sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9b798a4d43559c363bfce3319f7214a610ede6302975d71701e50d36d69575bc | Perl | 3,858 | 137 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
################################################################################
#
# --rnammmer_gff|R <string> rnammer superscaffold gff
#
# --transcript_scaffol... |
63178c246acad91dfff5c63d649d340c74a4083a11ee289417c95fe82eb4f208 | Perl | 3,900 | 144 | #!/usr/bin/env perl
# bin2hex.pl
########################################################################
# Copyright (C) 2001 by OpenEye Scientific Software, Inc.
# Some portions Copyright (c) 2002 by Geoffrey R. Hutchison
#
# This file is part of the Open Babel project.
# For more information, see <http://openbabel.... |
0978c4739df8a3e101f004c911f515fe612fd843c49130a9a743b50d08d022c1 | Perl | 3,968 | 171 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
my $usage = <<__EOUSAGE__;
###########################################################################... |
1d679d9704db8be5de8eb0d609afbacd30b67ba2fc2630b1f1784b7ea5b575f5 | Perl | 4,017 | 145 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
##############################################################... |
96bdafeb497fdb0a4ec00d61b144092240a44a6b3dd93462770a1f4ac0c4131e | Perl | 4,017 | 126 | #!/usr/bin/perl
use strict;
use warnings;
my $fasta = $ARGV[0];
my $read = $ARGV[1];
my $out = $ARGV[2];
my $link_A_bc = $ARGV[3]; #Any length, we use 6 bases
my $link_A_oligo = $ARGV[4]; #4 bases
my $end_A_oligo = $ARGV[5]; #4 bases
my $MIN_SEQ_SIZE = $ARGV[6];
my $MIN_ENH_SIZE = $ARGV[7];
my $MAX_ENH_SIZE = $ARGV[8... |
2821f4edac5c56107e847b3c808b51535f6d454e5c704bcebcb4a3c87fb759a6 | Perl | 4,036 | 135 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Data::Dumper;
my $usage = "usage: $0 Trinotate_report.xls.gene_ontology [include_transcript_ids]\n\n";
my $trinotate_go_report_file = $ARGV[0] or die $usage;
my $include_transcript_ids_flag = $ARGV[1] || 0;
my $go_slim_file = "$FindBin::Bin/../../PerlL... |
ea4f16bfc8c2801c63dae91861d45003c855e195c7d33a28af181d579156f05c | Perl | 4,093 | 156 | #!/usr/bin/perl
# trioEval.pl
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $vcf;
my @parents;
my @offspring;
my $mingq = 0;
my $filter;
die(qq/
trioEval.pl [arguments]
OR
cat vcf | trioEval.pl [arguments]
Arguments:
--vcf VCF file, can be (b)gzipped
--parents space-delimited VCF IDs of ... |
55aee860f2e6de5f7c468a1bed8979ef74b8d2d240b9087081e405b52d488d88 | Perl | 4,099 | 168 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
c84cb7dbd1c09b7831e853cf5d993159b0a3068210b29bc96da5293156be01e9 | Perl | 4,104 | 121 | #!/usr/bin/perl -w
use strict;
use warnings;
use List::Util qw(shuffle);
use Getopt::Long;
use File::Path qw(make_path);
# Default values
my $input_nodes = './graph_model/nodes.csv';
my $input_edges = './graph_model/edges.csv';
my $input_embeddings = './graph_model/node_embeddings.128_64.csv';
my $output_ppi_learning... |
fa1aa46e9950f42311ec9a03dba147451beee9e34bed7890dd5b843bc7f2c13b | Perl | 4,152 | 169 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
####################################################################... |
497cc831d73c52ee8d0969ad005b92aa10c8ac78e7800e522d9223488703183f | Perl | 4,237 | 169 | #!/usr/bin/env perl
## Pombert lab, 2019
my $version = '1.3a';
my $name = 'MashToDistanceMatrix.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Basename;
use File::Path qw(make_path);
#########################################################################
### C... |
9977dc96cefb19550fc8173b1ec10961ed306b2d0de649725c454558591d3e46 | Perl | 4,254 | 154 | #!/usr/bin/perl
# sampleLDVar.pl
use warnings;
use strict;
use Getopt::Std;
my ($snpfile, $plinkprefix, $outprefix);
my $minld = 0.5;
my $maxdist = 1000000;
my $focal = undef;
my $nsamp = 0;
die(qq/
sampleLDVar [options] <snpfile> <plinkprefix> <outprefix>
Input:
snpfile: 1-column file of SNPs (1 per row) <STRING>... |
a8466f781660636d981f3781c7bd043bc00a86c800c088f6fb225ebc868216cb | Perl | 4,313 | 165 | #!/usr/bin/env perl
## Pombert JF, Illinois Tech 2019
my $version = '0.5a';
my $name = 'queryNuccore.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
#########################################################################
### Command line options
#########################... |
2118bf8a3f38c212f0092b8a2e95e2093e77c8be6ea82ec791b1a820e1ee0e30 | Perl | 4,325 | 173 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use GO_DAG;
use DelimParser;
my $usage = <<__EOUSAGE__;
#######################################################################
#
#
# Re... |
732d73a835105acd9131cd85681f5861a47a88a1ee9fcad870a2c47c39a96ec1 | Perl | 4,336 | 173 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use GO_DAG;
use DelimParser;
my $usage = <<__EOUSAGE__;
#######################################################################
#
#
# Re... |
c467698e5e8aae1582024040361bcb8b5cda869841b840b6f163190f0cf0fa34 | Perl | 4,400 | 174 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Pipeliner;
use Carp;
use Cwd qw'abs_path cwd';
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use Fasta_reader;
use Process_cmd;
use File::Basename;
use threads;
use Thread_helper;
... |
5e4e985cd5a46eab8469b9d743c241c136e68cd8788fa6f3303a427ec26995f2 | Perl | 4,705 | 170 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Fasta_reader;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
#####################################################################################... |
e83e49b9da90823a52504c06a8bde73762199ca1102fe0a606780403412bc79a | Perl | 4,734 | 172 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use GTF_utils;
use DBI;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################... |
5058e6ec52f2b4fcce4a7dcafbb270a52490dd33426737d9cb4480addf345be5 | Perl | 4,889 | 179 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use GO_DAG;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
#######################################################################
#
# Req... |
d5db42e2aa9814301de15caf2c1dc7056856ad4f5246e2cf5fef55cbc0e0a013 | Perl | 4,984 | 181 | #!/usr/bin/env perl
## Pombert JF, Illinois Tech 2020
my $version = '1.4a';
my $name = 'queryNCBI.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
#########################################################################
### Command line options
###########################... |
6a3a65b6c17ca0f1343f83925b4e7c7162dc75cf3c270834d0481ee024cb467d | Perl | 5,064 | 184 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use Carp;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
my $usage = <<__EOUSAGE__;
############################################... |
a6aea52ed798d1ba6adf45d1b102eb435f906f8c6a20dde07527af82a535a46c | Perl | 5,241 | 253 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use EMBL_parser;
use Data::Dumper;
my $usage = "usage: $0 swissprot.dat out.prefix\n\n";
my $swiss_dat_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] or die $usage;
main: {
my $tmp_UniprotInde... |
a835db8d9ca0a721308794b410c51ab4560cc3033291e3a711b706a2f7959319 | Perl | 5,259 | 213 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;
my %options=();
getopts('ECMSA:', \%options);
#####
#
#-E = Print alignment error scores for each tag
#-C = Print CIGAR strings for each tag
#-M = Print MD tag for each tag
#-S = Print Start/Stop for oligo alignment
#-A = Alignment cutoff to use for barcode ... |
fd5bc2ff44e68c45e272575c660427cea5d1b84495ceea3771f40a73066751ca | Perl | 5,259 | 213 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;
my %options=();
getopts('ECMSA:', \%options);
#####
#
#-E = Print alignment error scores for each tag
#-C = Print CIGAR strings for each tag
#-M = Print MD tag for each tag
#-S = Print Start/Stop for oligo alignment
#-A = Alignment cutoff to use for barcode ... |
0c53b15a3c228bdee6caaf9aa7cd2e60d3f591dcc3e09051718aabd5401efe86 | Perl | 5,436 | 197 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Copy;
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use DelimParser;
use Process_cmd;
my $usage = "\n\n\tusage: $0 Trinotate_report.tsv output_prefix\n\n";
my $trinotate_report_file = $ARGV[0] or die $usage;
my $out_prefix = $ARGV[1] or die $usage;
my ... |
172366e605e47cfb355d84956892b60de8057acbfffd4116997f460c460923ef | Perl | 5,437 | 156 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $usage = "\tcnvnator2VCF.pl [-prefix prefix] [-reference reference_name ] file.calls [genome_dir]\n";
my ($file,$dir,$prefix,$reference);
die("not enough argyments. $usage\n") unless ( @ARGV );
$reference = '1000GenomesPhase3_decoy-GRCh37';
GetOptions( ... |
934d88179c0d7816b73e801a537217e84a868e59d8da65da49d79c3f4267ff31 | Perl | 5,661 | 171 | #! /usr/bin/perl
# Copyright 2000, 2001 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version... |
df96c2fccc7d2ca89ea998395904aef07fefd5b97e92b455a2b5fb34646c1e54 | Perl | 5,747 | 256 | #!/usr/bin/perl
#
#by Ryan Tewhey
use strict;
use warnings;
use Getopt::Std;
##################################
#
#4/27/2014 - Changed "RC" reporter to after SNP ID
##################################
my %options=();
getopts('CB', \%options);
#####
#
#-C = Use new cigar format =/M
#-B = Filter for 0 bitflag
#####
my... |
f387bd47d7a4b66a20e87ea169498f1c0ba1235904ee4f8085284ecab5664432 | Perl | 5,866 | 266 | #!/usr/bin/perl
#
# Includes
use strict;
use warnings;
#
# Documentation
my ($help_screen);
$help_screen = << 'Endofblock';
Usage: copy-code.pl (options) (input files)
This program copies code from the specified input files and produces LaTeX
documentation output.
The following options are recognized:
"--hel... |
54221dda2a4567942cf90da936c8439551aaa1ddc00f8545335adbd3f9842fbb | Perl | 5,962 | 256 | #!/usr/bin/perl
#
#by Ryan Tewhey
use strict;
use warnings;
use Getopt::Std;
##################################
#
#4/27/2014 - Changed "RC" reporter to after SNP ID
##################################
my %options=();
getopts('CB', \%options);
#####
#
#-C = Use new cigar format =/M
#-B = Filter for 0 bitflag
#####
my... |
9a0bb0c7afd5212de62533b91d033fa9d4f1cb78cb70bc289bf14569f1352150 | Perl | 6,004 | 195 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
#use Fasta_reader;
use GTF_utils;
use GFF3_utils;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
my $usage = <<__EOUSAGE__;
######################################################... |
fa60a1f8bed8d0d6a38e72b9c93676f518afa6abf1161e3414c13120fc55f024 | Perl | 6,118 | 227 | #!/usr/bin/env perl
## Pombert Lab, IIT, 2019
my $name = 'bam2fastq.pl';
my $version = '0.4a';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Basename;
use File::Path qw(make_path);
#########################################################################
### Command... |
2777aa249c8984858fc14ad1d93c88c6e879ffaa306592629769d655eed92ed6 | Perl | 6,148 | 162 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Pipeliner;
my $usage = "\n\n\tusage: $0 Database_prefix [no_cleanup_flag]\n\n\n";
my $prefix = $ARGV[0] or die $usage;
my $no_cleanup_flag = $ARGV[1] || 0;
my $UTILDIR = "$FindBin::RealBin/util";
my $RESO... |
98e05d7e4614aa999d70a875e77c81b83aef26f0daf2899d3d17f198bea5d687 | Perl | 6,235 | 191 | #!/usr/bin/perl
# annotate_summary.pl
use warnings;
use strict;
die(qq/
annotate_summary.pl <log directory> <log file prefix, '_[1-20,22-25].err' appended>
\n/) if (!@ARGV && scalar(@ARGV) < 2);
my $dir = $ARGV[0];
$dir =~ s/\/$//;
my $prefix = $ARGV[1];
my ($lines_total, $fail_total, $aa_total) = (0,0,0);
my ($li... |
77d392fcd28b34f3f86c009cf713fd95fa5bd5eb3db942a4d201a0ab9f332db6 | Perl | 6,606 | 240 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################... |
02352fa3a2d1db49830418634caf282946eac382aeb16985972c3f6f4a6aa800 | Perl | 7,059 | 265 | #!/usr/bin/perl
#
#by Ryan Tewhey
use strict;
use warnings;
##################################
#
##################################
my $mapped = $ARGV[0];
my $CT_COL = $ARGV[1]-1;
my $CMP_COL = $ARGV[2]-1;
open (MAPPED, "$mapped") or die("ERROR: can not read file (mapped): $!\n");
my $first = 0;
my $tmp_line;
my @la... |
1dc3ef24ada7ea0905895f1340f6fb13c86bfc12c3a9ed82912ed7ddfbaef6ed | Perl | 7,302 | 303 | #!/usr/bin/perl -w
# Copyright 2000, 2001, 2003, 2004, 2005 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Founda... |
fd92e6479181773ffe93626b9c30d9a757cce97c43817c3e9531e27501a7642b | Perl | 7,349 | 239 | #!/usr/bin/env perl
## Pombert lab 2019
my $version= '0.3b';
my $name = 'sort_stats.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Math::Complex;
use Getopt::Long qw(GetOptions);
###################################################################################################
### Command line optio... |
d082afee12e82433c030ffa18d2105521493e50ea7f5a7ab8f89176fed5c9fc8 | Perl | 7,446 | 21 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
for(my $i = $MIN_REP; $i <= $MAX_REP; $i++) {
my $line = sprintf("./discoal %d... |
17d8a762fac8056905227c1e49915a33149d0c60214122217cfa1c9f265b2f4e | Perl | 7,930 | 32 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
my $infreq_lower_log10 = log(0.001) / log(10);
my $infreq_upper_log10 = log... |
7575e31072f932c6caebf5d6e6663b976c83564c36a61e256539c25312493caf | Perl | 7,971 | 260 | #!/usr/bin/perl
# extractVariants.pl
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $version = '1.0.0';
my $skip_af;
die(qq/
extractVariants.pl v$version
extractVariants.pl [options] <input vcf>
OR
cat VCF | extractVariants.pl [options]
Input options:
--skip_af Do not check that at least one alle... |
0f8f55abc2928d74493cafcd1be93e569a6ec06d65ee00bfa8e63845e6f49ef1 | Perl | 7,987 | 240 | use warnings;
use strict;
use Data::Dumper;
main();
sub main {
InfoMsg("Commandline : $0 ".join(" ",@ARGV)."\n");
DuplicateParameterRemoval(@ARGV);
}
sub DuplicateParameterRemoval{
for my $shFile (@_){
InfoMsg("File $shFile does not exist!!!")if(! -e $shFile);
next if(! -e $shFile);
my $sh = ShLoader($shFil... |
84a58c51bb294303939f9224ae6b81a000018f2e7532006e1105cc39aab4e3a2 | Perl | 8,044 | 35 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
my $infreq_lower_log10 = log(0.001) / log(10);
my $infreq_upper_log10 = log... |
770782ebd1fabde46852ef9dd4956fcc8788fd3aca12af6f0dd4def02391c6b3 | Perl | 8,227 | 302 | #!/usr/bin/perl -w
use strict;
$ENV{'LANG'} = 'C';
my $gphoto2 = "gphoto2";
my $debug = 0;
##################################################
# auto configured
my $imageformat;
my $havecapture = 0;
my $havetriggercapture = 0;
my $havepreview = 0;
my $havecapturetarget = 0;
my %formats = ();
# internal
my $debugc... |
dc406a220cca0a8a233d44099b9c6ee166a25b885964d8e2bd2f522d87d21d83 | Perl | 8,985 | 310 | #!/usr/bin/perl
# extractBiallelicSnps.pl
# notes:
# requires bcftools to be in user's path (no longer true as of v 2.0.0)
# Assumes input VCF indels are left-aligned and normalized: bcftools norm -f <fasta>
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $version = '2.0.0';
my $minmaf = 0;
my $keep_o... |
cf6a75b39682ff79edf5b3bbbd9072a6002aa230db8ed7ebe8f117f00da96052 | Perl | 9,005 | 303 | #!/usr/bin/perl
# speciesFst.pl
use warnings;
use strict;
use Getopt::Long;
my $version = '1.2.0';
my $spfile = undef;
my $idfile = undef;
my $vcf = undef;
my $posfile = undef;
my $passonly = undef;
my $out = undef;
my $comptype = 'all';
die(qq/
speciesFst.pl v $version
speciesFst.pl [input]
Input:
--spfile 2... |
4aa1c95d727d99182e3e61c123e6d2656aca5da67bf5d92479f99279ab53eea9 | Perl | 9,119 | 212 | #!/usr/bin/perl -w
#
#******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# ... |
80856a0e82e657639d706ecfc3b7f09c51f9d2d4972174bcd58066f483323e2e | Perl | 9,260 | 195 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###########################################################################
#
# Requir... |
dd6be51d580388d8badc9a078bbfcc872bd0ea5870a3f706d76cd6cc787ffd4e | Perl | 9,779 | 400 | #!/usr/bin/perl
# queryMeta.pl
# requires bcftools and vcftools (installed and in PATH) for sum functions
use warnings;
use strict;
use Getopt::Long;
use Getopt::Std;
my $version = '1.2.1';
die(qq/
callsetTools.pl $version
Requires bcftools and vcftools to be installed and in \$PATH
callsetTools.pl [command]
co... |
146cefff28ad05e830178a76e75f721952581d749abe13d7e78bf27aa5a5c57c | Perl | 10,828 | 411 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
24c8d074f6758994f9fb3df9044b553072bd45f46868e30d8810be8e1a715cbb | Perl | 10,959 | 359 | #!/usr/bin/env perl
use strict;
use warnings;
use DBI;
use Text::NSP::Measures::2D::Fisher::twotailed;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Sqlite_connect;
use GO_DAG;
main: {
my $dbproc = &connect_to_db("Trinotate.sqlite");
print STDERR "-getting cluster analysis names\n";
... |
12d52a2dff0601c2c693599eaec1a90e7e60af60a4597a21aca181f17f5dea0e | Perl | 11,241 | 397 | #!/usr/bin/perl -w
use strict;
use Getopt::Std;
###
my $SNPFile = 'snp_set_100M.txt';
###
#Get command line arguments
our($opt_i,$opt_r, $opt_b, $opt_e);
getopt('irbe');
unless (defined($opt_r) && defined($opt_i) && defined($opt_e)){
print <<EOF;
SNP-level GO enrichment analysis
It requires the following arg... |
8da06b4e143cba6f7ef17e5489f0787be8deb8217a29c8ee0d00f251a1500163 | Perl | 11,263 | 398 | #!/usr/bin/perl
# extractBiallelicSnps.pl
# notes:
# requires bcftools to be in user's path
# Assumes input VCF indels are left-aligned and normalized: bcftools norm -f <fasta>
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $version = '1.0.0';
my $dpbounds = undef;
my $minmaf = 0;
die(qq/
extractBia... |
e55d01a9c7675338882e0a49ce1ceacd29e51d1f263bd37f3b30c5f3e93292ca | Perl | 11,629 | 416 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
8f9e42bef05add906fb84f0b8e6e5f6f30ad558d134f0995c1f9695c0668e5fb | Perl | 12,821 | 402 | #!/usr/bin/env perl
# Pombert lab 2019
my $version = '0.6a';
my $name = 'MashR_plotter.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
#########################################################################
### Command line options
#######################################... |
5f15f6da5dba52836b30508564f285f6d6183b024c24883733699230d9d4b504 | Perl | 12,823 | 408 | #!/usr/bin/env perl
## Pombert Lab, Illinois Tech
my $version = '2.0a';
my $name = 'SSRG.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Basename;
use File::Path qw(make_path);
use PerlIO::gzip;
####################################################################... |
fe6673172b1331f4c6c9ba6405cb330252ec8a164854503a102241208e43d802 | Perl | 13,611 | 441 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
##############################################################... |
e90e18d0b61b9450e439a21c8673b70a145f9fb61241761debebcb717254ad4a | Perl | 14,420 | 459 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
ec4eeeb9a960c692d35c59d084092d615c00ccfa78ff11728d15aa800ae5f0db | Perl | 16,620 | 579 | #!/usr/bin/perl
# insertAnnotations.pl
use warnings;
use strict;
use Getopt::Long;
use IO::Zlib;
#use warnings FATAL => 'all';
my $version = '0.2.0';
my $alfile = undef;
my $alfields = undef;
my $anctype = 'parsimony';
my $dpbounds = undef;
my $vcf = undef;
my $rmfilter = undef;
my $fstart = 4;
my $bedgraph = undef;... |
2f934a847d413118cea885940158e1059169cc58368d302e2653abe95342dc33 | Perl | 17,541 | 528 | #!/usr/bin/perl
## ACMdS, Illinois Institute of Technology, 2021
use warnings;
use strict;
use Getopt::Long qw(GetOptions);
use File::Basename;
use Cwd qw(cwd);
my $name = 'isoforms.pl';
my $version = '0.7';
my $update = '2023-06-20';
my $usage=<<"USAGE";
NAME ${name}
VERSION ${version}
UPDATED ${update}
SYNOPS... |
9ef13009d6711a55ce21069782309a3101142b7b0f50737605ea62075a7e4a3a | Perl | 18,103 | 624 | #!/usr/bin/perl
# insertAnnotations.pl
use warnings;
use strict;
use Getopt::Long;
use IO::Zlib;
use List::MoreUtils qw(uniq);
#use warnings FATAL => 'all';
my $version = '1.0.0';
my $alfile = undef;
my $alfields = undef;
my $anctype = 'parsimony';
my $dpbounds = undef;
my $vcf = undef;
my $rmfilter = undef;
my $fst... |
11335d9f1946b82b3532b9a6c2ad3d393b8b894bdcff25aa0f0aad18aed26f9d | Perl | 18,640 | 636 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Data::Dumper;
use Sqlite_connect;
use Trinotate;
use DelimParser;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#################################################... |
b98d65ee1bd6393818812aadd35c0b9bed305d124cc5f859c8fe4d2fc416d038 | Perl | 19,396 | 531 | #!/usr/bin/perl
## ACMdS, Pombert Lab, Illinois Institute of Technology, 2023
use warnings;
use strict;
use Getopt::Long qw(GetOptions);
use File::Basename;
use Cwd qw(cwd);
my $script_name = 'get_BAX.pl';
my $version = '0.1a';
my $update = '2023-02-22';
my $usage=<<"USAGE";
NAME ${script_name}
VERSION ${versio... |
39a668e7810e3c459b52ff784dbdd72d7e8d9fbdcbb140efe4b17cdd1222f56d | Perl | 22,779 | 815 | #!/usr/bin/perl -w
use strict;
use Getopt::Std;
###
my $SNPFile = 'snp_set_100M.txt';
###
#Get command line arguments
our($opt_i,$opt_r, $opt_b);
getopt('irb');
unless (defined($opt_r) && defined($opt_i)){
print <<EOF;
SNP-level GO enrichment analysis
It requires the following arguments:
-i [input file prefi... |
8df61846a7d13039172689e6de4abeace6c054a09e65f9a55a8d7d0cd8ace2cf | Perl | 28,945 | 810 | #!/usr/bin/env perl
## Pombert JF, Illinois Tech - 2020
my $version = '2.0f';
my $name = 'get_SNPs.pl';
my $updated = '2023-05-03';
use strict;
use warnings;
use File::Basename;
use File::Path qw(make_path);
use Getopt::Long qw(GetOptions);
#########################################################################
##... |
1fb047d9476fc967cde060c9105c7d9824d3d5235e6dd29a1e212ac26489ec91 | Perl | 36,456 | 1,322 | #!/usr/bin/perl
# Script to check plink .bim files against HRC/1000G/TOPMed for strand, id names, positions, alleles, ref/alt assignment
# W.Rayner 2015 - 2020
# wrayner@well.ox.ac.uk
#
# Version 4.2
#
# -v4.0
# - removes SNPs not in the reference panel
# - removes all A/T G/C SNPs with MAF >40% in the reference da... |
3ba6942deb8c58c467556f8270d5aa1f63fbc45b4e8b4411c3848d9317c3082d | Perl | 40,436 | 1,332 | #! /usr/bin/perl -w
# Copyright 2000, 2001, 2002 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation; eithe... |
4d28e0370b71829507bc42b1b66982b98c7823aa3c48a7fba6791c968dbebdd6 | Perl | 43,509 | 897 | #!/usr/bin/env perl
## Pombert Lab, 2017-2018 Illinois Tech
my $version = '0.5c';
my $name = 'synonymy.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Basename;
use File::Path qw(make_path);
########################################################################... |
e23e5ab041c5e1b655e4df46453d66c57226c5219b9e05d587c4eb2c2f7648d8 | Perl | 58,966 | 2,168 | #!/usr/bin/perl -w
# GMP perl module tests
# Copyright 2001, 2002, 2003 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free So... |
7132df993f79311f27ca1db208268a133416ea165ee4a36cd37d1ca119a368ac | Perl | 200,000 | 47 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../../../TrinotateWeb/cgi-bin/PerlLib/");
use CanvasXpress::Sunburst;
use CanvasXpress::Piechart;
use CanvasXpress::Barplot;
use CanvasXpress::PlotOnLoader;
use CGI;
my $usage = "usage: $0 report_prefix\n\n";
my $report_prefix = $A... |
edb2d1351aa8ad0b87dcfbf8acdfb38decc1d4554defa9287ffdf01cb0dc9f53 | Python | 7 | 1 | # Empty |
b000f4590d6af9cfe633ffe0faae301a05dde8e4ca7757d7566f899d61f240b8 | Python | 9 | 1 | import io |
9e856831265f20d432e22528cc07b4c06e22598ff68a475932c4f4f83d678b89 | Python | 16 | 1 | version = "0.2"
|
8bb2d14116a2b4e2011d6f5d87b0287ea7d0e9e8098336bcec316b3e3c423269 | Python | 18 | 1 | version = "0.6.2"
|
c966706fb1d75acd5dcee6c52e4f0985ae92024dc1d8d1865ef4dd13b8f54f25 | Python | 18 | 1 | """QE presets."""
|
e20d1aa48f3eddd8b27dd05a04eb7a54a6345865d32bc169c9b6cd4cc1cd476a | Python | 19 | 1 | from .util import * |
fcdab3dbb2b952fb2d05b5d2ee5c0a7a1991c6ef63762e1dca9cbdc2ee67ba8b | Python | 19 | 1 | from .m3cv import * |
97307b19581d3c1b4a785bf5ef5afea8ef82f09c6345c224423313143295999c | Python | 20 | 1 | import numpy as np
|
0bf8c7273997f0f238c6ad23a7399c4ccc696f9943b2ae28e55cb1433955ad91 | Python | 21 | 2 | __version__ = '3.4'
|
b8d446e48c3f005500a7fec851bcd5e202b6655d3c84670a0caab6a46c2604a7 | Python | 21 | 1 | version = "2.3.9rc2"
|
bb7014e5feb50d031f3b1a59edfe8700a2379034d405d8f1be47d958a7972496 | Python | 21 | 1 | from .module import * |
cdd6cefd1d5e3d59aa04575e235575b22455ce85c6f8130d176efb5ce030d929 | Python | 21 | 1 | from .render import * |
d3b3734170603659f0e6448de9963113d072fbf46e1f7272cb9f19ef8b088a8d | Python | 21 | 1 | __version__ = '0.0.1' |
eec35b79eef6af7a82015968166d914560936bd8158cc4bb9c225c27e511ce5e | Python | 21 | 1 | __version__ = '0.0.7' |
f6ddc7cbe2e119c937398de04e4d064976cc0110c5618bc7312fa595967ae3b4 | Python | 21 | 1 | from .clip import *
|
ffd84609a1f165f00c7dcfd704ddf0f86b4a7f3354a1812ae5688a4885e43bfd | Python | 21 | 1 | """tgan.research."""
|
13eeb00198e22d15489c0045c6b5a8a9d6253bfb7ecd584af1735f367683cb32 | Python | 22 | 1 | __version__ = '1.1.1'
|
17a74cad85ed9c8c68550221427aba8b5208bb0887a9e67164c1d38548ebdaf3 | Python | 22 | 1 | __version__ = "0.6.7"
|
1fd3564596fb35b79144f2cffd5d5f01198b357ada9e8ad533e38e63ef3fdae8 | Python | 22 | 1 | __version__ = "0.9.0"
|
329013e6180da079d3b46d57443fc657f03b42b1d553abc98c64b0ffca8c180e | Python | 22 | 1 | __version__ = "1.2.0"
|
3e6710d8f236a0ff22ae72ed24b25bcb661f5bab01bcb0262fe569001cd3ab07 | Python | 22 | 1 | __version__ = '0.2.1'
|
42f95587825397724bee34008daefac8ab53f88bc5e3adf50128d6635c12e804 | Python | 22 | 1 | __version__ = "0.0.2"
|
59fafba01c12f08ed6abe43212650bc07ea96ea186db5d74d3c4cb4a88c2a298 | Python | 22 | 1 | __author__='cheese63'
|
86a52aea3631c93c94c7c6ee49a60f35da20c6dd743e21a3728a1c11ec187eb7 | Python | 22 | 3 |
#def load_bowl_cup() |
9a5a6d9eee176bb37899cf47df586a8c70e4b0e53844767881b8945715d6a861 | Python | 22 | 1 | __author__ = 'fabian'
|
ceb713c313f7480dc5d49b3bf1a7eb7de699789afcc3684bb45b4466852a5268 | Python | 22 | 1 | __version__ = '0.4.2'
|
d9e896408e797ddfaba03764b781ef97d5b3ad3278c50a37dd5cc5b9de83d375 | Python | 22 | 1 | __version__ = '0.4.0'
|
f3f1356a89a932c16c98048e8db1b3c74139e6c058529f9f4560b4c1c4cf11b7 | Python | 22 | 1 | from .gwas import GWAS |
5eefd4cf311ab3da6b22a9228dec11766fd717b56957539d658b232e52b22b13 | Python | 23 | 1 | from ._options import * |
81754f762125f473adbcd513d65004e1990723271f979b169baab8da15c3a72e | Python | 23 | 1 | from .model import FPN
|
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