sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7346fd62a99a8460ad6fb6ff26046271932a07ea0b3e5ff93abde069d518f277 | Perl | 1,008 | 53 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 graphFromIwormFasta.out\n\n";
my $file = $ARGV[0] or die $usage;
main: {
my %graph;
open(my $fh, $file) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $node_id = shift @x;
my $spa... |
8509a62d7777a09be7f4488152ce7412eeeeeb26428892a3995e8e735948494d | Perl | 1,019 | 54 | #!/usr/bin/env perl
#
# Author: Jue Ruan <ruanjue@gmail.com>
#
use Getopt::Std;
use strict;
our ($opt_h, $opt_t, $opt_s, $opt_m, $opt_x, $opt_p);
getopts("ht:s:m:x:p:");
&usage if($opt_h);
&usage(1) if(@ARGV < 2);
my $ref = shift || &usage(1);
my $rst = $ref;
$rst=~s/\.fa$//;
$rst=~s/\.fasta$//;
my $ncpu = 4;
$ncpu... |
6a4554930161707c09db4bca15827e64c9635c2d95661ecbef61dfb54f6056e4 | Perl | 1,022 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 fpkm.matrix pct_of_top_fpkm\n\n";
my $expr_matrix = $ARGV[0] or die $usage;
my $pct_of_top = $ARGV[1] or die $usage;
main: {
open (my $fh, $expr_matrix) or die $!;
my $header = <$fh>;
chomp $header;
$header =~ s/^\s+//;
m... |
91ac74539cb881d03f38c610d20f726fe0846786f0c586157e998c95ca381490 | Perl | 1,023 | 46 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.audit_summary\n\n";
my $filename = $ARGV[0] or die $usage;
main: {
my %yes_no_counter;
my $total_reco = 0;
my $total_ref = 0;
my $total_FL = 0;
open (my $fh, $filename) or die $!;
while (<$fh>) {
if (/ref_fa/... |
fd257b5b1b576d65c30ca505096800c6ffd03d08b5a615e874a2e26b2853796e | Perl | 1,024 | 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, $opt_b, $opt_I);
getopts("hp:s:f:b:I");
die("Usage: $0 [-p name_prefix] [-s name_suffix] [-f trans_file] [... |
4a331b79f0c64bf7e579537084b459cef9daee61aa13386650ecb1f3fac22b65 | Perl | 1,030 | 44 | #!/usr/bin/env perl
use Getopt::Long;
my $description;
use Bio::SeqIO;
use Bio::Seq;
use File::Basename;
my $format = 'fasta';
#my $chunksize = 2500;
my $numchunks = 100;
my $file = 0;
my $pad = 0;
GetOptions(
"n:s"=>\$numchunks,
"f:s"=>\$file,
'pad'=>\$pad
);
my @suffixlist = qw(.gff .gff3 .gff2 .gtf .f... |
dd9451ab778468a746e6268b9c6fd9f0fe99e127d0d3feda91193d74787c9900 | Perl | 1,030 | 50 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$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);
while (my $sam_entry = $sam_reader->g... |
9e2ec998185c46fe42bbec3ad063a1d525c8c8f87c799557409bfade6bdeec33 | Perl | 1,043 | 55 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: all_diff_expr_results.txt min_abs_log_FC max_FDR\n\n";
my $dat_file = $ARGV[0] or die $usage;
my $min_logFC = $ARGV[1] or die $usage;
my $max_FDR = $ARGV[2] or die $usage;
my %best;
open (my $fh, $dat_file) or die $!;
while (<$fh>) {
my $line =... |
ff0b44a9100b009a03b24720b7936c6b29183c62d38d92c3f6e383aead34ddfb | Perl | 1,044 | 55 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 DE.graph\n\n";
my $DE_graph = $ARGV[0] or die $usage;
=color_panel
> colorpanel(10, 'black', 'purple', 'red')
[1] "#000000" "#28083C" "#501078" "#7818B4" "#A020F0" "#A020F0" "#B818B4"
[8] "#D01078" "#E7083C" "#FF0000"
=cut
my @colors = (
... |
dcbf95ddb3df3baa348a7fcdc95c94af0be2faaebdcee7f79c36061c99936214 | Perl | 1,049 | 61 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 coordSorted.sam max_per_position\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $max_per_pos = $ARGV[1] or die $usage;
main: {
my $sam_reader = new SA... |
75bf00cdafbb06fcff021fc5562a4db086521597358a473dab645a2bab2ccc65 | Perl | 1,068 | 57 | #!/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... |
2c6ed2016b01fa38b444a648541b29303c9d73475e5cd6d358c73a6a48e4f7f8 | Perl | 1,071 | 53 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 acc_list_file.txt target_db.fasta\n\n";
my $acc_list_file = $ARGV[0] or die $usage;
my $target_db = $ARGV[1] or die $usage;
main: {
my $samtools = `sh -c "command -v samtools"`;
unless ($samtools =~ /\w/) {
die "Error, need... |
e9b5462541a9fdfc204b15aa96d004e8b7e1f79f2c09972815bcb780834358e9 | Perl | 1,073 | 49 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 scaff_pairs_A.txt scaff_pairs_B.txt ...\n\n";
my @pair_files = @ARGV;
unless (scalar(@pair_files) > 1) {
die $usage;
}
main: {
my %top_pairs;
foreach my $pair_file (@pair_files) {
open (my $fh, $pair_file) or die "Error,... |
35341ad7fd7f49ed9e37438cbfc5f9eccf0aa10f53575012be7040f27d651a12 | Perl | 1,074 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 blastx.outfmt6 trinity.matrix\n\n";
my $blastx_file = $ARGV[0] or die $usage;
my $trinity_matrix = $ARGV[1] or die $usage;
main: {
my %blastx_top_hit; # store for transcript and component
{
open (my $fh, $blastx_file) or die... |
7dd28b3a21abac47e124f3f3559309dec924a4edf88643449a4984feca924166 | Perl | 1,090 | 48 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Process_cmd;
my $usage = "\n\n\tusage: $0 Trinity.fasta reads.fa [threads=1]\n\n";
my $trin_fa = $ARGV[0] or die $usage;
my $reads_fa = $ARGV[1] or die $usage;
my $CPU = $ARGV[2] || 1;
main: {
my $salmon... |
68df6dc2d5d715014ae8db9368ea6d037d48ba0490f25554f42f3bbc03f5e8bc | Perl | 1,102 | 51 | #!usr/bin/perl -w
use strict;
use warnings;
unless(@ARGV==3){
die "USAGE: Using the MIS value and the common taxon, this programe calcualtes the stability of the network across timeline.\nperl $0 <MIS.lst> <common_tax.xls> <stabliity.xls>\!\n";
}
my (%common_tax, %MIS_path);
#Store the common taxo
open IN, "$ARGV[1... |
0d856ffc1e504c933d7df98b76b4abf40dfb56d727b459482667fb758a7c7367 | Perl | 1,104 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 bfly.A.fasta [bfly.B.fasta ...]\n\n";
my @files = @ARGV or die $usage;
main: {
my %data;
foreach my $file (@files) {
open (my $fh, $file) or die "Error, cannot open file $file";
while (<$fh>) {
... |
9d4f60ee13a60f07fa593cca073bd5384b60be7940ca0135daba5af433bf1c2e | Perl | 1,106 | 44 | #!/usr/bin/perl -w
#
# Author: Jue Ruan <ruanjue@gmail.com>
#
use strict;
=pod
Transform <dbg>.[1/2/3/frg/ctg].dot into GFA format. <dbg>.[1/2/3/frg/ctg].dot is the assembly graph from wtdbg
TAG:
gl: gap length
rc: read count to support the link
sq: sequence can be substr from <rd_name>_<FR>_<off>_<len>, F fwd, R r... |
d89e5a8515206638fc6f37faa9469810a9278a1e2181b8bf47fb21c487ac6c5c | Perl | 1,127 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Data::Dumper;
unless ($ARGV[0] && $ARGV[1]) {
die "Usage: $0 \$fastaFile \$acc_listing\n";
}
my $fastaFile = $ARGV[0];
my $acc_listing = $ARGV[1];
open (ACC, "$acc_listing");
my %accs;
while (<ACC>) {
chomp;
my @x = split (/\s+/);
foreach... |
8760b3d62ca4b4a49ab78bfaf7c41e59a522c198a79bf3aa5db92c305769829d | Perl | 1,134 | 78 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 venn.txt\n\n";
my $venn = $ARGV[0] or die $usage;
my %class_to_att_count;
my %atts;
open (my $fh, $venn) or die "Error, cannot open file $venn";
while (<$fh>) {
chomp;
my ($feature, $class_list) = split(/\t/);
my @classes = split(/,/, $class... |
7713c828b0a818d0aab9a11154282be6e8cba710a085e23f8ec9527e8730bad2 | Perl | 1,146 | 53 | #!/usr/bin/perl
# miRDeep2 find-read-count 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 ... |
a6429d1d6e550693e327b7a6522fedeb0b604ab2f3e4a565c5e80aebe2db73f4 | Perl | 1,160 | 53 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
my $usage = "usage: $0 Trinity.fasta reads.{fa,fq}\n\n";
my $trinity_fasta = $ARGV[0] or die $usage;
my $reads_fasta = $ARGV[1] or die $usage;
main: {
my $cmd = "fasta_file_header_stripper.pl < $trinity_fasta > $trinity_fasta.noheader";
&pr... |
f200a17c2fbef6f9ba73fe4214bb94d898b2c169e08fe5a3042c94b5a06029a2 | Perl | 1,163 | 56 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.intron_analysis ...\n\n";
my @files = @ARGV;
unless (@files) {
die "$usage\n\n";
}
my @types = qw(
NOVEL
REF
NOVELCOMBO
REFCOMBO
SUBrefCombo);
print "#analysis\t... |
e27220cacc911350174108dc6c05558398a67e77ce216d12729f5a91a84c6922 | Perl | 1,166 | 58 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = <<__EOUSAGE__;
###############################################
#
# Usage: $0 Trinity.fasta new_feature_id_mapping.txt
#
# The 'new_feature_id_mapping.txt' file has the format:
#
# current_identifier <tab> new_identifier
# ....
#
#
# Only those entri... |
13c91386867470dced61f0ea68268a9f395280969e91d6d4325d9d133cc5eaa1 | Perl | 1,168 | 55 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "venn_pairwise_out.dat\n\n";
my $venn_txt = $ARGV[0] or die $usage;
main: {
my %combos;
my %sample_pair_to_combo_count;
open (my $fh, $venn_txt) or die $!;
while (<$fh>) {
chomp;
my ($feature, $sampleA, $sampleB, $comb... |
d030e18f4512bcb660b8491b354b135eac78b0a561b5c0dac3bfaee438bef6da | Perl | 1,169 | 71 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.maps\n";
my $file = $ARGV[0] or die $usage;
my %genes;
my %isoforms;
my %gene_merges;
my %isoform_merges;
open (my $fh, $file) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $genes = shift @x;
my @entries = split(/,/, ... |
b2cc70e1a1e657abc7bf9661b6580f7b8cc9dd66940389821bf1c8d13f0c20e0 | Perl | 1,175 | 48 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 iworm.fasta iworm_cluster_welds_graph.txt\n\n";
my $iworm_fa = $ARGV[0] or die $usage;
my $iworm_cluster_welds_file = $ARGV[1] or die $usage;
main: {
my %counter_to_iworm;
{
my $counter = 0;
open(my $fh, ... |
a9dce545dea7e06d046f9acc883a9ec6f4f5dd5d93d19045d9d8dfa80e360ff3 | Perl | 1,178 | 57 | #!/usr/bin/perl
# miRDeep2 remove-white-space-in-ID perl script
# 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 Free Software Foundation, either version 3 of the Licens... |
105eed51d4e28eded5931c1e038fb58864a6bde10459813bfbc382d8f3240260 | Perl | 1,184 | 62 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 file.frag_coords (LEND|REND)\n\n";
my $file = $ARGV[0] or die $usage;
my $end = $ARGV[1] or die $usage;
unless ($end eq "LEND" || $end eq "REND") {
die $usage;
}
main: {
my @histogram;
my $curr_scaffold = "";
open (my $fh, $... |
2bcf4d28a4dce9aac18ba2a3fdcac58651514a5c0383fcbc2d32475d9467df30 | Perl | 1,190 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
my $usage = "usage: $0 file.fastq\n\n";
my $fastq_file = $ARGV[0] or die $usage;
main: {
my $fastq_reader = new Fastq_reader($fastq_file);
my $tab_tmp_file = "$fastq_file.tab";
o... |
fa05093484ad48036a8bf88b0c90ab5ae0d23794baa749f4cf7f2ba8ef58a4ad | Perl | 1,193 | 59 | #!usr/bin/perl -w
use strict;
use warnings;
unless(@ARGV==3){
die "USAGE: This program helps to find the common taxo across the timeline.\nperl $0 <mean_abundance.lst> <AD or WT> <Common_tax.output>\!\n";
}
my (%path, $target, %abun, %taxo);
$target = $ARGV[1];
#To get the path for the mean_abundance.file
open IN... |
e61a94db2facfb1f616fe3a6401a164c44a57da64873f9e39813eeb1ad97b21c | Perl | 1,197 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 roku.dat expr.dat\n\n";
my $roku_dat = $ARGV[0] or die $usage;
my $expr_dat = $ARGV[1] or die $usage;
my %acc_to_info;
main: {
{
open (my $fh, $roku_dat) or die $!;
while (<$fh>) {
chomp;
my @x = spli... |
9395d50816cf82b0a6dba2ef8eb6fdd9cb653239494bb9623af5cfdac5b87061 | Perl | 1,203 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
my $usage = "\n\nusage: $0 interleaved.fq [left_output_filename.fq right_output_filename.fq]\n\n";
my $interleaved_fq = $ARGV[0] or die $usage;
my $left_out_filename = $ARGV[1] || "unweaved.le... |
3ab2283bbd583932cc9179954e4ee09979987e68d617134a52be46bbcd39f640 | Perl | 1,207 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 genome.fasta left.fq right.fq [output_dir]\n\n";
my $genome_file = $ARGV[0] or die $usage;
my $left_fq_file = $ARGV[1] or die $usage;
my $right_fq_file = $ARGV[2] or die $usage;
my $output_dir = $ARGV[3] || "bowtie.$$.dir";
while ... |
fd564b3dbcd5af6c88a8032ebdb465601b16cf5ac67c27de519dd8db62fc835f | Perl | 1,225 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
## Given a subset of the venn, extracts all entries from the original files containing the pairwise DE data.
my $usage = "\n\nusage: $0 venn.selected pw1.summary pw2.summary ...\n\n";
my $selected_file = $ARGV[0] or die $usage;
shift @ARGV;
my @pw_summaries = @ARGV;
u... |
ae35f6bf5657495ad95110f47608ebb7ae58f9ada83a27094a846a368e1a27cf | Perl | 1,230 | 74 | #!/usr/bin/perl -w
#
#Author: Ruan Jue
#
use strict;
use Getopt::Std;
use DB_File;
our ($opt_l, $opt_h);
getopts("l:h");
my $level = $opt_l || 0;
&usage if($opt_h);
my $dbf = shift or &usage;
if($dbf!~/\.dbm$/){
$dbf .= ".dbm" if(-e "$dbf.dbm");
}
my @nodes = @ARGV;
if(@nodes == 0){
while(<>){
chomp;
push(@... |
c8c735574ed30d0f69045582ad74446f6a030d539c5cc4661c249e8301b3bf86 | Perl | 1,239 | 52 | #!/usr/bin/env perl
# kj2 08.10.2020
use strict;
use Getopt::Long;
my $fa;
my $printfa;
my $split;
my $help;
GetOptions (
"fa:s" => \$fa,
"printfa" => \$printfa,
"h" => \$help,
"help" => \$help,
"split" => \$split,
);
if (($help) || (!$fa)) {
print "This script takes a fasta file and produ... |
8758471ae68b785fb70073eb31e59eb028c932b07c9c08402dd8494539a592da | Perl | 1,244 | 70 | #!/usr/bin/env perl
use strict;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "usage: $0 nameSorted.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_coun... |
811b926402a0d97d381ab2e7af6db7556f83f6baade69f14da51cb99a0f7ebb5 | Perl | 1,249 | 46 | #!/usr/bin/perl -w
use strict;
die "Usage: perl $0 <ref> <kmer_length> <step_size> <output>\n" unless @ARGV == 4;
my $storefile = &FastaReader($ARGV[0]) or die "fasta file is required!\n";
print STDERR "ref loading finished!\n";
my $length = $ARGV[1];
my $step = $ARGV[2];
open (OUT, ">$ARGV[3]") or die "permission deni... |
70e9c4b02d546ad4a9001f3544f2c6831c2fd7c4be4aea20721979358ab0a03c | Perl | 1,270 | 50 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib("$FindBin::Bin/../../PerlLib");
use Pipeliner;
use Cwd;
my $usage = "\n\n\tusage: $0 input.fasta reads.left.[fq|fa] reads.right.[fq|fa]\n\n";
my $target_fa = $ARGV[0] or die $usage;
my $left_reads = $ARGV[1] or die $usage;
my $right_reads = $ARGV[2... |
875436e82c31f836e8e5689c2bc816db54cc081959bd1032a5334af5d84d326c | Perl | 1,277 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 (count|percent) A.org_rep B.org_rep ...\n\n";
my $type = shift @ARGV;
my @org_rep_files = @ARGV or die $usage;
unless ($type eq 'count' || $type eq 'percent') { die $usage; }
main: {
my %matrix;
my %species_to_total_percentage;
... |
92322db39ebc20234463b2927484eed2db979e6cb5ee96117f4a6e6d01ac104a | Perl | 1,286 | 74 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
my $usage = "usage: $0 strand_coverage.wig strand[+-]\n\n";
# need strand value to include in the GFF file.
my $wig_file = $ARGV[0] or die $usage;
my $strand = $ARGV[1] or die $usage;
main: {
m... |
d31de02ac2ece9e58d1d632020500e1e55130c93bae58591c94716d44d89bfca | Perl | 1,301 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
use lib($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "\n\n\tusage: $0 trin_before.fa trin_after.fa\n\n";
my $trin_before_file = $ARGV[0] or die $usage;
my $trin_after_file = $ARGV[1] or die $usage;
main: {
my %trin_seqs_before = &parse_trin_fa($trin_before_f... |
22a485b0252429f8039b7152aee52373f21f3a5d1fc18beefe28e339bc452916 | Perl | 1,311 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
my $usage = "\n\nusage: $0 left.fq right.fq\n\n";
my $left_fq = $ARGV[0] or die $usage;
my $right_fq = $ARGV[1] or die $usage;
main: {
my $left_fastq_reader = new Fastq_reader($left_fq);
... |
ee33e8a5064a1a37a0b2ef7f3df4d06a3ecdca4f7a5c9a03e4b16cdf7e25dc46 | Perl | 1,314 | 55 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 iworm_bundles_fasta_file sorted_reads_to_components_file\n\n\n";
my $iworm_bundles_fasta_file = $ARGV[0] or die $usage;
my $reads_to_components_file = $ARGV[1] or die $usage;
main: {
my %component_to_LRs;
{
open (my $fh, $r... |
2dced2d943596853eec0ca752a64e3964e253d708605d4be3487b47979b761d4 | Perl | 1,320 | 71 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use Fasta_reader;
my $usage = "usage: $0 transcripts.cdna.fasta\n\n";
my $transcripts_fasta = $ARGV[0] or die $usage;
my $graphs_per_dir = 100;
main: {
my $fasta_reader = new Fasta_reader($transcripts_fasta) or die $!;
... |
793818a97139d4b4988bb64835de345cfa104d3b5136e22a6fa07bfa872514b2 | Perl | 1,330 | 68 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = <<__EOUSAGE__;
###############################################
#
# Usage: $0 matrix.txt new_feature_id_mapping.txt
#
# The 'new_feature_id_mapping.txt' file has the format:
#
# current_identifier <tab> new_identifier
# ....
#
#
# Only those entries ... |
fb5a78d7da5695b62c39094e5eb7365cb2fd4a07f255495ce6055df0ccec6732 | Perl | 1,336 | 70 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\tusage: $0 A.FL_selected B.FL_selected [RESTRICT_TO_FAILURES]\n\n";
my $A_stats_file = $ARGV[0] or die $usage;
my $B_stats_file = $ARGV[1] or die $usage;
my $RESTRICT_TO_FAILURES = $ARGV[2] || 0;
my $MIN_PER_LEN = 99;
my $MAX_PER_GAP = 1;
main: {
... |
369f4ec9f393a9cd6b0186d402af2b3af318fda4d5ec4425ac85fc15680a96e4 | Perl | 1,337 | 61 | #!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
use Config::Simple;
die "ERROR: Not enough argument.\nUSAGE: ./getChr15.pl <filedir> <ts>\n" if(@ARGV<2);
my $dir = dirname(__FILE__);
my $cfg = new Config::Simple($dir.'/app.config');
my $chr15dir = $cfg->param('data.chr15');
my $filedir = $ARGV[0];
$fil... |
1505a1b111e62b466471af86803c96638709ed895cf63530665bc019d2753fac | Perl | 1,346 | 70 | #!/usr/bin/env perl
use strict;
use warnings;
use lib ($ENV{EUK_MODULES});
use WigParser;
use Gene_obj;
my $usage = "usage: $0 clip.wig\n\n";
my $clip_wig = $ARGV[0] or die $usage;
main: {
my %mol_to_clips = &get_clip_pts($clip_wig);
foreach my $mol (keys %mol_to_clips) {
my @clip_... |
b97beecfdd994c3f397bb7c09280f3a599c1f9a6cb20bfbc2d35f145b76a1dce | Perl | 1,346 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = <<__EOUSAGE__;
###############################################
#
# Usage: $0 matrix.txt samples_with_relabeling.txt
#
#
# where samples_with_relabeling.txt has the format:
#
# sample_name <tab> current_column_name <tab> new_column_name
# ....
#
# On... |
da4c33802900dbb50963994e56ae90278f3117d7d6fdea890b3f42d5d6aea7ae | Perl | 1,379 | 68 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\tusage: $0 cd-hit.clstr\n\n" .
"try running cd-hit first like so:\n" .
"\tcd-hit-est -o cdhit -c 0.98 -i Trinity.fasta -p 1 -d 0 -b 3 -T 10\n\n";
my $cdhit_file = $ARGV[0] or die $usage;
main: {
my $num_bad_clusters = 0;
my $cluster... |
978c7d2d93f4baea88310df8aac3570014cee97cca584df3a9b06ffc510a6d5e | Perl | 1,382 | 77 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
my $usage = "usage: $0 wigA [ wigB ... ]\n\n";
my @wig_files = @ARGV;
unless (@wig_files) {
die $usage;
}
main: {
my @data_arefs;
my $max_pos = 0;
foreach my $wig_file (@w... |
8c39c518fd9248805e4eb81af1b001e3dd8813b9b88ca37c2666c2b2371d0d74 | Perl | 1,388 | 49 | #!/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";
`rm -rf ./trinity_out_dir*`;
`rm -rf ./bowtie_out` ... |
d90e7d2a8918a45d6c4d149e7565e3107f313cbd62af90ae0dd0da7bdaa813a3 | Perl | 1,410 | 47 | #!/usr/bin/perl
# miRDeep2 mirdeep-to-BED 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
# (a... |
f35cd3c50a0f8713e29d1c749e53ab78dd3d4d4571a37259216d928a8eac6ad1 | Perl | 1,410 | 53 | #!/usr/bin/perl
# miRDeep2 FASTQ-to-FASTA 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... |
d0aee9f679890672a9cdfa72afd38d79201189c1586bd7de69117dd27b42086f | Perl | 1,413 | 70 | #!/usr/bin/perl -w
#
#Author: Ruan Jue
#
use strict;
use DB_File;
my $dot_file = shift or die("Usage: $0 <dot_file>\n");
die("$dot_file.dbm already exists!!!") if(-e "$dot_file.dbm");
open(IN, "<", $dot_file) or die;
my %hash;
tie %hash, 'DB_File', "$dot_file.dbm", O_RDWR | O_CREAT, 0644, $DB_HASH or die "Cannot op... |
0ce520780b9c4fd1887cdb8dbecbf95705a24ef90ef09f0ba1a70f334dedff4c | Perl | 1,418 | 79 | #!/usr/bin/perl
## support for gzip files
use strict;
my $id;
my $seq;
my @species = split(",",$ARGV[1]);
die "Error: Specify species or comma separated list of species\n\nUsage:\n\tperl $0 miRBase_fasta_file species [mature/star]\n\te.g. $0 mature.fa cel mature\n\tfiles can be gzipped\t=>no reason to decompress th... |
6b1a55a67897421942fa4de2e9cbe3b0e32b4e7f0319e08d8d7b8c28da04f15d | Perl | 1,430 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 all_diff_expression_results.txt\n\n";
my $results_summary_file = $ARGV[0] or die $usage;
my @signif_results;
{
open (my $fh, $results_summary_file) or die "Error, cannot open file $results_summary_file";
while (<$fh>) {
chomp;
... |
b05df65ad3c45297b2934a3259bc222f175d5c911d59db1cef14eb86cbaa13e5 | Perl | 1,452 | 81 | #!/usr/bin/perl
# miRDeep2 Illumina-to-FASTA 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
# (a... |
cf4300e5f24556e473c5dfaff6849f94deba5dcc746f007282cbfc546e2f1259 | Perl | 1,457 | 60 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 rsem.out blast.outfmt6 [transcripts.fasta]\n\n";
my $rsem_out = $ARGV[0] or die $usage;
my $blast_out = $ARGV[1] or die $usage;
my $transcripts_fasta = $ARGV[2];
main: {
... |
364b9cc14ce5297465d8c11a3265cd7c55c99001a7f2a32169b36b5edd035a8e | Perl | 1,460 | 71 | #!/usr/bin/env perl
use strict;
use warnings;
use Cwd;
use FindBin;
my $usage = "\n\nusage: $0 reads.fa hash_size\n\n";
my $reads_file = $ARGV[0] or die $usage;
my $hash_size = $ARGV[1] or die $usage;
my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";
my $CPU = 4;
my $min_kmer_cov = ... |
6f840bd57ad73f9d23997783c2cd62896adde7623bdf08d49d4c425d9ae9c8c4 | Perl | 1,467 | 56 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 chrysalis_component_listing.txt min_seq_length\n\n";
my $comp_list_file = $ARGV[0] or die $usage;
my $min_seq_length = $ARGV[1] or die $usage;
main: {
my $ret_val = 0;
... |
b01358fe94c9c5c9a374ffa2cee76fb0bb1df45df042e8daf2a7d628c5bdb142 | Perl | 1,468 | 55 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fastq_reader;
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;
main: {
my $left_fq_reader = new Fastq_reader($left_fq);
my $... |
a1eda47e0b4dbad04b712e62583326eb65cffa56fea9778f9c32f505b25d4f5a | Perl | 1,469 | 65 | #!user/bin/perl -w
use strict;
use warnings;
unless(@ARGV==3){
die "USAGE: This program calcuates the efficiency and EDR for the network without nodes.\nperl $0 <shortest.path.csv> <MIS.xls> <efficiency.xls>!\n";
}
my(%nodes, $n);
#Get the names of nodes
open IN, "$ARGV[1]"||die $!;
<IN>;
while(<IN>){
chomp(my $li... |
979e9931e86b43d11bdd343d5502a5fb898c4d15cba09b17182312de2e235c3b | Perl | 1,485 | 78 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use WigParser;
my $usage = "usage: $0 strand_coverage.wig min_coverage strand[+-]\n\n";
# need strand value to include in the GFF file.
my $wig_file = $ARGV[0] or die $usage;
my $min_coverage = $ARGV[1] or die $... |
39f4882b02450eab6b411dadf606d5ed51da6aa0283d75a9c9954984e3eecbf8 | Perl | 1,495 | 77 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$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);
while ($sam_reader->has_next()) {
my $sam_en... |
5164a9203312f6d090e79a78b070a3aba3c925f9704d71a388ba72763a63e5e8 | Perl | 1,500 | 67 | #!/usr/bin/env perl
use strict;
use warnings;
## Just identifies and counts transcripts that are predicted to encode multiple ORFs
# of those that encode an ORF of min length, how many encode multiple ORFs of min length?
my $usage = "\n\nusage: $0 transdecoder.pep [min_prot_length=300]\n\n";
my $transdecoder_pep_f... |
36a7eb152f0455cfe810adbfb928d47f99d6b01b5e5a2286b26ae67d848440c2 | Perl | 1,511 | 62 | #!user/bin/perl -w
use strict;
use warnings;
unless(@ARGV==4){
die "USAGE: This program calculates the MIS (abundance-weighted Mean Interaction Strength) for all nodes in the specific network.\nperl $0 <mean_abundece.csv> <correlation.matrix.csv> <AD or WT> <MIS.results>\!\n";
}
chomp(my $target =$ARGV[2]);
my (%ab... |
e187d9cf9e306ab74a8316b120bdfe31284e503fae1888b8cb98cf4eedd518ec | Perl | 1,528 | 65 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Process_cmd;
my $usage = "\n\n\tusage: $0 Trinity.fasta [out_prefix='GC_content']\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] || "GC_content";
main: {
my $dat... |
8ae9ca8f72325bed98206d65e7a4ce28828aee715b633c4568999e0283e91d1a | Perl | 1,557 | 31 | #!/usr/bin/env perl
use Cwd qw(abs_path);
use File::Basename;
$bam = shift;
#$bam =abs_path($bam);
$ANNO='/home/weiqi/project/00.DATABASE/GRmm38/Annotation/gencode.vM24.annotation.bed';
$GENOME = '/home/weiqi/project/00.DATABASE/GRmm38/GRCm38.p6.fa';
$SIZE = '/home/weiqi/project/00.DATABASE/GRmm38/GRCm38.p6.fa.size';... |
05399e7afddcbd182c21052145efeac65ab7929b59fd71e36eee08729ebe79b6 | Perl | 1,572 | 68 | #!usr/bin/perl -w
#use strict;
use warnings;
unless(@ARGV==3){
die "USAGE: This program evaluates the Robustness for a network through simulations of Random-Attack or Target-Removal.\nperl $0 <MIS.xls> <Hub.info> <Robustness.xls>\!\n\nThe format for the Hub.info file:\nFile Type\tPath to file\tRandom select number\n"... |
a9390c2ec86b74c2e8518e16e201aa7417488d2440b6ae112b892a2b51a71d3f | Perl | 1,578 | 77 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 inputFile out.cleanReads out.malformedReads\n\n";
my $inputFile = $ARGV[0] or die $usage;
my $cleanReads = $ARGV[1] or die $usage;
my $malformedReads = $ARGV[2] or die $usage;
open (my $ofh_clean, ">$cleanReads") or die "Error, can't write to $cl... |
a1118f8b115088c0bb4a3a8914a9cf90c0809becf98ba0c3f9ec4d14e8794bac | Perl | 1,584 | 91 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use List::Util qw(shuffle);
my $usage = <<__EOUSAGE__;
######################################################################################
#
# Required:
#
# --cmds <string> ... |
555f97be3121ec6aeb93433f6230f61d29efcb1b2a1d35430377c091e0a37256 | Perl | 1,603 | 65 | #!/usr/bin/perl -w
use strict;
use Data::Dumper;
die "Usage:perl $0 <gff|gff.gz> <Mammalia.gene_info> <tax id> <annovar result> <out>\n" unless @ARGV == 5;
my $gff = $ARGV[0];
open (GFF,($gff =~ /\.gz$/)? "gzip -dc $gff |" : $gff) or die "gzipped gff file required!\n";
open (OUT, ">$ARGV[4]") or die "permission denied!... |
733e09ba18ef94d348c322d00a8242b2f746e2ecba0ec28512a13c0581643faa | Perl | 1,609 | 70 | #!/usr/bin/perl
use strict;
use warnings;
#use autodie ':all';
# use Compress::Zlib <- don't use this - too slow
use Time::HiRes 'time';
use Getopt::Std ;
our ($opt_h, $opt_f,$opt_q, $opt_v, $opt_t);
getopts("hvqf:t:");
&usage if $opt_h;
sub usage {
die "FindMethylatedCoordinatesForAllStrainsInOneTissue.pl -f <... |
b9c79906d106dd6a33626c1d61b7b395558b362b13a0fb48bfb1712a659a8d87 | Perl | 1,644 | 95 | #!/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... |
6fdcc0a6bfe7a43cc6904241e7cb82edc70d1b796546410ef18aef0c8e04261a | Perl | 1,662 | 61 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 flag_number\n\n";
my $flag = $ARGV[0] or die $usage;
my @tokens;
my $pair_flag = ($flag & 0x0001) ? "PAIRED" : "unpaired";
push (@tokens, $pair_flag);
my $query_unmapped_flag = ($flag & 0x0004) ? "query_unmapped" : "QUERY_MAPPED";
push (@token... |
40f1e6141aae27b497f851e5a702d5e5b585f0ebeb5b63fe3f1db98f05099ae4 | Perl | 1,668 | 84 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = "\n\nusage: $0 --prefix \$prefix fileA.sra [fileB.sra ...]\n\n\n";
my $prefix;
&GetOptions ('prefix=s' => \$prefix);
my @sra_files = @ARGV;
unless (@ARGV) {
die $... |
91bd18a79e1de466f25b8fca4a5b3184a20290352fd3e73d8670cac488e60091 | Perl | 1,675 | 83 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
####################################################################################
#
# usage: $0 --reads_list_file <string> --out_token <string> [Trinity params... |
472409c326d325a78c77df290961168955b7497134577bb7d60f492c01d85026 | Perl | 1,689 | 62 | use marisa;
$keyset = new marisa::Keyset;
$keyset->push_back("cake");
$keyset->push_back("cookie");
$keyset->push_back("ice");
$keyset->push_back("ice-cream");
$trie = new marisa::Trie;
$trie->build($keyset);
print("no. keys: ", $trie->num_keys(), "\n");
print("no. tries: ", $trie->num_tries(), "\n");
print("no. node... |
d16f034df533e0ad21c78a4c8cf7058b646cb92b1705fd69ee3705ebeba1b0b5 | Perl | 1,708 | 78 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib", "$FindBin::RealBin/../../PerlLib/KmerGraphLib");
use Fasta_reader;
use StringGraph;
use StringNode;
use ColorGradient;
my $usage = "usage: $0 Butterfly.fasta\n\n";
my $butterfly_fasta_file = $ARGV[0] or die $usag... |
0f25bd4f2a1b441444ab3cd231d9e513e271722bad2eb7fd014d46c2f6b37434 | Perl | 1,717 | 82 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 annot.gff3 target_file.txt\n\n";
my $annot_gff3 = $ARGV[0] or die $usage;
my $target_file = $ARGV[1] or die $usage;
main: {
my %trans_id_to_annot = &parse_trans_names($annot_gff3);
open (my $fh, $target_file) or die "Error, cannot open ... |
827c24b7485eb4345a43d6c790ea85e86ba2d6c03749c3ca3cbee867fe15853b | Perl | 1,723 | 84 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\nusage: $0 RSEM.genes.results\n\n";
my $rsem_file = $ARGV[0] or die $usage;
main: {
my @entries;
open (my $fh, $rsem_file) or die $!;
my $header = <$fh>;
my $max_fpkm = 0;
while (<$fh>) {
chomp;
my @x = split(/\t/);... |
9641392078f883b77aab7fb73623b5d4ef2390adb660b4c7a5120e33af00d3c1 | Perl | 1,726 | 74 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fasta [require_proper_pairs_flag] [include_volcano_spread]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $require_proper_pairs_flag = $ARGV[1] or die $usage;
my ... |
dc6002a25e9f1bd8c137f94f240c1ca32a8db132216e13997e88f4e05beb2d1e | Perl | 1,726 | 82 | #!/usr/bin/env perl
use strict;
use warnings;
## sums up reads per gene, but uses the single isoform with the highest sum counts as the representative entry in the reported 'gene' matrix.
my $usage = "usage: $0 trinity_trans_matrix > trinity_rep_trans_matrix\n\n";
my $trans_matrix_file = $ARGV[0] or die $usage;
m... |
6533d50ccec63c8638a45cba7f9aa96301b113bc63427174c5913cd13387c248 | Perl | 1,737 | 58 | #!/usr/bin/perl
use strict;
use warnings;
use Vcf;
die "ERROR: not enough arguments\nUSAGE: ./exacext.pl <filedir>\n" if(@ARGV < 1);
my $filedir = $ARGV[0];
#local my $file = "/media/sf_Documents/VU/Data/ExAC0.3/ExAC.r0.3.sites.vep.vcf.gz"; #local
my $file = "/data/ExAC/ExAC.r0.3.sites.vep.vcf.gz";
my $in = $filedir.... |
9d94fefc813d2cb8eaa04d31dfde92397ac59ba8376b1749f4f7d63b1f846fdf | Perl | 1,738 | 85 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Nuc_translator;
my $usage = "usage: $0 file.sam out_prefix\n\n";
my $sam_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] or die $usage;
main: {
my $sam_reader... |
286ba234a2e1f9c81d11b5f7f584b4ca0cd6e90230f00d3bda7004e985fb84b2 | Perl | 1,746 | 62 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
print STDERR "\n\n\tNOTE - longest transcript isn't always the best transcript!... consider filtering based on relative expression support ... \n\n";
my $usage = "usage: $0 Trinity.fasta\n\n";
m... |
c05e22fd445abe873c718641175f80f63d81528a2972d1f4caa617cd19ade2c1 | Perl | 1,770 | 85 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Nuc_translator;
my $usage = "usage: $0 blat.psl.nameSorted.sam reads.tab.nameSorted\n\n";
my $sam = $ARGV[0] or die $usage;
my $seqs = $ARGV[1] or die $usage;
main: {
open (my $sam_fh, "$sam") or die... |
787b487821d87d2c9a015d6c34d814f4d9c226ccc06ee648c85f0e2b5167d5c4 | Perl | 1,779 | 66 | #!/usr/bin/perl
# miRDeep2 convert-bowtie-output perl script
# 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 Free Software Foundation, either version 3 of the License, ... |
fc3d77c9740b531a16dc0918678fced6b7ef0e759fbd66368cf3695bff5462a7 | Perl | 1,783 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 summary_file num_top_ranks\n\n";
my $summary_file = $ARGV[0] or die $usage;
my $num_top_ranks = $ARGV[1] or die $usage;
main: {
my %method_pairs;
open (my $fh, $summary_file) or die $!;
while (<$fh>) {
chomp;
my ... |
7c7d1e44dc6411ed97df8b895950bfebd3307fb8b337bd9add8dac83e7eaa9ce | Perl | 1,794 | 98 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fasta [kmer_length=25]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $kmer_size = $ARGV[1] || 25;
main: {
my $fasta_reader = new Fasta_reader($fasta_file);... |
7b3724a1d3eec3409e9727918277574dc9562fefba4c178a903c9bb5602aaf01 | Perl | 1,798 | 80 | #!/usr/bin/env perl
use strict;
use warnings;
no strict 'subs';
#use BSD::Resource;
main: {
print "\n\nBefore unlimit stack space:";
system("bash -c ulimit -a");
print "Attempting to unlimit stack space...";
try_unlimit();
print "After unlimit stack space: ";
system("bash -c u... |
b33d422f09283eda6ce4b6f92e348fcfd0bc8279e326a7765e8cde0d87b189bb | Perl | 1,836 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use List::Util qw(min max);
my $usage = "\n\n\tusage: $0 blast.outfmt6 query_fasta target_fasta\n";
my $blast_file = $ARGV[0] or die $usage;
my $query_fasta = $ARGV[1] or die $usage;
my $target_fasta... |
0aad3029fd7247c57149dca4cb7238689df28197b4c7587e1bd27f9f6fa46dc9 | Perl | 1,842 | 84 | #!/usr/bin/perl
# miRDeep2 GEO-to-FASTA perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... |
6c49a790c439d0382f7e8e7501722a5d36ba3f47e79e64c5e4a26e50d0f6468f | Perl | 1,855 | 95 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Gene_obj;
my $usage = "usage: $0 transcripts.gtf\n\n";
my $gtf_file = $ARGV[0] or die $usage;
main: {
my %genome_trans_to_coords;
open (my $fh, $gtf_file) or die "Error, cannot open file $gtf_file";
... |
1e6cdc0264392fc48bcb58766b948c02be234992a4a1f63253213b17be239017 | Perl | 1,858 | 103 | #!/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);
my $usage = <<_EOUSAGE_;
##################################################################
#
# Required:
#
# --target <string> : transcript sequences (eg. ... |
dc928711866be25e2e62474c38b9569f90c76074f7bd312fa38524b7a7cd5238 | Perl | 1,861 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 MAX_FDR MIN_FC\n\n"
. " \n\tRun this in the edgeR results directory.\n\n";
my $MAX_FDR = $ARGV[0] or die $usage;
my $MIN_FC = $ARGV[1] or die $usage;
my $MIN_LOGFC = log($MIN_FC)/log(2);
main: {
my @DE_files = <*.DE_results>;
my... |
88ce0a3ec6afdd6572d93e42824e5b5fcc6c65487c285b0636c6dd66e4147736 | Perl | 1,870 | 76 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 gmap.gff3 transcripts.fasta\n\n";
my $gmap_gff3 = $ARGV[0] or die $usage;
my $trans_fa = $ARGV[1] or die $usage;
main: {
my %trans_coords_matched;
open (my $fh... |
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