sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7edc4e2e6dc09032aabab123883d89f52ff3fd74c085aca66bf6f8743d10fdaf | Perl | 8,771 | 285 | #!/usr/bin/env perl
# NOTE FOR WEB GUIDE http://trinityrnaseq.sourceforge.net/genome_guided_trinity.html
# % samtools view gsnap_out/gsnap.coordSorted.bam > gsnap.coordSorted.sam
# change to run samtools view with -F4 or -F12 if you are plannign to use --no_single
use strict;
use warnings;
use FindBin;
use lib ("$Fi... |
dda4c05aac4dfbfa8473a4e8bfb192e249bc8c8d0f5e8f93ffe4d8a0868cd80f | Perl | 8,883 | 421 | #!/usr/bin/perl
# miRDeep2 excise-precursors perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (a... |
94e6263dff3f5114ee61c9cb25cde07db4f8c628e8d93f1283a438c7f8e44c64 | Perl | 9,085 | 291 | #!/usr/bin/env perl
=pod
=head1 NAME
=head1 USAGE
-in input file in FASTA/Q or posmap length file (e.g. posmap.scflen)
-genome genome size in bp for estimating N lengths and indexes
-single FASTA/Q has sequence in a single line (faster)
-overwrite => Force overwrite
-reads => Force processing as read data (no ... |
f7042ed0c156668a5ed73f5454cfaa7ea7bb70f9ba137d59f011380d59f72e91 | Perl | 9,136 | 306 | #!/usr/bin/env perl
# parse_prot_tran_data.pl
# ver 0.1
# 2014/09/13
#
# Po-E (Paul) Li
# B-11
# Los Alamos National Lab.
#
# 2017/07/21
# - add support for metabolic expression data
# 2015/05/23
# - add codes to take average proteomic data if genes has multiple expression level
use strict;
use Getopt::Long;
use FindBi... |
2f53e8d2c3e04cea3a46e6878b2b61016421fd8d982cfa8173a02ea3bea43112 | Perl | 9,328 | 440 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use SingleLinkageClusterer;
use PSL_parser;
use Process_cmd;
use Getopt::Long qw(:config no_ignore_case bundling);
use DelimParser;
use File::Basename;
my $usage = <<__EOUSAGE__;
###########################... |
0719a946e33e65f2e145b10989ce93d2f7bbe6aa98bf8ffc52ae3a0950090fb4 | Perl | 9,336 | 354 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Cwd;
my $volcano_spacing = 25;
my $usage = <<__EOUSAGE__;
#################################... |
4d7c840d41180a314984c542a9e066562235455cd68c7f4c35f835e96887b463 | Perl | 9,451 | 286 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib "$FindBin::Bin/../../../PerlLib";
use Pipeliner;
use File::Basename;
my $CPU = 2;
my $top_genes_plot = 50;
my $usage = <<__EOUSAGE__;
#######################... |
1cebe584a763028978c7ce9bf4c536bf1e03e5625e54f5bf06985d12d3a68e42 | Perl | 9,578 | 297 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Fasta_reader;
my $help_flag;
my $usage = <<__EOUSAGE__;
###############################################################... |
caa961b4c4e44962fd48234e985ee5ea966e1ad1328d100bc57a4cc608c00d5e | Perl | 9,631 | 348 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Data::Dumper;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use SingleLinkageClusterer;
use Overlap_piler;
my $usage = "usage: $0 gmap.gff3 Trinotate.annot_mappings\n\n";
my $gmap_gff3 = $ARGV[0] or die $usage;
my $trinotate_mapping_file = $ARGV[1] ... |
2f1ef8d1fbe90bbf3882055a6978efd25c5e3b74ad09cdb369260ed1f6314365 | Perl | 10,180 | 257 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###############################################################################################
#
# --factor_labeling <string> tab delimited file with forma... |
5b9eb86a1567171d42cbc208263ff362467af378afc15dcce1258102ff282c28 | Perl | 10,520 | 269 | #!/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... |
101b0f139cd5410a3566245d9fd94157a7f9dd443c63a58e3959786f6d1b0c4c | Perl | 10,682 | 477 | #!/usr/bin/perl
# miRDeep2 excise-precursors-iterative-final 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 F... |
9d1ca25506adb1485d746e946057f14d27badc211bd5ccaefa823a71ee851d7e | Perl | 11,184 | 405 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Carp;
my $usage = <<__EOUSAGE__;
####################################################################################
#
# Usage: $0 --est_method <method> sample1.res... |
32decffa93ee048ce99f140f129c28c2d029c97f3b59eb6b716339271c1b529f | Perl | 11,984 | 380 | #!/usr/bin/perl
use strict;
use Getopt::Std ;
our ($opt_h,$opt_i, $opt_g, $opt_G, $opt_e, $opt_c, $opt_b, $opt_m, $opt_a, $opt_R, $opt_K, $opt_x);
getopts("hig:c:Gb:mae:RKx");
&usage if $opt_h;
sub usage {
die "MatchToGenes -c <coordinates file> -g <gene file> (refseq format)
e.g. ./MatchToGenes.pl -c coord
defa... |
7dd8aeacbd89eb8e8a713dfd5913a219ea7bceeb121d75f5c9827c7d19469a63 | Perl | 12,758 | 642 | #!/usr/bin/perl
# miRDeep2 survey perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your opti... |
5b2a39540114017f27ff33eba4fde2c6235af85af3364ebd7c9c2da16378c43f | Perl | 12,977 | 461 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$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 $VERBOSITY_LEVEL = 10;
my $help_flag;
my $ref_trans_fa;
my $B... |
d48eaf9ff153fb48592a36019ce3049e1879e3a48cba6e211ea66339f148a209 | Perl | 14,803 | 584 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our($opt_h, $opt_t,$opt_f, $opt_z, $opt_b, $opt_F, $opt_S, $opt_v, $opt_c, $opt_T, $opt_C, $opt_V, $opt_H, $opt_M, $opt_m, $opt_S);
getopts("hf:bT:c:CV:vHS:z:");
&usage if $opt_h;
sub usage {
die "FindCpGs.pl -c chromosome (assumes sequence file to process is of the fo... |
4900c68d90edaf5f186548c20675fc50413fa29a776172e13b1b06cbd87a525e | Perl | 16,609 | 471 | #!/usr/bin/env perl
## Youtao Lu <luyoutao@sas.upenn.edu>
## Copyright (c) 2017-2022, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2017-2022, James Eberwine, Perelman School of Medicine, University of Pennsylvania
## All Rights Reserved.
## This Source Code Form is sub... |
50ce817f1f6ae84afab7b3402de13d610a2182792cc2bf8ef387a31a12c28267 | Perl | 16,762 | 629 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib/");
use Gene_obj;
use GFF3_utils;
use GTF_utils;
use SAM_reader;
use SAM_entry;
use Overlap_info;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
use Overlap_piler;
$ENV{LC_ALL} =... |
ae2b9bb015b75d4dd34ca37fd066be01226f357805fd6156f71ad4dd224ae5aa | Perl | 17,213 | 379 | #!/usr/bin/perl
# ats-repair.pl v3.2
# Author: Glenn J. Tattersall
#
# ============================================================
# PLAIN ENGLISH GUIDE TO WHAT THIS SCRIPT DOES
# ============================================================
#
# WHAT IS A JPEG FILE?
# A JPEG file is not just raw image pixels. It i... |
7e6a328f71240a09802fa91dd4afe7cfff4e59af6fa826327e18cff4a8c643b8 | Perl | 17,400 | 740 | #!/usr/bin/perl
# miRDeep2 select-for-randfold perl script
# Copyright (C) 2008 - 2011 Marc Friedländer
# Copyright (C) 2009 - 2011 Sebastian Mackowiak
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software F... |
04436a7bcc89df12f740711019c05ef115b8cdfe45732ffe7dcc681e7b7ee05e | Perl | 18,797 | 667 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use SAM_reader;
use SAM_entry;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Carp;
use Data::Dumper;
$ENV{LC_ALL} = 'C'; # critical for proper sorting using [system "sort -k1,1 ..."] w... |
16b19a2d52d7f11664df63f6de7a0de237ed8ec795b7285ebd5c16a00b4ed4ba | Perl | 19,267 | 576 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
####################################################################################
#
# Required:
#
# --matrix|m <string> TMM.E... |
8beb30f3fcc47ed187a03474ec6714da1e6b66cf26447c5963ee802132fcdbef | Perl | 19,336 | 690 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our($opt_h,$opt_p,$opt_H, $opt_m, $opt_t, $opt_d, $opt_t,$opt_f, $opt_a, $opt_z, $opt_C);
getopts("hpf:d:Hamz:Ct:");
&usage if $opt_h;
sub usage {
die "SumByDensity.pl -f <file>
-z compressed file
-d density (default is 10)
-m sum by density of methylated sites rather t... |
f64741e27e0f3ad5cab4160c545477990a0f4e62ffa53e81bdf5f3adb0c0ba52 | Perl | 19,419 | 484 | #!/usr/bin/env perl
use warnings;
use strict;
use Getopt::Long;
use Pod::Usage;
use File::Spec;
our $REVISION = '$Revision: 871849c7dd7b3842a6f3acecc3ce47beb5e1e920 $';
our $DATE = '$Date: 2015-12-14 13:51:19 -0800 (Mon, 14 Dec 2015) $';
our $AUTHOR = '$Author: Kai Wang <kai@openbioinformatics.org> $';
our ($verbos... |
b18134c674c967e50e159b7d9be99b0a0968940751fe0df3e23be3bee44727e7 | Perl | 19,806 | 485 | #!/usr/bin/env perl
## 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 subject to the terms of the Mozilla Publi... |
11b2c5e9d0a95e5b7ac06608923ffc8cb44a66c18e0da6ce2d94312fbfdd696f | Perl | 20,117 | 495 | #!/usr/bin/env perl
#
# cmsearch-deoverlap.pl: remove lower scoring overlaps from cmsearch
# --tblout files.
#
# EPN, Mon May 8 08:41:36 2017
#
# The EMG Team took a SNAPSHOT of this script on Thurs July 13 2017 from src:
# https://raw.githubusercontent.com/nawrockie/cmsearch_tblout_deoverlap/m... |
bb8719a02e473568c7c4e7b62951f056ca21630d2a2640befb8b263ef74511db | Perl | 20,860 | 735 | #!/usr/bin/perl
use strict;
use Getopt::Std ;
use Compress::Zlib;
use List::Util qw(max);
use Carp qw< croak >;
use List::Util qw< sum >;
use POSIX;
our ($opt_h, $opt_f, $opt_t, $opt_o, $opt_m, $opt_z, $opt_s, $opt_S, $opt_v, $opt_H, $opt_M, $opt_d, $opt_M, $opt_z, $opt_l, $opt_R, $opt_D);
getopts("hf:t:z:sSvHM:m:lRD"... |
ff3a0930198f0f51d177c25808f7970ed84a9bf17b3b8ee29f2fe87466372771 | Perl | 21,134 | 703 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Gene_obj;
use GFF3_utils;
use Nuc_translator;
use Data::Dumper;
#DB::disable_profile(); # Devel::NYTProf
my $usage = <<__EOUS... |
0c4eadd915f70912776ba9e04d52869b61e59d19be0a2e13361063b657f8e958 | Perl | 22,577 | 848 | #!/usr/bin/perl
# miRDeep2 install perl script
# Copyright (C) 2009 - 2012, 2014 - 2017, 2019 Sebastian Mackowiak
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Lice... |
aadfda49f58969bd3bfedaae1b2dd543d10bbd6f9d6cf59ab775cace40d628a9 | Perl | 23,285 | 844 | #!/usr/bin/perl
use strict;
use Getopt::Std;
our($opt_h, $opt_t,$opt_f, $opt_z, $opt_b, $opt_F, $opt_s, $opt_v, $opt_c, $opt_T, $opt_C, $opt_V, $opt_H, $opt_M, $opt_m, $opt_S, $opt_i, $opt_A, $opt_a, $opt_H, $opt_Y);
getopts("hf:b:T:c:C:VvHS:s:Fi:Aa:Hm:M:Y");
&usage if $opt_h;
sub usage {
die "PairwiseComparison.... |
f1538889ac133ae01d1d995d9f680f9663fb53ed34234ef48af40678e246e43b | Perl | 23,608 | 762 | #!/usr/bin/perl
# miRDeep2 mapper perl script
# Copyright (C) 2008 - 2012 Marc Friedländer
# Copyright (C) 2009 - 2012, 2014, 2016 - 2019 Sebastian Mackowiak
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Soft... |
8cb747da3559be25e9991317598d519bcd6e1cc740f1d293231c5482c90ab1f9 | Perl | 23,716 | 776 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib "$ENV{TRINITY_HOME}/PerlLib";
use Simulate::Uniform_Read_Generator;
use Overlap_info;
use GFF3_utils;
use GTF_utils;
use Gene_obj;
use Fasta_reader;
use SAM_entry;
use Data::Dumper;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use C... |
521fb47e5aae9f9879614a73b3b414be6a81948e403af52fd3cbf3f8f08f6d51 | Perl | 27,473 | 745 | #!/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... |
c39167246764da4e3245213b7033f635fde6d967bc3ec2cc070b6270b66c0d19 | Perl | 28,133 | 712 | #!/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... |
3369029ed9c48934a3075b4bc6c4d9d07a2acc7cef5f2d4c483805fbb48f32ab | Perl | 29,464 | 1,050 | #!/usr/bin/env perl
use strict;
use warnings;
use threads;
no strict qw(subs refs);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use File::Basename;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case pass_through);
use Fastq_reader;
use Fasta_reader;
use threads;
use Data::Dumper;
use COMMON;
use... |
1c0f5f8e80182b1c34bde4ccab17ea507f57b4b2e6285a78b01a8cfbeca2d541 | Perl | 29,608 | 1,015 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Cwd;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
my %aligner_params = (
############
## Bowtie-1
############
'bowtie_RSEM' => '--all --best --strata -m 300 --chunkmbs 5... |
257860327d8ed5a2925b03ec020b2794af8b9b6ecfedd2ac4dd427d4d23daf47 | Perl | 30,125 | 809 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Cwd;
use FindBin;
use File::Basename;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Data::Dumper;
my $ROTS_B = 500;
my $ROTS_K = 5000;
my $MIN_REPS_MIN_CPM = "2,1";
m... |
687b3deb74b769d5ab35e32ff8080541de8c5a11b5e2e5f7efe51dc4add7aed3 | Perl | 30,665 | 679 | #!/usr/bin/perl
# ats-split.pl v4.0
# Author: Glenn J. Tattersall, 2026
#
# ============================================================
# WHAT THIS SCRIPT DOES
# ============================================================
#
# Converts a FLIR ATS video file (.ats) into a flat binary
# .raw file that ImageJ can open ... |
47606558d0947e3641b1f9869312b21c767f72410b191ccd0227f28ee2c8b7ea | Perl | 30,973 | 932 | #!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
my $tapscan_version = "v4.76";
print "Running TAPscan Classify version $tapscan_version \n\n";
# Written by Gerrit Timmerhaus (gerrit.timmerhaus@biologie.uni-freiburg.de).
# Changes included by Kristian Ullrich, Per Wilhelmsson, Romy Petroll and Saskia Hi... |
8eda5f2615ae853e8a5a7fd295ba9ff3a6e2d19bc6c1cb2a34358e60f4f5bee2 | Perl | 36,122 | 870 | #!/usr/bin/env perl
use warnings;
#CHANGELOG
#05Jun09 - Added option to ignore X/Ns when estimating size of Query
# (to allow blasting specific strains of an assembly only after convert_project and replacing @s with Xs)
# Provide the initial fastafile used to blast or
#11Jun09 - Added option to extract hits an... |
f77915d5078b83c921ba10a350eee055ba07e7fcbc5452f7a4e41b8a9c20ff5a | Perl | 36,381 | 1,136 | #!/usr/bin/perl
# miRDeep2 perl script
# Copyright (C) 2008 - 2012 Marc Friedländer
# Copyright (C) 2009 - 2012, 2014 - 2019 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 Foundati... |
3d48262531a70e608d3f98d77b89f5c9b3b8c8918898f1e617fb039d0fd6e17b | Perl | 38,999 | 1,032 | #!/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... |
78b7955154e499d474fe2b030330177104edc42a9a73de5b1634e8d6af6831cf | Perl | 42,178 | 1,137 | #!/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... |
ed09a41b62aa366662ee993b3618bf19dca7b34f985a78954c5db1398170b2ec | Perl | 47,571 | 1,746 | #!/usr/bin/perl
# miRDeep2 core-algorithm perl script
# Copyright (C) 2008 - 2012 Marc Friedländer
# Copyright (C) 2019 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, e... |
95f45cc9c1aaab57f46531593e15e7395826b2622a6b3b64de453acd727415d0 | Perl | 47,713 | 1,514 | #!/usr/bin/perl
# quantifier module from the miRDeep2 software package
# Copyright (C) 2009 - 2012, 2014 - 2017, 2019 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, eith... |
5b82555798264f03f4e398097d42f62205466ea839e432cf0fea7ad14d9271ed | Perl | 48,148 | 1,244 | #!/usr/bin/env perl
#############################################################################
##
## Copyright (C) 2016 The Qt Company Ltd.
## Copyright (C) 2016 Intel Corporation.
## Contact: https://www.qt.io/licensing/
##
## This file is part of the build configuration tools of the Qt Toolkit.
##
## $QT_BEGIN_LIC... |
53e56bbd15dbf328bcb1db4bf6204bc20b1558e3dd465789c2924278320b8674 | Perl | 56,138 | 1,125 | #!/usr/bin/perl
# ats-xml.pl v4.0
# Author: Glenn J. Tattersall
#
# Extracts metadata and calibration constants from a FLIR ATS video file
# (.ats) or RJPEG (.jpg). Default output is ExifTool-style: a flat list
# of "Tag : Value" lines with NO section headers, intended to be parsed
# programmatically (e.g. by ThermIm... |
99314dfb553a55649c879163552417ea1d85ac3a4a98956a90b963381e6c346b | Perl | 61,011 | 1,443 | #!/usr/bin/perl
use warnings;
use strict;
use FindBin '$Bin';
#use lib "$FindBin::Bin/";
#use lib "/home/wsimp/perl5/lib/perl5";
use Getopt::Long;
use Cwd 'abs_path';
use Pod::Usage;
use Bio::Graphics;
use XML::Twig;
use Bio::SeqFeature::Generic;
use Math::Round;
use UniProtFileParser;
use List::Util qw[min max sum];
u... |
17fcae04d1ef3f786e45b86e767e390e2a8f1519b35da22c8566e9bdf1bcb9f4 | Perl | 68,608 | 2,168 | #!/usr/bin/perl
# miRDeep2 make-HTML2 perl script
# Copyright (C) 2009 - 2012, 2019 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
# ... |
ba7d3958fe0ca50662df58f3fe4957a05425456e687a2a5921ddcab1261219e1 | Perl | 91,115 | 2,479 | #!/usr/bin/perl
#use feature ':5.10';
use File::Basename;
use lib dirname($0); # search skript directory for modules
use strict 'vars';
use warnings;
use Getopt::Long;
use Pod::Usage;
#use List::Util qw/ min max /;
#use StructureLibrary::RNAtoolsConfig;
#use StructureLibrary::Sequence;
use Cwd qw(getcwd abs_path);... |
4dd54863ed94a5c23a61d28d3d476e82c33f9c47d30af10fb8e98382fe1949fd | Perl | 125,771 | 3,947 | #!/usr/bin/perl
# miRDeep2 make-HTML script
# Copyright (C) 2009 - 2012, 2014 - 2015, 2018 - 2019 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 L... |
868c071ea97a569e4f98eaea98eab62b8ab2c648ac017d4dd1d29005b2f7f795 | Perl | 200,000 | 4,090 | #!/usr/bin/env perl
use warnings;
use strict;
use Pod::Usage;
use Getopt::Long;
use File::Spec;
use Cwd;
our $REVISION = '$Revision: 11f4bb33cd1289ba7c43dadc20b3e9982b5a9a00 $';
our $DATE = '$Date: 2016-02-01 00:11:04 -0800 (Mon, 1 Feb 2016) $';
our $AUTHOR = '$Author: Kai Wang <kai@openbioinformatics.org> $';
our... |
2106c36011520fe73876d45bfb9ef8bf7b2e9f4362096a320376d8ee9b27ef12 | Python | 4 | 1 | |
337e547a950fc8a98592f10d964c1e79a304961790a8da0ce449a1f000cefabb | Python | 4 | 1 | TODO |
edcb4d68a1e239ad9f55e3dc74a3d4f49fbf6d0d24d631476a86650875d8d2f5 | Python | 14 | 1 | """Fixups."""
|
c9d4ad2f6ee937034a473d9ec791fd9c9a332c1ff3586df9d07dbd86338d66e6 | Python | 15 | 1 | #import .utils
|
019e7cb76637344ba205a7b4e72a69e7a0771f01e3f9ff768574e32a8158b296 | Python | 17 | 2 |
# __init__.py
|
e013538dfb86642a24d80bab77e475541fd42d4f01ab6d72566c57720b5e95cb | Python | 17 | 1 | name = "psychrnn" |
61db20d6b43e6a5c017db1a0f0eaa19e3f45d4075d9328a243211d06acc4a16c | Python | 18 | 1 | # here for a test
|
973185b3299fd03b40ff5a0065c3db790e79ee263ed414647a485f036a9a161f | Python | 18 | 1 | VERSION = "1.0.0"
|
cbdf546cbe6007bfae9eb9eb97145fe9728def0b010cdaa9642573acb92bb115 | Python | 18 | 1 | #import lib.utils
|
1527e449844a8c3a88b84884677f4eb6f7b9d2a4b18bb40e6cd9cdac71cfc79b | Python | 19 | 1 | """tests module"""
|
6fd583e5ad1a4b1bbf0275ff814f0afe586ed05ef5a036a721f0bd800734ccc1 | Python | 19 | 1 | VERSION = "0.26.2"
|
78c1e561d0c0598aa61405d205634de95b3cd73548a7afabfd8322104d9bb3c0 | Python | 19 | 1 | type ImageId = str
|
b822da1e755db2b467c6c3276fa4281a1de4ebe915bf144b85bed866666fd517 | Python | 19 | 1 | from .svg import *
|
ffe089582cd14d8cf57f125ee77661e95e33faa296a8bb37dcbff5835c9d1cc8 | Python | 19 | 1 | from .tdr import *
|
03751bed9daad8e10e369ad79c2e63950f31e76e587df806f77840f4ce030089 | Python | 20 | 1 | __version__ = '2.0'
|
2e07fd91e057eda1bf24416de94612ca214a726f81606b6693da21a50858a729 | Python | 20 | 1 | __version__ = "0.1"
|
4af14e0799e7ff237e242698140b737ac2f4cd4d0e8a1429d2cd1d38fd7e30a1 | Python | 20 | 1 | """tests for gnn"""
|
992106b26de4ae968fdf67480baa348df4a954fcbe59cace7e86ad56f4419d5e | Python | 20 | 1 | __version__ = '0.3'
|
a268b766f75d4583c92d0aeacd6c6b437e5feaefe59ade54dc0177b0b648095c | Python | 20 | 2 | """BCBio module
"""
|
0cb2929f780090a70ea986c83828c9d5c7b50ade7f6a71de792f8454d013530b | Python | 21 | 1 | """IO sub-module."""
|
52fa5b55dcea998ddb03a311a0f873f29fd4645a3286a745e1d2e7762598aa17 | Python | 21 | 1 | __all__ = ["tracker"] |
6a83725a98861f86211a9e19dda257f2e868b8a42a5ecd4a3ccf3568e28929f1 | Python | 21 | 1 | from .config import * |
7253774e7c98cade53ff05092d5066bad4b69182cb0444f82450764179d19b64 | Python | 21 | 1 | __version__ = '0.2.0' |
9cefa2a61a17883a1c8bf640325f8f1b6cdd77863b9bcf2304320b4d8cf01b2e | Python | 21 | 1 | __version__ = "18.1"
|
b099ad96b64e9a2bb553d13794b5844d785856a06dd6f0be6c0e3d7596cf5e29 | Python | 21 | 1 | from .tools import *
|
c7b4969f1f21a3e55a0c72ed2bbe48b48b9ba09f52a5c47fbf2d86bd73665380 | Python | 21 | 1 | __version__ = "1.0.1" |
e00c251ae1eabb533c9f522cee05e1b7782822f5454c1d0df214d211fbff075d | Python | 21 | 1 | __version__ = '0.8.2' |
e79857145e23828b6d256f53a6b3d130185d16f7c62ae0e85f96b146c4f5231a | Python | 21 | 1 | from .mdata import *
|
1373fa01b9c2c1a5a4ea7751d7336a94e4d579b5fdcf9aeff6fa25b5cef5768b | Python | 22 | 1 | __version__ = "3.0.1"
|
35c8e8c432d83a66e9e1f3f6b1d388edfad4985b0ffce98844ba6915438cc094 | Python | 22 | 1 | __version__ = '1.2.3'
|
49a0c06077dd531d3367010c26cf02b618526365f82347680114cf817daf3b03 | Python | 22 | 1 | __version__ = "3.4.0"
|
7080f58cb9c2fef8f8f0680c37a61bd4503726c43de73366087991604f131616 | Python | 22 | 1 | __version__ = "0.6.0"
|
9639c9098c5a4fef50e3b25994da65a3429c2dd399ac1d30a082613ead75a43d | Python | 22 | 1 | __version__ = "3.3.2"
|
9ba93268da7005c3f55d872aade957da84b73c9b8e9c494e7117416bda446fc7 | Python | 22 | 1 | __version__ = "0.2.2"
|
9fb485e0a01b8d077af8e26fd220187d7297c6737b474225170e0759177a9e31 | Python | 22 | 1 | import celery # noqa
|
cbb3d556fd968b3d66b00e63a8a3ae07905b0785330a60d9fa99a5f61210ca3a | Python | 22 | 1 | """tests for utils"""
|
e65d0b81da6213158844240b97cbc9b0184fc7fb0b8837bbdcd05a53a482c56c | Python | 22 | 1 | from .trainer import * |
f3030cfbcd9f5e8b438d3b6130b56d414b58a98f19d5c216877b892343a3577b | Python | 22 | 1 | __version__ = "1.8.3"
|
2b9aa45600ba385813e5adcfa25dd47a06f53949088fd58d4a6fb97d531cbf99 | Python | 23 | 1 | """MS COCO dataset."""
|
3c20d0604062d50287196e131f8b5475c57638094ae3178c44e42345dad820ea | Python | 23 | 1 | from .disk import disk
|
97acb0d8bb359dd85555c498734e7d9008d0dbe5680c6657c6705a825159e33a | Python | 23 | 1 | """Tests for linalg"""
|
a559d8b8b70d9d939217e1c0e5635ba5e8ae2435859fd6b739728bb85f5b9f6e | Python | 23 | 1 | __version__ = "0.6.15"
|
ae464ed06a0c973966bb3d54c49eb1b108e7cd8bd01b5ea2a64adef17a30556d | Python | 23 | 1 | __author__ = 'quentin'
|
ba12dca2594f354600a3c5d8b2177443059450ea1b94977d35c203e4a8d54b86 | Python | 23 | 1 | from . import tracking
|
d33bd5be8f87f6f36f78dd4a45e77cbe77ef8d51e10fff428725de453fc12931 | Python | 23 | 1 | __author__ = "quentin"
|
d6437dd9d7f58c3a77802ea6ac6119236784fa438450829d38e1d101daf2d9ad | Python | 23 | 1 | """Result Backends."""
|
d8a34298df384db749a2be7b13e0805b8627bfcc1568630e3347ec3ad4f5c5d3 | Python | 23 | 1 | """Dataset package."""
|
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