985 | Perl | 6,003 | 246 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use PSL_parser;
require "overlapping_nucs.ph";
# note, align to genes
my $usage = "usage: $0 blat_output.pslx [STRAND_SPECIFIC=0]\n\n";
my $blat_output = $ARGV[0] or die $usage;
my $strand_specific = $ARGV[... |
79b12c6ee044d05c13044c0ab8d9109692f85b192af04cf5ead36eb7536a6d6b | Perl | 6,009 | 233 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
#################################################################################################
#
# Required:
#
# --details <string> compreh_in... |
a455b77f0daad3afbec261d34d91fbcd7655142071161f752b5950da1ee147c5 | Perl | 6,093 | 259 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Path;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Nuc_translator;
use SAM_reader;
use SAM_entry;
my $usage = <<__EOUSAGE__;
################... |
edeb03795182f8d4220af7866976ff5c3927a2b599720b5853f32f4a3b990107 | Perl | 6,182 | 236 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::RealBin/../../PerlLib");
use Pipeliner;
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###############################################################... |
bf4cb7e2c391e0ba1519b118341558d0c1160d39d9a8815df9933f9bb0aa84cd | Perl | 6,195 | 264 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Path;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Nuc_translator;
use SAM_reader;
use SAM_entry;
my $usage = <<__EOUSAGE__;
################... |
f655524a3ee058eaadbf5b80ae6d6c57c1d4ce210b85c1ff556b1270f29245bd | Perl | 6,222 | 212 | #!/usr/bin/perl -W
# miRDeep2 sanity-check-reads-ready-file perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
# Copyright (C) 2009 - 2011 Sebastian Mackowiak
#
# 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 Fr... |
160f8666082a6b977e2d241a163f231d0520854e9fde3db53b1ce1429fc9904a | Perl | 6,328 | 250 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#########################################################################
#
# --deBruijns <string> bundled_iworm_contigs.fasta.deBruijn
# --compo... |
c282fe371f2c5acf8fa0be1deb2b83071be113daf13ea898b9387dfd9911d3f7 | Perl | 6,344 | 179 | #!/usr/bin/env perl
#############################################################################
##
## Copyright (C) 2016 The Qt Company Ltd.
## Contact: https://www.qt.io/licensing/
##
## This file is part of the porting tools of the Qt Toolkit.
##
## $QT_BEGIN_LICENSE:LGPL$
## Commercial License Usage
## Licensees h... |
108ec7cddca5a307ab22c5c9e2e3337c9005e72eee537fc21b9155844091c7c9 | Perl | 6,464 | 258 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $help_flag;
my $FDR_thresh = 0.05;
my $usage = <<__EOUSAGE__;
###############################################################
#
#
# Required:
#
# --trans_DE_results_dir <string> /pat... |
90a3fae232b28c9d1fd46a70680ab8eee4ebd92ca7ad7428df5ee0f255403a7e | Perl | 6,523 | 279 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Fasta_reader;
use SingleLinkageClusterer;
use File::Basename;
use Process_cmd;
my $usage = <<__EOUSAGE__;
#####################################... |
e035a35087198744633dc4ded01fc14319f777ca0871365671938a7686192040 | Perl | 6,603 | 249 | #!/usr/bin/perl
# miRDeep2 parse-mappings perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at y... |
7755c2e7bf03fd0fc5f3f1b0d2487057ed16ede82039e23720dbe883ae9857bd | Perl | 6,622 | 223 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
my $DEBUG = 0;
my $usage = "usage: $0 left.fq right.fq\n\n";
my $left_fq = $ARGV[0] or die $usage;
my $right_fq = $ARGV[1] or die $usage;
open (my $left_PP_ofh, ">$left_fq.... |
5560cb6a90c696f93588b636093b242e515456752c0384779746165ac1fc8704 | Perl | 6,709 | 260 | #!/usr/bin/perl
# miRDeep2 get-precursors perl script
# Copyright (C) 2012 - 2014 Sebastian Mackowiak
#
# 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
# (a... |
2a8e2a8900c62ede4a504eebd126e90db3cd8ba3093ddf832545f2ca45a6b479 | Perl | 6,741 | 262 | #!/usr/bin/env perl
# written by
#
# Bob Freeman, Ph.D.
# Acorn Worm Informatics, Kirschner lab
# Dept of Systems Biology, Alpert 524
# Harvard Medical School
# 200 Longwood Avenue
# Boston, MA 02115
# 617/432.2294, vox
#
# bob_freeman@hms.harvard.edu
=from_Bob
I wrote a small script in Perl that gi... |
e0911a0e3907813bf0f3c181c810ffc85afc5c1cc2149cbabbda99607b0ec975 | Perl | 6,806 | 217 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
my $usage = <<__EOUSAGE__;
###################################################################################
#
# -K <int> define K clusters via k-mean... |
a8f11c4d525330e4ec0267820e04abd49babb31e420a4901a940df2ce0accc89 | Perl | 6,885 | 268 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Gene_obj;
use GFF3_utils;
use BED_utils;
use Carp;
use Nuc_translator;
use Fasta_reader;
my $usage = "\n\nusage: $0 reference.gff3,bed target.gff3,bed [genome.fa restricts to introns w/ consensus splices]\n\... |
a2ef2885f8a88f6de78bdd9007df449ffefd790cdc3324db4aec13793999e170 | Perl | 6,895 | 234 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
use Carp;
use Nuc_translator;
use Data::Dumper;
my $usage = "\n\nusage: $0 gff3_file utr_trim_dat [DEBUG]\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my $utr_trim_... |
75a0bb9a9cb5c689d9740f2d6700543036e9d2ef02eb66d4222f7304ad313613 | Perl | 6,914 | 258 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::RealBin/../../PerlLib");
use Pipeliner;
use File::Basename;
use Cwd;
use List::Util qw(min);
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#######################################... |
7914011de909fc630c28808005428a26b436d57fbac4bab91d98fd2d960a09f6 | Perl | 6,957 | 253 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use DelimParser;
use File::Basename;
use Data::Dumper;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $help_flag;
my $usage = <<__EOUSAGE__;
###########################... |
42f3f72b295728fade1c39b134cc3cf377e65e1754d457467b5017a5ab016797 | Perl | 7,024 | 262 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
use FindBin;
use File::Basename;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
#######################################################... |
77a7f9f640af9b87519cf946a88964a0742b5cf8768b9a5a431f106447200176 | Perl | 7,116 | 242 | #!/usr/bin/env perl
use strict;
use warnings;
################
# blat format: # Q=cDNA T=genomic
################
# 0: match
# 1: mis-match
# 2: rep. match
# 3: N's
# 4: Q gap count
# 5: Q gap bases
# 6: T gap count
# 7: T gap bases
# 8: strand
# 9: Q name
# 10: Q size
# 11: Q start
# 12: Q end
# 13: T na... |
3328818b981e1b192f5f3cc553b4be736a8cbae85c371c48ed3efc045530e0a2 | Perl | 7,269 | 312 | #!/usr/bin/perl -w
use strict;
use Getopt::Long;
use POSIX qw(ceil floor);
my $maxLength = 400;
my $desiredLength = 200;
my $help = 0;
GetOptions(
"maxLength:i" => \$maxLength,
"desiredLength:i" => \$desiredLength,
"help" => \$help,
"h" => \$help
);
if ($help) {
p... |
1cdb6ed34740b9a83453bd8ce8ea69dd5ba5562c73004b51e0d561d6ae87ddd9 | Perl | 7,298 | 288 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
my $jaccard_file;
my $trough_win = 200;
my $min_jaccard_delta = 0.35;
my $max_jaccard_trough_val = 0.05;
my $coverage_w... |
528d57b0b7728aca0383810cbc38d178963607800c374adc4113821d9a61bb7d | Perl | 7,526 | 308 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$ENV{TRINITY_HOME}/PerlLib/");
use Fasta_reader;
use Cwd;
use Data::Dumper;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use List::Util qw (shuffle);
my $help_flag;
my $ref_trans_fa;
my $MIN_REFSEQ_LENGTH = 100;
my ... |
2591ca7ac57acaec230d7dfd05d8ee01bce07d9c3b8fda8dc1b8886451585426 | Perl | 7,555 | 238 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
use SAM_reader;
use SAM_entry;
use Data::Dumper;
my $FASTA_LENGTH = 60;
my $usage = "usage: $0 alignments.sam target.fasta [JUST_ALIGN_STATS=0]\n\n";
my $sam_alignments = $ARGV[0] or die $usage;
my $target_fasta = $ARGV[1... |
1f15a59ca67a91ce3780e82de0fd146a9d5a4f2ff6a2a61f59406dc44b9042f6 | Perl | 7,666 | 277 | #!/usr/bin/env perl
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use strict;
use warnings;
use threads;
use Fasta_reader;
use Process_cmd;
use Thread_helper;
use Getopt::Long qw (:config no_ignore_case bundling);
use vars qw ($DEBUG $opt_h $opt_g $opt_t $opt_c $opt_o $opt_B $opt_I);
my $CPU = 1;
my... |
04114969000c43e65a1f730dbda48d37ae34b1ebb603da4ba74ca30761e483d9 | Perl | 7,695 | 276 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "\n\nusage: name_sorted_paired_reads.sam [debug]\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $DEBUG = $ARGV[1] || 0;
if ($sam_file =~ /coord/i) {
die "Your file... |
c1f77a7c51b0eeca59fdd20360d550abc02002caec0da8870b0c2a15d6cf6b10 | Perl | 7,727 | 246 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib "$FindBin::Bin/../../PerlLib";
use Pipeliner;
use File::Basename;
my $CPU = 2;
my $top_genes_plot = 50;
my $usage = <<__EOUSAGE__;
##########################... |
600bff88f9e3e05399422ce7f3301c929b9b573b28b7fc16b41436ead89c317b | Perl | 7,767 | 308 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Path;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Nuc_translator;
use SAM_reader;
use SAM_entry;
my $usage = <<__EOUSAGE__;
###################... |
52ed189cd387aafe7e62ac264998af5019a0ce6e156bbc5ac5f8f6d17eb08698 | Perl | 7,998 | 304 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Data::Dumper;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $help_flag;
my $MIN_PCT_MAX_EXPR = 5;
my $CPU = 2;
my $REF_MIN_PCT_LEN = 90;
my $us... |
d50465cda90d5809b7f499b4670a48b1f4911e9793570e339872de3fea70f391 | Perl | 8,024 | 250 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Fasta_reader;
use Data::Dumper;
=ExampleCommands
# make blastable
makeblastdb \
-in refTranscripts.fasta\
-out refTranscripts -dbtype nucl
# run blast+
blastn -query Trinity.fasta -db refTranscripts -ou... |
1243791694dfa522d51a3b3678b2a13bf90114cfa5efb032774ed8c2e2c1f91e | Perl | 8,174 | 384 | #!/usr/bin/perl
# miRDeep2 bwa-SAM-converter perl script
# Copyright (C) 2009 - 2012 Sebastian Mackowiak
#
# 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
#... |
8eabe94f8ea6a5dfb7dc374f3066e9c8fbdcb1c929f03519463253cf85513735 | Perl | 8,203 | 287 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use SAM_entry;
my $usage = "\n\nusage: $0 nameSorted.sam iworm_fasta_file\n\n";
my $name_sorted_sam_file = $ARGV[0] or die $usage;
my $iworm_fasta = $ARGV[1] or die $usage;
my $SAM_OFH;
main: {
open ... |
9b25f0d33abef61f4bf08d898e10e6aa1e2f0dabc43de9f5417ec9b3f126d64f | Perl | 8,380 | 298 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 summary.dat [outprefix=argv[0]]\n\n";
my $file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] || $file;
main: {
my %up_to_down;
my %feature_to_sample_expr_val;
open (my $fh, $file) or die $!;
while (<$fh>) {
chomp;
... |
a0060c2045a554e94aed60e18cb42c75875c3f4af23ea6c102413e80af5ee33d | Perl | 8,409 | 299 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 summary.dat [outprefix=argv[0]]\n\n";
my $file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] || $file;
main: {
my %up_to_down;
my %feature_to_sample_expr_val;
open (my $fh, $file) or die $!;
while (<$fh>) {
if (/^\... |
a15acdd54cb7a7695f4a101d6dae90c9ca9c83249743120343f2becba88a08bb | Perl | 8,560 | 327 | #!/usr/bin/env perl
use strict;
use warnings;
use List::Util qw(min);
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Data::Dumper;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $MIN_CONTAINMENT = 96;
my $KMER_LENGTH = 25;
my $usage = <<__... |
b52ac592eaa1dde650ee67e5d472d77bb964c4da2244f1d40dca91d657cedc61 | Perl | 8,633 | 338 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Cwd;
use File::Basename;
use Carp;
use Data::Dumper;
use Getopt::Long qw(:config no_ignore_case bundling);
$ENV{PATH} .= "\:$FindBin::RealBin/../trinity-plugins/rsem/sam/"; # include samtools in path, already included in rsem build.
$ENV{LC_ALL} = 'C'... |
fde9375a5caedb7c57f303b44004c060ad866346bf02f778f836f7b175ff7494 | Perl | 8,659 | 326 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our($opt_h, $opt_p,$opt_f, $opt_z,$opt_a,$opt_r, $opt_c, $opt_d, $opt_F, $opt_S, $opt_i, $opt_A, $opt_R);
getopts("hf:a:p:r:c:vd:F:S:i:A:R:");
&usage if $opt_h;
sub usage {
die "CombineModalities.pl -d density file (e.g. pairwise) -r rna DESEQ file -R RNA count file -a a... |
a3add4169c153c5436adcb271c93f088c0a34b937a42f66533424b84d5094748 | Perl | 8,669 | 295 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Data::Dumper;
my $help_flag;
my $usage = <<__EOUSAGE__;
############################################... |
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