sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7b8d2dd9068267c4a2f7eea5f41d72798c955999df1dc1ad34e7d0d0a4fbb147 | Perl | 3,019 | 121 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey). Apache 2.0.
#scalar(@ARGV) >= 1 && print STDERR "Usage: summarize_warnings.pl <log-dir>\n" && exit 1;
sub split_hundreds { # split list of filenames into groups of 100.
my $names = shift @_;
my @A = split(" ", $names);
my @a... |
0bb678f1e19dd5fc5e218049423e3056647be78a7f0f1e5c2af3d6d12464fb2c | Perl | 3,026 | 123 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
use Data::Dumper;
$Data::Dumper::Indent = 1;
binmode STDOUT, ":utf8";
binmode STDIN, ":utf8";
sub permute {
my $last = pop @_;
unless(@_) {
return map([$_], @$last);
}
return map {
my $left = $_;
map... |
5818e4ab8d756481ae05172161c1fd7cb0ce6156f642055b9c1094d42a014ff5 | Perl | 3,031 | 107 | #!/usr/bin/perl
use warnings; #sed replacement for -w perl parameter
#
# Copyright 2013 Daniel Povey
# Apache 2.0
if (@ARGV != 2) {
print STDERR "Usage: $0 <path-to-LDC99S79> <path-to-output>\n";
print STDERR "e.g. $0 /export/corpora5/LDC/LDC99S79 data/swbd2_phase2_train\n";
exit(1);
}
($db_base, $out_dir) =... |
9730d7d7fdb0864859142e7caddeb8f26615f190e0439981e82f98009b4c375f | Perl | 3,036 | 76 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
c547f30dac7f2bc852dfa3e756c90972bcdb924a408c8740289422e3e5f75d21 | Perl | 3,048 | 98 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey)
# Apache 2.0.
# This program is a bit like ./sym2int.pl in that it applies a map
# to things in a file, but it's a bit more general in that it doesn't
# assume the things being map... |
95e698dbf0d27b22a3d1b1aff863725a0495acc0574966831ca1c6b624ec4858 | Perl | 3,054 | 101 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey). Apache 2.0.
# 2013 University of Edinburgh (Author: Pawel Swietojanski)
# This takes as standard input path to directory containing all the usual
# data files - segments, text, utt2spk and reco2file_and_channel and cre... |
ce73570371b9f836e98407d0ba45bf6c57b4b371fdb9c4f9a6f04ff05af2653b | Perl | 3,055 | 108 | #!/usr/bin/env perl
# Copyright 2014 QCRI (author: Ahmed Ali)
# Apache 2.0
use warnings;
use strict;
use Encode;
use utf8;
if (@ARGV !=2 )
{#
print "usage: $0 <inFile> <onlyArabicFile>\n";
exit (1);
}
# <\check usage>
my $inFile = shift (@ARGV);
my $ouFile = shift(@ARGV);
open INFILE, "<$inFil... |
b352c051d71996070ed670a1948f1330358bbbe2e3a03427abfbc8e531c47f18 | Perl | 3,091 | 129 | #!/usr/bin/perl
use strict;
my $filein = $ARGV[0];
my $fileout = $ARGV[1];
my $matrix = $ARGV[2];
my $min_x = 100000;
my $max_x = 0;
my $min_y = 100000;
my $max_y = 0;
my $n=0;
open(OUT,">$fileout");
open(F,$filein);
while(<F>){
if (/<path style=" stroke:none;fill-rule:nonzero;fill/){
if (/d=\"M ([\s\d\.]+) L... |
14ee037a53ef5388efcbff702ac230a4ccc6e38cbdf5ce2df97ef6e8bd6c0507 | Perl | 3,101 | 121 | #!/usr/bin/perl
use strict;
my $indir = $ARGV[0];
my $matrix = $ARGV[1];
my $out = $ARGV[2];
my $strain_names = $ARGV[3];
my %strains_of_gb;
open(F,$strain_names);
while(<F>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my ($gb,$strain) = split(/\t/,$line);
$strains_of_gb{$gb} = $strain;
}
close(F);
my @str... |
b978ab020d7659bf10128febed3dca53bb85295b4d79f2425bd77c0aeb5ecbc1 | Perl | 3,102 | 102 | #!/usr/bin/perl
#require "Parse_Form.lib";
#&Parse_Form;
require "./cgi-lib.pl";
my (%formdata, # The form data
%cgi_cfn, # The uploaded file(s) client-provided name(s)
%cgi_ct, # The uploaded file(s) content-type(s). These are
# set by the user's browser and may be unreliable
... |
a705c09fa92fc51d82d712daf3f73ca264344678ad4929a67615120c02d5a4f0 | Perl | 3,111 | 59 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
582d42846cf09083cbaa6f1a936d78a4bf53f6dbd0eee56068fd61dac9906639 | Perl | 3,113 | 73 | #!/usr/bin/env perl
use File::Basename;
($tmpdir)=@ARGV;
$trans="$tmpdir/callhome_train_transcripts.flist";
$reco="$tmpdir/reco2file_and_channel";
open(T, "<", "$trans") || die "Can't open transcripts file";
open(R, "|sort >$reco") || die "Can't open reco2file_and_channel file $!";
open(O, ">$tmpdir/text.1") || die "... |
27c5902b3d57d8ee805e5f43e00c67edaf0cd44731e3111b5cd216d20bba37be | Perl | 3,114 | 59 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
f5ea970fe3b105bd2f59a5231502e529985ad1a3462898713fd9ee43565f98aa | Perl | 3,125 | 123 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
use Data::Dumper;
$Data::Dumper::Indent = 1;
binmode STDOUT, ":utf8";
binmode STDIN, ":utf8";
sub permute {
my $last = pop @_;
unless(@_) {
return map([$_], @$last);
}
return map {
... |
96ccf49dd72a4370dc8e69998d283c430620c7ca7357f12050a65052e3fd07be | Perl | 3,137 | 123 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Yenda Trmal)
# Apache 2.0.
use Data::Dumper;
$Data::Dumper::Indent = 1;
binmode STDOUT, ":utf8";
binmode STDIN, ":utf8";
sub permute {
my $last = pop @_;
unless(@_) {
return map([$_], @$last);
}
return map {
... |
b2e1912696535184cb8bb5893ca3127e603238d0936c7941b522d927d5825cb6 | Perl | 3,166 | 80 | #!/usr/bin/perl
use warnings;
use strict;
use autodie;
use Getopt::Long;
use Bio::SeqIO; # bioperl module to handle sequence input/output
my $usage = << "USAGE";
##################################################################
# $0 -i seq_file -f in_format -o out_format #
# ... |
0c6fe0121cbab33cd959b12a67cd3bf89598e88dec5abe842462c524015fe0dd | Perl | 3,189 | 138 | #!/usr/bin/perl
use Hmm;
use Fsm;
use strict 'vars';
my $eps = ",";
my $boundary = "#";
my $final_symbol = "-2";
my $max_boundary_id = 0;
if (open(FILE, "boundaries")) {
$max_boundary_id = <FILE>;
chomp $max_boundary_id;
close(FILE);
}
$Hmm::verbose = 0;
my $hmmfile = shift @ARGV;
my $hmms = Hmm::read($hmmfil... |
c8186e0eb9ba9098b4dc75dedd12db5f18a47f14b8d4e3960dd6ec7ad1211c8d | Perl | 3,197 | 74 | #!/usr/bin/env perl
# Copyright 2014 Gaurav Kumar. Apache 2.0
use utf8;
use File::Basename;
($tmpdir)=@ARGV;
$trans="$tmpdir/callhome_train_transcripts.flist";
$reco="$tmpdir/callhome_reco2file_and_channel";
open(T, "<", "$trans") || die "Can't open transcripts file";
open(R, "|sort >$reco") || die "Can't open rec... |
373aa47e3aad41a57e372a350e92276d511659fa1a8838a78d49d06ff26ac351 | Perl | 3,220 | 120 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
my $Usage = <<EOU;
Usage: subset_atwv.pl [options] <keywords|-> <bsum.txt>
e.g.: subset_atwv.pl keywords.list bsum.txt
This script will compute the ATWV for a subset of t... |
2da13e3bb6a20a11133907274faac342123f5494a1c33cae6736137ae2487b87 | Perl | 3,223 | 120 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
my $Usage = <<EOU;
Usage: subset_atwv.pl [options] <keywords|-> <bsum.txt>
e.g.: subset_atwv.pl keywords.list bsum.txt
This script will compute the ATWV for a subset of t... |
f1c8fb19e889e4c5eaec498a4c2de5ea1dde6300dc89a5e776e5dfc23ad394e5 | Perl | 3,245 | 103 | #!/usr/bin/perl
use Finished;
use Chrom;
use Contig;
$ref = "hg19";
@finished_species = (mm9);
@chrom_species = qw(equCab2 canFam2 bosTau4 oryCun2 rn4 monDom5 taeGut1 galGal3);
@contig_species = qw(loxAfr3 cavPor3 anoCar1 xenTro2);
@all = qw(hg19 equCab2 canFam2 bosTau4 oryCun2 mm9 rn4 monDom5 taeGut1 galGal3 loxAfr... |
d33f71c15acbc3dbc749f6844e1f72a0fb7b6e760fbc6273534f02a0eeb36d82 | Perl | 3,256 | 101 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
0e9d27544e9dcc3fdbc0552fb32b7a7acbb07cec99527b3a4478346225f03aaf | Perl | 3,265 | 101 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
b560ed2c96341a46328551aa6a3aade0b229b439822d7801807be80b5ed60f39 | Perl | 3,267 | 124 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
my $Usage = <<EOU;
Usage: annotated_kwlist_to_KWs.pl [options] <kwlist.annot.xml|-> <keywords|-> [category]
e.g.: annotated_kwlist_to_KWs.pl kwlist.annot.list keywords.lis... |
02da7f10139da87e0908d7c804ea77e0dd79120612f75af7a68c2f674dc4a9a6 | Perl | 3,269 | 124 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
my $Usage = <<EOU;
Usage: annotated_kwlist_to_KWs.pl [options] <kwlist.annot.xml|-> <keywords|-> [category]
e.g.: annotated_kwlist_to_KWs.pl kwlist.annot.list keywords.lis... |
5736b20db5e0732f1fda31520da5e7200206d583ee96c65ec64aef66f3ae88e5 | Perl | 3,321 | 117 | #!/usr/bin/perl
use strict;
my $gff = $ARGV[0];
my $window_size = $ARGV[1];
my %counts;
my %hash;
open(F,$gff);
while(<F>){
if (/^#/){next;}
my @infos = split("\t",$_);
my $chr = $infos[0];
#$chr =~s/chr//g;
my $source = $infos[1];
my $feature = $infos[2];
my $start = $infos[3];
my $end = $infos[4];
my $win... |
1e335c850edd8ebc5f851820ddcf2373ab43033b585c3f52676420b01199ed3a | Perl | 3,369 | 110 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
177da2dca441a4b99aabcf8ca9ae00d2432418f722f940200d887df504969662 | Perl | 3,370 | 95 | #!/usr/bin/perl
# This script creates the denominator hmmnets required for discriminative
# training. Note that this will also generate the normal numerator hmmnets
# to ensure conformity of the two hmmnets. If you want to disable the
# writing of numerator hmmnets, remove the -n switch from create_hmmnets.pl
# call.
... |
077788622448d0534b0ba763156d77d2827f27a2533c222959a21b75598a2c02 | Perl | 3,428 | 193 | #!/usr/bin/perl
=head
this script is used to find chip-seq intensity in certain region
input files are: region_location_file in bed format and chip-seq_BedGraph_file
output file is: chip-seq_peak_intensity_file
=cut
use List::Util qw(first max maxstr min minstr reduce shuffle sum);
print "command line: perl grep... |
4e5444fcf52cb8b8575fe8d0bcf0a15f8420710a526630c3b9d657722f89c8c1 | Perl | 3,436 | 179 | #!/usr/bin/env perl
use warnings;
use strict;
use List::Util qw(reduce);
use Data::Dumper;
sub cartesian_product {
reduce {
[ map {
my $item = $_;
map [ @$_, $item ], @$a
} @$b ]
} [[]], @_
}
sub gen_range {
(my $begin, my $step, my $end) = split(':', $_[0]);
my @range = ();
for (my $... |
0f62bd9e739c4c1447c81b0597e88635159887879a730381dc691a8b0d51be5b | Perl | 3,452 | 179 | #!/usr/bin/env perl
use warnings;
use strict;
use List::Util qw(reduce);
use Data::Dumper;
sub cartesian_product {
reduce {
[ map {
my $item = $_;
map [ @$_, $item ], @$a
} @$b ]
} [[]], @_
}
sub gen_range {
(my $begin, my $step, my $end) = split(':', $_[0]);
my @range = ();
for (my $... |
532aea8ad2df1aa3747357e44bbe9cf6ba81f612999ca22b007423a1756fe9b0 | Perl | 3,470 | 111 | #!/usr/bin/env perl
# Copyright 2014 QCRI (author: Ahmed Ali)
# Apache 2.0
use warnings;
use strict;
use Encode;
use utf8;
if (@ARGV !=2 )
{#
print "usage: $0 <inFile> <onlyArabicFile>\n";
exit (1);
}
# <\check usage>
my $inFile = shift (@ARGV);
my $ouFile = shift(@ARGV);
open INFILE, "<$inFil... |
39aa452250b993c9b5bc82191c6c35cadc6c25b378eac08d1cc67840ff92d2b5 | Perl | 3,471 | 151 | #!/usr/bin/perl
# Copyright 2020 Ivan Medennikov (STC-innovations Ltd)
# Apache 2.0.
# This script takes 4 scp files $filein{1,2,3,4} with the same utterance-ids,
# and produces 4 shuffled versions of them.
# Moreover, the same shuffling is performed with 4 utt2spk files $utt2spk{1,2,3,4}.
use List::Util qw(shu... |
677b87d82db1d246fbd497b44fa89e9a364ad2313eed4706d1891d9b5304c477 | Perl | 3,471 | 109 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Milos Janda; Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... |
d11daff8e6850db89407f2a4184cec8c3add18e7b4410a01b090a1a70503bce2 | Perl | 3,491 | 129 | #!/usr/bin/perl
# Reads monophone transcripts (with or without time and state information)
# from transcript fields of the recipe file and rewrites them as triphonized
# versions.
# Input: RECIPE
use locale;
use strict;
my $recipefile = shift;
die "Usage: triphonize_monophone_phns.pl RECIPE" if (!defined($recipef... |
07e286cefeb5fdae6ee18efa940396109657a04bae4d28913ffc312a307b47e2 | Perl | 3,507 | 137 | #!/usr/bin/perl
use strict;
my $matrix = $ARGV[0];
my $out = $ARGV[1];
my $strain_names = $ARGV[2];
my $bed_dir = $ARGV[3];
my $fasta_dir = $ARGV[4];
my %strains_of_gb;
open(F,$strain_names);
while(<F>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my ($gb,$strain) = split(/\t/,$line);
$strains_of_gb{$gb} = $... |
360bc3601707fdd050b3bb311006b5cf53083696eb5c119d7ac20b7aaec9e690 | Perl | 3,510 | 121 | #!/usr/bin/perl
#
# Generates LNA files with possible Gaussian clustering, recognizes
# the utterances and deletes the LNAs in the end. Enables parallel
# operation for both LNA generation and recognition.
#
use lib '/share/puhe/x86_64/lib'; # For GridManager (or use aku/scripts dir)
use locale;
use strict;
use GridM... |
1817f5cab98ff6f3bf2f23a3292582eefb758b273fcdb23c8d70a90eaef46034 | Perl | 3,511 | 153 | #!/usr/bin/perl
use strict;
my $nb_file_found = 0;
open(LS,"ls *Nfowleri.snp |");
while(<LS>){
$nb_file_found++;
}
close(LS);
if ($nb_file_found < 1){
print "No file found with extension \".Nfowleri.snp\". This script allows to merge multiple SNP files (named as follows \"strainname.Nfowleri.snp\") obtained with Va... |
2907dc7674d49ff324873cc153ca288d65bc49c5b0ddba6617dc4c376699001c | Perl | 3,523 | 110 | #!/usr/bin/perl
use strict;
use warnings;
use List::Util qw/shuffle/;
#hardip@rstudio-nci:~/pacific$ # /media/dstore/covid19/seqid.vs.genomeinfo.txt
#hardip@rstudio-nci:~/pacific$ # /media/dstore/covid19/virus.genbank.20200324.fa
#V1 V2 V3 taxid assemblyname organism lineage
#GCA_000837105.1 ViralMultiSegProj14079 L1... |
a06f5d832ca2906f4761b31d2b020d10478e606950237bf7d902639cc78c9508 | Perl | 3,550 | 104 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
87d3bd6b562ff5af266b744f092f04ee92321cb62831951e245a0818d236bcd1 | Perl | 3,553 | 106 | #!/usr/bin/perl
# LMU Munich. AG Enard
# Pipeline to filter reads based on Barcode base quality.
# Author: Swati Parekh
# Contact: parekh@bio.lmu.de or ziegenhain@bio.lmu.de or hellmann@bio.lmu.de
if(@ARGV != 11)
{
print
"\n#####################################################################################
Usage: p... |
e8379e62cad778c9ce72c4f9a50c1871b3e681b31c6d97e6348c33eab34e76c0 | Perl | 3,599 | 120 | #!/usr/bin/env perl
# Copyright 2017 John Morgan
# Apache 2.0.
# heroico_recordings_make_lists.pl - make acoustic model training lists
use strict;
use warnings;
use Carp;
use File::Spec;
use File::Copy;
use File::Basename;
my $tmpdir = "data/local/tmp/heroico";
system "mkdir -p $tmpdir/recordings/train";
system "... |
6f8f1bbf269e3fd1a9d90c1f98cc8a759d24221b0853f9199e8d2a24a4176d83 | Perl | 3,605 | 103 | #!/usr/bin/env perl
# This program enforces the rule that
# if a "more specific" rule applies, we cannot use the more general rule.
# It takes in tuples generated by get_candidate_prons (one per line, separated
# by ";"), of the form:
# word;pron;base-word;base-pron;rule-name;de-stress[;rule-score]
# [note: we mean th... |
e03c799d09d2ad4e94e7e64908436ff03137d14bfb8b942a74754090f378a293 | Perl | 3,624 | 112 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Milos Janda
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICE... |
ed83c16f9d7ffb58df8680cc7b7f39af87d90b1058415503d749da9429a7e73a | Perl | 3,717 | 125 | #!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
our $VERSION = 0.01;
#our $DIR = '/bwdata1/jfryan/72-MNEMIOPSIS/09-SEBE_RERUN/UMI_tables/Mnemiopsis';
our $DIR = 'print_coexp_all.dir';
our @INNEXINS = qw(ML25993a ML25997a ML25998a ML25999a ML32831a ML47742a ML218922a ML129317a ML07312a ML223536a ML036514... |
879ff822108ccacc5ef089f56ec0b8b1eb4eb1c13cda7f1a9f1f8deae30fc45c | Perl | 3,723 | 106 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal; Milos Janda
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... |
4ac930d74214ae9037dc5af171276b92063820426cb2cc82c35b8f451239fe60 | Perl | 3,731 | 106 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal; Milos Janda
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... |
4987d2a43e5d9c5885c2ae5d94c34020f76e97487b44d0f8dc7d43b75578204b | Perl | 3,785 | 116 | #!/usr/bin/env perl
# Copyright 2014 QCRI (author: Ahmed Ali)
# Apache 2.0
use warnings;
use strict;
use Encode;
use utf8;
if (@ARGV !=2 )
{#
print "usage: $0 <inFile> <onlyArabicFile>\n";
exit (1);
}
# <\check usage>
my $inFile = shift (@ARGV);
my $ouFile = shift(@ARGV);
open INFILE, "<$inFil... |
5f5b108b63f7890fe44c87a053782f0c315d40af865967ad0330714866354a80 | Perl | 3,791 | 127 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
my $Usage = <<EOU;
Usage: build_edit_distance_fst.pl <phones.txt|-> <fst_out|->
Buld a edit distance FST at the phone level.
Allowed options:
--confusion-ma... |
0521e5252da4fad87f03f87dd36d484ac837d181f85ee56d5a4e7d7cb8bba067 | Perl | 3,816 | 114 | #!/usr/bin/perl
use strict;
use Cwd;
use File::Spec;
use File::Basename;
# directory of where this script is called
my $cwd = dirname($0);
# databases to annotate against to
my $REF="$cwd/../external_databases/hg19_random.fa";
my $dbSNP_142="$cwd/../external_databases/dbSNP142_All_20141124.vcf.gz.modified.vcf.gz"... |
8c172415e8705c1e820bfc3d3725840d65909801e87f913713fd16feebeb0238 | Perl | 3,873 | 123 | #!/usr/bin/env perl
# Reads a dictionary (for prons of letters), and an OOV list,
# and puts out candidate pronunciations of words in that list
# that could plausibly be acronyms.
# We judge that a word can plausibly be an acronym if it is
# a sequence of just letters (no non-letter characters such
# as "'"), or some... |
6d8cd6c45aad568a2c6854683647af9dc6cd71ecbd32a7da64f4e0c225df3b3e | Perl | 3,896 | 154 | #!/usr/bin/perl
use strict;
my $pav = $ARGV[0];
my $ref = $ARGV[1];
my $strain_info = $ARGV[2];
my $gff = $ARGV[3];
my $ordering = $ARGV[4];
my $outfile = $ARGV[5];
my $circos_exe = "circos/bin/circos";
#my $circos_exe = "circos";
my %metadata;
open(M,$strain_info);
while(my $line = <M>){
chomp($line);
my ($id,$n... |
4d64b63c0e3f0c6d654f99ae8c424fdde55545abaa43255192c3684fddf6eb90 | Perl | 3,978 | 151 | #!/usr/bin/env perl
use warnings;
use strict;
use utf8;
use Data::Dumper;
sub float_gt {
my ($A, $B) = @_;
#print Dumper(\@_);
if ( ($A - $B) < 1e-12 ) {
return 0;
} elsif ($A > $B ) {
return 1;
} else {
return 0;
}
}
binmode(STDOUT, ":utf8");
binmode(STDERR, ":utf8");
my $datadir=$ARGV[0]... |
a4afd4e2ad6c6ec1c675b1f198d7d49a4bb5fa50e2fc00acfeb2d01a561f2915 | Perl | 3,988 | 151 | #!/usr/bin/env perl
use warnings;
use strict;
use utf8;
use Data::Dumper;
sub float_gt {
my ($A, $B) = @_;
#print Dumper(\@_);
if ( ($A - $B) < 1e-12 ) {
return 0;
} elsif ($A > $B ) {
return 1;
} else {
return 0;
}
}
binmode(STDOUT, ":utf8");
binmode(STDERR, ":utf8");
my $datadir=$ARGV[0]... |
9b7507670a600c07c909b9a627afd47f90b50b1a57011bcb3339925ebfa15606 | Perl | 4,001 | 140 | #!/usr/bin/env perl
# Copyright 2013 Hong Kong University of Science and Technology (Author: Ricky Chan Ho Yin)
#
# Apache 2.0.
#
# A script to convert Kaldi Chinese words transcription to Chinese characters transcription.
# This is helpful for Chinese character error rate scoring.
#
# If no option... |
69e23ffeb00b505ff8ae9762a4592772163d441928a48b3f17ccc6f2867937b4 | Perl | 4,016 | 101 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
b116a7b06474698c6e4751e174be0fa3886bf00e3feb232f4bf3fa3261725d4b | Perl | 4,020 | 163 | #!/usr/bin/perl
use strict;
my $gfa = $ARGV[0];
my $bed = $ARGV[1];
my $out = $ARGV[2];
my %segment_is_covered_by_genes;
my %coordinates;
my %store_gene_paths;
my %allgenes;
my %coding_positions;
open(LENGTH,">$out.gene_length.txt");
open(F,$bed);
while(my $line = <F>){
chomp($line);
my @infos = split(/\t/,$l... |
32b31f54ee7b54cbc21ae9193583020072a6189fb0c076cc5d3f8b27b8d464c6 | Perl | 4,079 | 208 | #!/usr/bin/perl
#
#######################################################################################
#
# this script is used to find rna per-base value from a .bedGraph file
#
# input files are: annotaion_file, chrsize file, and bedGraph files
# output file is: rna_per-base_signal_tab_file
#
######################... |
804612ebc0f880fe4c2c74314825ab033db05ebee5f3f1f2c9d57a2131f90b0e | Perl | 4,086 | 110 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (Author: Jan Trmal)
# Apache 2.0.
#This script takes the original BABEL STM file (part of the IndusDB)
#and replaces the "Aggregated" field with a correct speaker ID.
#As a result, the scoring will be do... |
8840954862b6f74fcc66bb273126ae5e2e6fd072d4aa613a9971d50d65049b40 | Perl | 4,101 | 110 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (Author: Jan Trmal)
# Apache 2.0.
#This script takes the original BABEL STM file (part of the IndusDB)
#and replaces the "Aggregated" field with a correct speaker ID.
#As a result, the scoring will be do... |
d45cc67f341210523612c13ae4a3bb0cfbca15e59e52990d0a07fc94d1810cac | Perl | 4,102 | 110 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Johns Hopkins University (Author: Jan Trmal)
# Apache 2.0.
#This script takes the original BABEL STM file (part of the IndusDB)
#and replaces the "Aggregated" field with a correct speaker ID.
#As a result, the scoring will be do... |
2345ea7a390c96ea4db3947fed67d3dc701417f2808f85e42eae950f7de8c4fa | Perl | 4,121 | 122 | #!/usr/bin/env perl
# Copyright 2010-2011 Microsoft Corporation
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THIS CODE IS PROVIDED *AS IS... |
7fd1a01559614b129b0db339d67fe5430e62d7f1b5ae525a0eb22f82e76d4f90 | Perl | 4,191 | 154 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2015 Johns Hopkins University (Author: Yenda Trmal<jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# ... |
4660a3335182a692793f236e60cfd683528aed921b0f2c127f1529f5a38d8996 | Perl | 4,213 | 140 | #!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use List::Util qw/shuffle/;
my ($dataid, $testclass, $maxreads, $testproportion) = @ARGV;
my %seqcounts = (
"Coronaviridae.genomes.fasta" => 12,
"Homo_sapiens.GRCh38.cdna.e99.canonicaltranscripts.fasta" => 22499,
"Influenza.genomes.fasta" => 1024,
"Metap... |
ae6be61fcc1aaf0cce5ff8c4d22fd792ef27974f4556005f41d7ce7848b7964c | Perl | 4,229 | 168 | #!/usr/bin/perl
use strict;
use Graph::Undirected;
my $strain_info = $ARGV[0];
my $bed_directory = $ARGV[1];
my $PAV = $ARGV[2];
my $threshold_coverage = $ARGV[3];
my %strains;
open(S,$strain_info);
while (my $line = <S>) {
chomp $line;
my ($id,$name) = split(/\t/,$line);
$strains{$id} = $name;
}
close(S);
my %... |
df04e236d8b1a7c19a7bd82be9ac59e20391442411b8fbb27061e1e2b325c6ed | Perl | 4,234 | 134 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2015 (Author: Yenda Trmal <jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy o... |
a7538ed5cd101df2e987b40fabe67e7e2538fa306fa1ec082aef370fbe9d7d12 | Perl | 4,292 | 159 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
my $cf_needed = 0.9;
my $cf_needed_upper = 1;
my $extend_segments = 0.0 ;
my $Usage = <<EOU;
Generate kaldi text and segments file (for use during unsupervised training)
Usage: ctm_to_training.pl [options] <ctm_in|-> <text_out|->
Allowed options:
... |
50fd1491dc5640fbf1a31f20a75494e828a0bcba6003b42e47c88b9b3b139cf9 | Perl | 4,312 | 159 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
my $cf_needed = 0.9;
my $cf_needed_upper = 1;
my $extend_segments = 0.0 ;
my $Usage = <<EOU;
Generate kaldi text and segments file (for use during unsupervised training)
Usage: ctm_to_training.pl [options] <ctm_in|-> <text_out|->
Allowed options:
... |
672b0f405f0dc6f44454bb1afc8773925b5c7ec0c163bc4566f7fe8205649cdb | Perl | 4,384 | 156 | #! /usr/bin/perl
#
use strict;
use warnings;
my $summitInstance = shift;
my $filterInstance = shift;
my $window = shift;
&main ();
sub main
{
$window = 10 if ( not defined $window );
my $nrSummitInstance = $summitInstance . ".nr";
rmRdp ( $summitInstance, $nrSummitInstance );
filter ( $nrSummitInsta... |
a5cefa4480b88418516d57cb7eaf75b8ef89fce5e2f25db36ce6e1ff58863b17 | Perl | 4,403 | 166 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2016 (Author: Yenda Trmal <jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy o... |
38c511531f6de7b5eed3ed7b4b56bbf1a6bec05d3866a7be3a60da1149401e8e | Perl | 4,426 | 180 | #!/usr/bin/perl
use strict;
my $gfa = $ARGV[0];
my $gff3 = $ARGV[1];
my $out = $ARGV[2];
my %segment_is_covered_by_genes;
my %coordinates;
my %store_gene_paths;
my %allgenes;
my %coding_positions;
open(LENGTH,">$out.gene_length.txt");
open(F,$gff3);
while(my $line = <F>){
chomp($line);
my @infos = split(/\t/,... |
d8728b3d8a274148e1fe85ea99c06712e8e34bc764e6b406f2af5a5a41a4f407 | Perl | 4,431 | 150 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Milos Janda
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICE... |
4208f0f8d2abe8d41c5d3d528ea407039eacc6fb79b5d5e37559ce7bd051109d | Perl | 4,487 | 131 | #!/usr/bin/env perl
#===============================================================================
# Copyright (c) 2017 Johns Hopkins University
# (Author: Jan "Yenda" Trmal <jtrmal@gmail.com>)
# 2017 Vimal Manohar
#
# Licensed under the Apache License, Version 2.0 (the "Licens... |
f9ad38f0c4f28f48b0a63f4bb7cf4c5fa16c56eb112c8e2d9273df1e5cc11c42 | Perl | 4,527 | 179 | #!/usr/bin/perl
use strict;
my $gfa = $ARGV[0];
my $bed = $ARGV[1];
my $out = $ARGV[2];
my $pattern = $ARGV[3];
my %segment_is_covered_by_genes;
my %coordinates;
my %store_gene_paths;
my %allgenes;
my %coding_positions;
open(F,$bed);
while(my $line = <F>){
chomp($line);
my @infos = split(/\t/,$line);
my $ch... |
8ac6f8494f6bbe2c71d7d20496699eff975892375c8f184a0d000c53ed13f64d | Perl | 4,536 | 191 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
# ------------------------------------------------------------
# Usage:
# perl gff_crispr_matrix.pl /path/to/gff_directory output.tsv
#
# Example:
# perl gff_crispr_matrix.pl ./gff crispr_presence_absence.tsv
# -------------------------------------... |
6a6995533e8fd15cf14d36e857da2c85ef42f25c5223c050eb2b3add0bcbeb0f | Perl | 4,585 | 123 | #!/usr/bin/perl
#
# Copyright 2018 Ewald Enzinger
# 2018 David Snyder
# 2019 Soonshin Seo
#
# Usage: make_voxceleb1_v2.pl /export/voxceleb1 dev data/dev
#
# The VoxCeleb1 corpus underwent several updates that changed the directory and speaker ID format.
# The script 'make_voxceleb1.pl' works for ... |
7edb6d6794270c36610fb906e0942d7304ea08b651b7c0d4d249f49df4b9c50a | Perl | 4,644 | 130 | #!/usr/bin/perl
#
# Copyright 2018 Ewald Enzinger
# 2018 David Snyder
#
# Usage: make_voxceleb1.pl /export/voxceleb1 data/
if (@ARGV != 2) {
print STDERR "Usage: $0 <path-to-voxceleb1> <path-to-data-dir>\n";
print STDERR "e.g. $0 /export/voxceleb1 data/\n";
exit(1);
}
($data_base, $out_dir) = @ARGV;... |
bf9b1d77ef995fd361da36df6969eb11f87cc691acc61fa3fbf113cbce7fd81f | Perl | 4,703 | 169 | #!/usr/bin/perl
use strict;
use Graph::Undirected;
my $strain_info = $ARGV[0];
my $bed_directory = $ARGV[1];
my $PAV = $ARGV[2];
my $threshold_coverage = $ARGV[3];
my %strains;
open(S,$strain_info);
while (my $line = <S>) {
chomp $line;
my ($id,$name) = split(/\t/,$line);
$strains{$id} = $na... |
26918d65de761a8c9eef338d2fa8bb0bc96d490490edad6e9733c53f5e2ce723 | Perl | 4,811 | 141 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
3aa5855a8874bab26f0437875a6375edc70b684c5cd8433a4eb45bcf8347c195 | Perl | 4,817 | 189 | #!/usr/bin/perl
use strict;
my $pav_matrix = $ARGV[0];
my $cog_of_clusters = $ARGV[1];
my $output = $ARGV[2];
my %categories = ("Unknown"=>1);
my %cog_categories;
my %cogs_for_cluster;
open(COG,$cog_of_clusters);
while(<COG>){
my $line = $_;
$line =~s/\n//g;$line =~s/\r//g;
my ($cluster,$cog,$category) = split("... |
5cf1c186725636c3eeb6bc5c3df63a7415ddfea544b326dd87c83b712b40e6c1 | Perl | 4,947 | 113 | #!/usr/bin/perl
use strict;
use warnings;
$| = 1; # Autoflush output
sub run_ft2_to_json_and_binary {
my ($input_file, $file_name_prefix, $execDir) = @_;
# Construct the command
my $command = $execDir . "deep-picker/release/plot_spectrum_2d "
. "-in $input_file "
. "-out-... |
799782779130a62e0c1c67c5d538a050261dea130d1b385bbb310f06aac6988a | Perl | 5,019 | 154 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal; Milos Janda
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... |
60ef6d0d2c578b054107c0ee0ce920c13a18f4b70cffb0330594846be5acb1f2 | Perl | 5,068 | 147 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
7d0f7b02b2ef43360023b54182c0f29571f6d227b24d647249b7016c3e432468 | Perl | 5,133 | 189 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2015 (Author: Yenda Trmal <jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy o... |
9b065521743603e579e256a3e2b7d34bf77d32ad4a9c6cdb544160a08ad681b4 | Perl | 5,199 | 190 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
sub KeywordSort {
if ($a->[0] ne $b->[0]) {
$b->[0] <=> $a->[0];
} else {
$b->[1] <=> $a->[1];
}
}
my $Usage = <<EOU;
This script reads a alignment.csv file ... |
cbf4e6129d4465d6dacd30012e95b60b5307344676bef20646a34a7bf45a4013 | Perl | 5,383 | 151 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LI... |
7a467b6edff5e02f3be5798caea370994d15881fb174811bc2f0e6a79bc079db | Perl | 5,443 | 139 | #!/usr/bin/perl
use strict;
use warnings;
sub run_fid_to_ft2_hsqc {
my ($hsqc_acquisition_seq, $neg_imaginary, $execDir) = @_;
my $command_step1 = $execDir . "deep-picker/release/fid -nus none -phase-in none -in hsqc_fid_file hsqc_acquisition_file hsqc_acquisition_file2 none";
$command_step1 .= " -aqseq $... |
c44f78b6482c45184aee768cf3ff828cbc56e93e50ec233076c735d9b8f89942 | Perl | 5,572 | 200 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
sub KeywordSort {
if ($a->[0] ne $b->[0]) {
$b->[0] <=> $a->[0];
} else {
$b->[1] <=> $a->[1];
}
}
my $Usage = <<EOU;
This script reads a alignment.csv file ... |
99250728507032a4260494b410e9fc06aaa8371a91a7e6471a39db31a210b900 | Perl | 5,974 | 203 | #!/usr/bin/env perl
#===============================================================================
# Copyright 2015 (Author: Yenda Trmal <jtrmal@gmail.com>)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy o... |
dd0bee3bc9399873cee1b26ca1b93fe3d7ddf7b5ed37cab452b55015eaf1ffd1 | Perl | 6,051 | 233 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
use XML::Simple;
use Data::Dumper;
use File::Basename;
my $tolerance = 0.5;
sub ReadKwslist {
my $kwslist_in = shift @_;
my $source = "STDIN";
if ($kwslist_in ne "-... |
46952f5cb37d11f56c50666a4f681b30e8399ef417ddcba31e1a9085b9ab184f | Perl | 6,097 | 207 | #!/usr/bin/perl
#######
# POD #
#######
=pod
=head1 NAME
C<revcom_seq.pl> - reverse complement (multi-)sequence files
=head1 SYNOPSIS
C<perl revcom_seq.pl seq-file.embl E<gt> seq-file_revcom.embl>
B<or>
C<perl cat_seq.pl multi-seq_file.embl | perl revcom_seq.pl -i embl
E<gt> seq_file_cat_revcom.embl>
=head1 DE... |
251655fe65c138bac15283c28b377f33401d75b44285429066be5e75ef1bbba1 | Perl | 6,132 | 234 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
use XML::Simple;
use Data::Dumper;
use File::Basename;
my $tolerance = 0.5;
sub ReadKwslist {
my $kwslist_in = shift @_;
my $source = "STDIN";
if ($kwslist_in ne "-... |
4dd14cde804153b2e3574c616b154e3de7390be8aab87b9aa716ca128258005b | Perl | 6,134 | 234 | #!/usr/bin/env perl
# Copyright 2012 Johns Hopkins University (Author: Guoguo Chen)
# Apache 2.0.
#
use strict;
use warnings;
use Getopt::Long;
use XML::Simple;
use Data::Dumper;
use File::Basename;
my $tolerance = 0.5;
sub ReadKwslist {
my $kwslist_in = shift @_;
my $source = "STDIN";
if ($kwslist_in ne "-... |
3da03d335b4bb2054950e922e7325e78911e5459ba6367fb8512d8d020e51d06 | Perl | 6,343 | 197 | #!/usr/bin/env perl
use warnings; #sed replacement for -w perl parameter
# Copyright 2012 Milos Janda; Arnab Ghoshal
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... |
bcfbcac3979af6abc9b2f6a3d3925477928d5ce536e67e2b085b7f78e591bc68 | Perl | 6,656 | 265 | #!/usr/bin/perl
#######
# POD #
#######
=pod
=head1 NAME
C<rename_fasta_id.pl> - rename fasta IDs according to regular expressions
=head1 SYNOPSIS
C<perl rename_fasta_id.pl -i file.fasta -p "NODE_.+$" -r "K-12_" -n -a c E<gt> out.fasta>
B<or>
C<zcat file.fasta.gz | perl rename_fasta_id.pl -i - -p "coli" -r "" -... |
b2f9dd4544f83599583485f63c39e1758cad8806284bd8fee65af3a27f81a4b5 | Perl | 6,671 | 228 | #!/usr/bin/env perl
#===============================================================================
# Copyright (c) 2017 Johns Hopkins University (Author: Jan "Yenda" Trmal <jtrmal@gmail.com>)
# 2017 Vimal Manohar
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
66bee2dcc73ec399472fbf203f643950e178ae4d936360e1fed1dd3b84d2f697 | Perl | 6,678 | 229 | #!/usr/bin/env perl
#===============================================================================
# Copyright (c) 2017 Johns Hopkins University (Author: Jan "Yenda" Trmal <jtrmal@gmail.com>)
# 2017 Vimal Manohar
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
d6473c147ce1fe391030dcbde06080c4451dfb6a3fb321c788e2d6dff83f199f | Perl | 6,678 | 232 | #!/usr/bin/perl
use strict;
use Graph::Undirected;
my $strain_info = $ARGV[0];
my $bed_directory = $ARGV[1];
my $PAV = $ARGV[2];
my $threshold_coverage = $ARGV[3];
my %strains;
open(S,$strain_info);
while (my $line = <S>) {
chomp $line;
my ($id,$name) = split(/\t/,$line);
$strains{$id} = $na... |
41579747ef4472c37694c9299e7f99a7cbfedb28036c8ff31d2e087c02c4bd55 | Perl | 6,746 | 217 | #!/usr/bin/perl
#######
# POD #
#######
=pod
=head1 NAME
C<transpose_matrix.pl> - transpose a delimited TEXT matrix
=head1 SYNOPSIS
C<perl transpose_matrix.pl input_matrix.tsv E<gt>
input_matrix_transposed.tsv>
B<or>
C<perl prot_binary_matrix.pl blast_hits.tsv | perl
transpose_matrix.pl E<gt> binary_matrix_tran... |
c407972a7a0b8632735e4e7a15ec8306db852f313194af534b8c73f70c026a42 | Perl | 6,785 | 218 | #!/usr/bin/env perl
# Copyright 2014 University of Edinburgh (Author: Pawel Swietojanski)
# The script - based on punctuation times - splits segments longer than #words (input parameter)
# and produces bit more more normalised form of transcripts, as follows
# MeetID Channel Spkr stime etime transcripts
#use List:... |
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