sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
edc57ca899329697e0e68b6ded52befb0ceca512d8d171fec4ee29be5a554a27 | Perl | 2,853 | 90 | use strict;
use warnings;
if (@ARGV < 1) {die "Please provide a GEO series matrix file for a single-cell RNASeq experiment.\n"}
open(my $ifh, $ARGV[0]) or die $!;
my @FILES = ();
while (<$ifh>) {
if ($_ =~ /^!Series_geo_accession\s+"(GSE\d+)"/) {
print STDERR "Acc: $1\n";
}
if... |
190641ef23c4229d2ededcdc4565339b4b5a91994e33d0a2fb03c30883573dfb | Perl | 2,870 | 87 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
42862c8591f7214a5ff3c46c1989cd75407805b72d939192bebb754672d83c22 | Perl | 2,967 | 78 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
40ace3f8ae6d63d7165be7e999fe256a07696283b7fc061bac9cf15351c9b554 | Perl | 2,996 | 127 | #!/usr/bin/perl -w
use strict;
use FindBin qw($Bin $Script);
unless (@ARGV==4) {
print "perl $0 <best.nk> <cds> <distance> <outdir>\n";
die ;
}
my %config;
parse_config("$Bin/config.perl.txt",\%config);
my ($bed,$cds,$distance,$outdir)=@ARGV;
my (%pairwise,%hash,%genome);
open (IN,$bed) or die $!;
while (<IN>) {... |
8d90065dfb05ec9600b015a1d77b19b94f9ff3c50f5c461d05da82674174a4a2 | Perl | 2,998 | 54 | #! /usr/bin/perl
# Test that HMM naming in hmmbuild works as advertised.
# Written to test for #h50.
# SRE, Tue Apr 28 14:00:51 2009
#
# Usage: ./i5-hmmbuild-naming.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i5-hmmbuild-naming.pl .. .. tmpfoo
$builddir = shift;
$srcdir = shift;... |
b5a4c014ab3ef09021530823a270a5f85b80634ab1aecda68a64e0d9ea741691 | Perl | 3,090 | 103 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use GAL::Annotation;
use IO::Prompt;
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#--------------------------------------------------------------... |
a5d5a71582c49ab0cf8bd37b092ccb91026ad2a3266e7283fdf30f41a363dedb | Perl | 3,162 | 74 | #! /usr/bin/perl
# Regression test of handling a nonresidue '*' character. By design,
# '*' residues score 0 in insert states and N,C,J; and -inf in match
# states. Test case verifies that an inserted * is handled within one
# alignment, and a consensus * breaks an alignment in two.
# Implemented as a regression test ... |
42808c0ad3571aa8cb023d52d59878ce48dbbf5d127948a07e24efe2b76b757b | Perl | 3,294 | 113 | #! /usr/bin/perl
# Run the testsuite under Valgrind, to check for memory leakage.
#
# First you have to do a 'make dev' or 'make check', or equiv;
# all the unit test drivers need to be compiled and present.
#
# Usage:
# valgrind_report.pl <top_builddir> <top_srcdir>
#
# Example, in a single directory (source+buil... |
a00711244d9263990bd3146fec139747aabde4c2f2c8e32a366a7097aab645f1 | Perl | 3,418 | 111 | #! /usr/bin/perl
# Check how we handle duplicate names, for both queries and targets.
# Indexing HMM or sequence files does require unique names/accessions.
# Aside from SSI indexes, other HMMER operations do not require unique
# names/accessions.
#
# Usage: ./i10-duplicate-names.pl <builddir> <srcdir> <tmpfile pre... |
f1c7640ba6f2d4b0cbbaa0cbf0e5c520d3109eae72466e26ddc9f40526b77f79 | Perl | 3,679 | 142 | #!/usr/bin/env perl
use Getopt::Std;
getopts('n:f');
$numIterations = $opt_n ? $opt_n : 10000;
if (@ARGV < 2) {
print "usage: [-n <iterations>] [-f] <model1> <model2>\n";
print "\twhere -f indicates only to compare sentences of length <= 40\n";
exit 1;
}
$model1name = $ARGV[0];
$model2na... |
c5b83ddfc57207ca51cbefbc483aaae805ff245e1bc72949f617dca6201e6c7b | Perl | 3,718 | 107 | #! /usr/bin/perl
# The top level script that runs speed benchmarks
#
# Usage:
# ./speed-master.pl <top_builddir> <top_srcdir> <resultdir> <nproc> <nthread> <joblist> <querydb> <targetdb> <script>
#
# <top_builddir>: Top level directory for finding executables to be
# benchmarked. This is passed on ... |
e6fc4312c462f5db2beaa660ab10fc94432fa8176171adcc5dbc24d71ce5d08a | Perl | 3,772 | 113 | #! /usr/bin/perl -w
# The top level script that runs a pmark benchmark.
#
# Usage:
# ./pmark-master.pl <top_builddir> <top_srcdir> <resultdir> <nproc> <benchmark prefix> <benchmark script>
#
# <top_builddir>: Top level directory for finding executables to
# be benchmarked. This is passed on to the <benchmark scr... |
ae78e6b24eebc84cc62a8ac1254943a717ea9a747de6f3876db9e906cf9af8af | Perl | 3,863 | 152 | #!/usr/bin/perl -w
use strict;
use FindBin qw($Bin $Script);
unless (@ARGV==5) {
print "perl $0 <best.nk> <identity.file> <cutoff> <outdir.file> <fasize> \n";
die ;
}
my ($bed,$idfile,$cutoff,$outfile,$fasize)=@ARGV;
my (%RBH,%RBHpaired,%RBHsolo,%RBHraw,%pairwise,%hash,%out,%FA);
open (FASIZE,$fasize) || die "$... |
c19538c737cba717c9a623c77027247abbf90d50716b877f746310188aa4aef5 | Perl | 3,938 | 112 | #! /usr/bin/perl
# Look for any problems in hmmalign that corrupt the input sequences.
#
# Usage: ./i13-msa-integrity.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i13-msa-integrity.pl .. .. tmpfoo
#
# SRE, Tue Mar 9 09:19:22 2010 [Janelia]
$builddir = shift;
$srcdir = shift;
$tmppfx =... |
4c41769429966321589a3c53ab616a3d623ac0a030c800829bcb1eed726d9128 | Perl | 4,012 | 94 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
c18ee1a5d21ac1315e0ee86ddef96d6b703db6e68be85077c12f69af3a441d53 | Perl | 4,134 | 195 | #!/usr/bin/perl
# todo:
# black box nodes with no edges
# use strict;
# use warnings;
use File::Spec;
use GraphViz2;
use Log::Handler;
# ---------------
$notes =
"usage: $0 file format {format2 {format3 ... }}
file contains list, space indent separated to determine linkage
duplicate names ok, they will be mult... |
99511dab381d75cedc1599fcd7aef1b4a36974bd7561402956ea1fedf93b112f | Perl | 4,174 | 133 | #! /usr/bin/perl
# Measures testsuite coverage (as percentage of source lines),
# using gcov.
#
# Assumes you've already compiled the library, with test drivers only.
#
# Usage:
# coverage_report.pl <top_builddir> <top_srcdir>
#
# Example usage, in a single directory (source and build):
# ./configure --enable-... |
8e95c4d6097d8804382852ccbe7ebed18083ba67bc754a6b6512dd1f0d4d0afe | Perl | 4,273 | 147 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
use GAL::Annotation;
use IO::Prompt;
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#--------------------------------------------------------------... |
1dc8a94d84852a69abda372df88471b0e59b61311a4b76008ba45c2ec130e9d7 | Perl | 4,281 | 92 | #! /usr/bin/perl
# Integrated test of esl-mask miniapp.
#
# Usage: ./esl-mask.itest.pl <esl-mask binary> <tmpfile prefix>
# Example: ./esl-mask.itest.pl ./esl-mask foo
#
# SRE, Sun Nov 1 09:26:45 2009 [Casa de Gatos]
$eslmask = shift;
$tmppfx = shift;
if (! -x "$eslmask") { die "FAIL: didn't find esl-... |
70035c9fbbd7ae0ba7e906dd2e26a37aac653ecfde9dffcb3ae21af4d0606fb9 | Perl | 4,497 | 143 | #! /usr/bin/perl
# Integrated test of the esl-seqrange miniapp.
#
# Usage: ./esl-seqrange.itest.pl <esl-seqrange binary> <esl-sfetch binary> <tmpfile prefix>
# Example: ./esl-seqrange.itest.pl ./esl-seqrange ./esl-sfetch foo
#
# EPN, Wed Mar 24 10:19:28 2010
$eslseqrange = shift;
$eslsfetch = shift;
$tmppfx ... |
fc7b5c84710b205c53cb0ff7e8ab0f51f622c24ebcc24ebbba9407b13aa31529 | Perl | 4,728 | 120 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
b4b2a298c700a391e604cfcbe4af62c49c0d5663605161521cb6cf8d1f4d85f5 | Perl | 4,741 | 138 | #! /usr/bin/perl
# Test that the search tools (hmmsearch, phmmer, nhmmer)
# produce the correct set of hits when the target sequence
# database is rewound. This aims to avoid a bug found by
# TW in 2016, in which a second pass through an NCBI
# database would miss hits to the first sequence of that
# database.
#
# ... |
88c4f22ba0f3082283f872a77014f28c3f6ac7175cae64b8bef8072459dd17d2 | Perl | 4,752 | 111 | #! /usr/bin/perl
# Check that we can deal with HMMs with no optional annotation, in either
# hmmscan or hmmsearch mode.
# Bug #h69 segfaulted on this test.
#
# Usage: ./i9-optional-annotation.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i9-optional-annotation.pl .. .. tmpfoo
#
# SRE, Sun Nov 29... |
3ec0f7ec808ea1b38528fa28be344808b5297a324597f10f12503a009f7a5da1 | Perl | 4,791 | 169 | #! /usr/bin/perl
# Test of makenhmmerdb and the core fm-index search functionality, using extactmatch
#
# Usage: ./i20-fmindex-core.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i20-fmindex-core.pl .. .. tmpfoo
#
BEGIN {
$builddir = shift;
$srcdir = shift;
$tmppfx = shift;... |
3e8364c9ddee74acb1679de6880433de72242666fc3682664bd194b2cb61eb66 | Perl | 4,925 | 225 | #!/usr/bin/perl
$qt = $ENV{QTDIR} || die "environment variable QTDIR must be defined (did you \$ module swap ultrascan/gui-build )";
$qwt = $ENV{QWTDIR} || die "environment variable QWTDIR must be defined";
$us = $ENV{ULTRASCAN} || die "environment variable ULTRASCAN must be defined";
$notes = "usage: $0 sys... |
ef3788f60fc0c04557d0dd4134e932ee925aab0d8744b766d59891f7fcb6bc6e | Perl | 4,930 | 127 | #! /usr/bin/perl
# Test of hmmbuild/nhmmer as used to build a DNA model, then query a
# a database of long (1MB).
#
# Usage: ./i18-nhmmer-generic.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i18-nhmmer-generic.pl .. .. tmpfoo
#
# TJW, Fri Nov 12 11:07:31 EST 2010 [Janelia]
BEGIN {
$build... |
f5e9e6c50c7c48861abbadbbc500bcd4792f53889946de9f2d95171167a2e99a | Perl | 5,250 | 143 | #! /usr/bin/perl
# Integrated test of the esl-alimap miniapp.
#
# Usage: ./esl-alimap.itest.pl <esl-alimap binary> <tmpfile prefix>
# Example: ./esl-alimap.itest.pl ./esl-alimap foo
#
# EPN, Tue Feb 2 13:19:44 2010
$eslalimap= shift;
$tmppfx = shift;
if (! -x "$eslalimap") { die "FAIL: didn't find... |
8d59be8e30fea16314136821f894b09c7e88f6d1db96d24f0c8541e87366694e | Perl | 5,276 | 109 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
9cfeb74fb2b9f649539d40dc01a0423be41cf4ea515403ecc4a3dea872d3e899 | Perl | 5,285 | 145 | #! /usr/bin/perl
# Testing that we can read FASTA files, even if they have NCBI
# formatted BLAST databases in the same directory.
#
# (This failed in Jan 2010 because the embryonic NCBI db parser
# automatically opened the NCBI files instead of the FASTA file,
# but did not have an implementation of esl_sqio_ReadWind... |
2e173749ad066ddb3c2319538de3a43c762af49caba7950fc6f1a1881500e45b | Perl | 5,306 | 110 | #! /usr/bin/perl
# Integrated test of the esl-compalign miniapp.
#
# Usage: ./esl-compalign.itest.pl <esl-compalign binary> <tmpfile prefix>
# Example: ./esl-compalign.itest.pl ./esl-compalign foo
#
# EPN, Tue Feb 2 13:19:44 2010
$eslcompalign= shift;
$tmppfx = shift;
if (! -x "$eslcompalign") { d... |
5eb889fd7eec69e1e9de9218f360bcc837a5f2f2cf416dc4aab38f721b6d8641 | Perl | 5,595 | 98 | #! /usr/bin/perl
# Integration tests of reading all valid protein sequence residue characters.
#
# Usage: ./i1-degen-residues.pl <top_builddir> <top_srcdir> <tmpfile prefix>
# Example: ./i1-degen-residues.pl .. .. foo
#
# SRE, Tue Feb 2 13:09:58 2010 [Janelia]
$top_builddir = shift;
$top_srcdir = shift;
$tmppf... |
cc465531613bb81bc70d8fe1ddd607b770b9e82c90a6f7d01929247744247c93 | Perl | 5,650 | 153 | #! /usr/bin/perl
# Usage: autobuild.pl <srcdir> <cmdscript>
# Example: autobuild.pl ~/src/hmmer/trunk intel-linux-gcc
#
# Builds HMMER from source in <srcdir>, in build directory
# <srcdir>/ab-<cmdscript>, using the <cmdscript>, which is
# assumed to be in <srcdir>/autobuild/<cmdscript>.
#
# <srcdir> is the root o... |
f1a42f95cecfe7337be4717edb8d8682c9d4cbfc0814e213e28c4cf4b715606e | Perl | 6,273 | 222 | #!/usr/bin/perl
# $debug++;
$dir = shift || die "usage: $0 develop directory\n";
die "usage: $0 develop directory\n" if $dir =~ /^-/ || !-d $dir;
$us3 = $ENV{'us3'} || die "can't find env variable us3\n";
while ( $ARGV[ 0 ] =~ /^-/ )
{
$arg = shift;
if ( $arg =~ /-d/ )
{
$debug++;
n... |
f046838d11f84c0a0f9a81c348b03e1329aca7642838bebe8d3566b40ddc211f | Perl | 6,625 | 151 |
###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##... |
a679b81b723f3773ee1af96f6c97c1cf68f623477217d4d9a05db57c862638b1 | Perl | 6,631 | 169 | #!/usr/local/bin/perl -w
################################################################################
# launchMotifEnrichmentAnalyses.pl 1.0.1 #
# Authors: P. Poullet, S.Liva (Institut Curie) #
# Contact: myproms@curie.fr ... |
e193bd4107314043f4dfbedc16ae62887077c1f790abd76d88dbbd1aa012a0bb | Perl | 6,874 | 146 | #! /usr/bin/perl
# Testing the esl-afetch miniapp
#
# Usage: ./esl-afetch.itest.pl <esl-afetch binary> <tmpfile prefix>
# Example: ./esl-afetch.itest.pl ./esl-afetch foo
#
# SRE, Fri Nov 11 09:16:49 2011
$esl_afetch = shift;
$tmppfx = shift;
if (! -x "$esl_afetch") { die "FAIL: didn't find esl-afetch ... |
71355bdc1cf8ec5bbb565d33d38c05c1dc0100d591cac1bf489d994ac6ee449e | Perl | 6,896 | 171 | #!/usr/local/bin/perl -w
################################################################################
# launchExploratoryAnalyses.pl 1.1.0 #
# Authors: P. Poullet, S.Liva (Institut Curie) #
# Contact: myproms@curie.fr ... |
17a345673397d3e72bcc9b91b8f98c29b2963cc15ca176606519bd4ddef7b3a2 | Perl | 7,088 | 144 | #!/usr/local/bin/perl -w
################################################################################
# runPathwayAnalysis.pl 1.0.2 #
# Authors: P. Poullet, S.Liva (Institut Curie) #
# Contact: myproms@curie.fr ... |
76dfe67a0ff89bc652e0273fd6071870a4d332b441647a08ab59b16a6ac41b42 | Perl | 7,725 | 227 | #!/usr/local/bin/perl -w
################################################################################
# myproms4datFiles.pl 1.0.9 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
4685b77e70b1b31c1fb7400032c42094cd515644f3e390b733ae19811531fec2 | Perl | 7,977 | 325 | #!/usr/bin/perl
# $debug++;
$dir = shift || die "usage: $0 develop -or- develop_stage\n";
die "usage: $0 develop -or- $0 develop_stage\n" if $dir !~ /^develop(_stage|)$/;
$us3 = $ENV{'us3'} || die "can't find env variable us3\n";
while ( $ARGV[ 0 ] =~ /^-/ )
{
$arg = shift;
if ( $arg =~ /-d/ )
{
... |
75e7bb4faee14c8bf1eb803935b725aee0a3dc58f9b2c272b18a4e08b7f390b3 | Perl | 8,364 | 207 | #!/usr/local/bin/perl -w
################################################################################
# scanDatabank.pl 3.0.9 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
a33417324611154f31c37318502fcbbbd52a5ccb0104b726e6acf5938d577606 | Perl | 8,727 | 159 |
# remove commas within tokens (e.g. "10,000")
while ( s/:(\S*),/:\1-comma-/ ) { }
########## INHERITANCE DEPENDENCIES
# node identification/equivalence...
#s/(\S+),=,(\S+)/\1,e,\2/g;
# cin deps...
s/(\S+)r,\d+,(\S+)c(?=\s)/\2,c,\1/g;
#s/(\S+)r,\d+,(\S+)c(?=\s)/\2r,c,\1r \2s,c,\1s/g;
# re-sort...
#s/,c,/r,00,/g;
$_... |
7aa5a6aac1f88e178eedde6325ee69720b7b72142545e0d0a480e2f2049db667 | Perl | 8,961 | 149 | #! /usr/bin/perl
BEGIN {
$builddir = shift;
$srcdir = shift;
$tmppfx = shift;
}
if (! -x "$builddir/miniapps/esl-translate") { die "FAIL: didn't find esl-translate program in $builddir/miniapps"; }
if (! -x "$builddir/miniapps/esl-reformat") { die "FAIL: didn't find esl-reformat program in $builddir/... |
47dd409e578a1a12cc932a101365aa510c24b9e130642b92569d406b75773d2b | Perl | 9,106 | 160 | #! /usr/bin/perl
# Integrated test of the esl-construct miniapp.
#
# Usage: ./esl-construct.itest.pl <esl-construct binary> <tmpfile prefix>
# Example: ./esl-construct.itest.pl ./esl-construct foo
#
# EPN, Tue Feb 2 13:19:44 2010
$eslconstruct= shift;
$tmppfx = shift;
if (! -x "$eslconstruct") { d... |
068b5b78cee7b5f768eb7fe07081e7bd976549246977466a9761ece935db9450 | Perl | 9,108 | 319 | #!/usr/bin/env perl
###############################################################################
#
# calc.kmerfreq.pl
#
# Calculates kmer frequency in fasta files.
# Length restriction, variable kmer, and rc kmer to remove strand bias.
#
# Copyright (C) 2012 Mads Albertsen
#
# This program is free ... |
5d8fde01d13c7c5292aaa4faa098093d7dfadef71a35e12189db866ae4d0abda | Perl | 9,245 | 258 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie Kapusta
# version : see below / see changelog
# email : 4urelie.k@gmail.com
# github : https://github.com/4ureliek?tab=repositories
#######################################################
#load modules
use warnings;
... |
69c447d02b4bfac357478fe0048d112af1457bea7f1fac925a4fe0a69fcb6f2c | Perl | 9,381 | 332 | #!/usr/bin/perl
=head1 Name
fishInWinter.pl -- get out all the fishes which match to the given baits
=head1 Description
Here I use "fishInWinter" to name this program, which do like fishing with baits.
The name is for memory of a college classmate met on Nankai bbs, and
"fishInWinter" is just her bbs id. I wonde... |
c0e933158af91bc7303011f8105ee12e9a244d1be83c2b787e008b0d46e484d7 | Perl | 9,478 | 531 | @colors = (
'black',
# 'antiquewhite' ,
# 'antiquewhite1' ,
# 'antiquewhite2' ,
# 'antiquewhite3' ,
# 'antiquewhite4' ,
# 'aquamarine' ,
# 'aquamarine1' ,
# 'aquamarine2' ,
# 'aquamarine3' ,
'aquamarine4' ,
# 'beige' ,
# 'bisque' ,
# 'bisque1' ,
# 'bisque2' ,
# 'bi... |
51310f5d5cb89a6cc1d999b5114610c561846576b4200dc4a8258c34f6eeabe1 | Perl | 10,648 | 227 | #!/usr/local/bin/perl -w
################################################################################
# launchProtRulerQuantif.pl 1.0.8 #
# Authors: V. Laigle (Institut Curie) #
# Contact: myproms@curie.fr ... |
2b9fe9c371b28866d5c486f33f97f93b66b26c684dedc8db768868b498320485 | Perl | 10,721 | 167 | #! /usr/bin/perl
# Bug #h80: hmmconvert can't read H2 Nucleic files
#
# Usage: ./i15-hmmconvert.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i15-hmmconvert.pl .. .. tmpfoo
#
# SRE, Tue May 18 13:32:40 2010 [Janelia]
BEGIN {
$builddir = shift;
$srcdir = shift;
$tmppfx = shift... |
fdc9b8921641c79c0581873cfa8e454979af401853b8e7887154efca7d7ca3e3 | Perl | 11,883 | 481 | #!/usr/bin/perl
=head1 Program Description
This program is designed to be a universal fasta format dealer, including attribution
statistics, large file cutting, word patterning, fragment substructing, and sequence
reforming.
For fasta file cutting, you can either specify the sequence number in each
sub file or sepe... |
4725f978f97356d391ec8021eb655f1d976e5789f2ff9e37517ead315d71805c | Perl | 12,362 | 381 | #!/usr/bin/perl -w
#----------------------------------------------------------------------------
# Author : Aurelie Kapusta
# email : 4urelie.k@gmail.com
# PURPOSE : parsing Repeat Masker .out output and merge interrupted repeats
#----------------------------------------------------------------------------
use wa... |
7aeb9410c8929d95b80d1bf3ae11d8a6cd7fb2c88e7f6d0faf4553bf96ae88e4 | Perl | 12,398 | 297 | #!/usr/bin/env perl
#
# FASTA Splitter - a script for partitioning a FASTA file into pieces
#
# Version 0.2.6 (August 1, 2017)
#
# Copyright (c) 2012-2017 Kirill Kryukov
#
# This software is provided 'as-is', without any express or implied
# warranty. In no event will the authors be held liable for any damages
#... |
0fb349f9bac9311d13e09c11e326d21f9f968cb7fc630d5fb21ced30aeeb45ca | Perl | 13,447 | 328 | #!/usr/local/bin/perl -w
################################################################################
# runGSEA.pl 1.0.0 #
# Authors: V. Laigle (Institut Curie) #
# Contact: myproms@curie.fr ... |
f665dcdd0b38e15a960a0b6dbfaa31ca23f40da6f51f947e9a95212710e476bc | Perl | 13,752 | 233 | #! /usr/bin/perl
# Integrated test of the esl-alistat miniapp.
#
# Usage: ./esl-alistat.itest.pl <esl-alistat binary> <tmpfile prefix>
# Example: ./esl-alistat.itest.pl ./esl-alistat foo
#
# EPN, Tue Feb 2 13:19:44 2010
$eslalistat= shift;
$tmppfx = shift;
if (! -x "$eslalistat") { die "FAIL: didn't... |
1464634a28d6db9c7094f8420c6d0c2ad757607fb759d9fff76379b1bb22f663 | Perl | 13,807 | 364 | #!/usr/bin/env perl
###############################################################################
#
# cytoscapeviz.pl version 1.0
#
# Indicates connections between scaffolds and produces cytoscape
# files for an easy visualization
#
# Copyright (C) 2012 Mads Albertsen
#
# This program is free sof... |
6d976048a8889fc3d265a4942fbda5d40b4766ac87d52f76535acb692f85bb02 | Perl | 14,059 | 439 | #!/usr/local/bin/perl -w
################################################################################
# myproms4databanks.pl 1.2.2 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
173eeeb7e3b167b27e82fcfe816a4ca94b78bcb178e205278ba8096e35426a19 | Perl | 14,224 | 400 | #!/usr/local/bin/perl -w
#############################################################################
# correctPepQuantification.pl 1.0.0 #
# Authors: P. Poullet (Institut Curie) #
# Contact: myproms@curie.fr ... |
1ad63330f3e5ac5db991979eaaeddfaa3a48824a15a21f97dacbd92392b97c8d | Perl | 14,259 | 211 | #! /usr/bin/perl
# Integrated test of esl-alimerge miniapp.
#
# Usage: ./esl-alimerge.itest.pl <esl-alimerge binary> <tmpfile prefix>
# Example: ./esl-alimerge.itest.pl ./esl-alimerge foo
#
# EPN, Wed Nov 25 11:23:55 2009
$eslalimerge = shift;
$tmppfx = shift;
if (! -x "$eslalimerge") { die "FAIL: ... |
0f3e6cfd759121b4b7a9950787665756d0aed85c6cf1d5e90d87194f49e74e46 | Perl | 14,386 | 269 | #!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic
# TAJ 6/23/08 last mod 7/10/08
# Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format
# Based upon my "blastn2gff.pl" script.
#
# OUTPUT GFF2 format:
# ------------------
# CONTIG METHOD TYPE START END SCO... |
33ba832ba8338fe432c51d912470c736e31556c6ed3d34087ab59995418dbbfd | Perl | 15,375 | 333 | #!/usr/local/bin/perl -w
################################################################################
# runemPAIQuantification.pl 1.1.11 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
d4bf054cc5399970e128c2cffee02a0524df6c371b6810275232fd50d9231013 | Perl | 17,315 | 474 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie Kapusta
# version : see below / see changelog
# email : 4urelie.k@gmail.com
# github : https://github.com/4ureliek?tab=repositories
#######################################################
#load modules
use warnings;
... |
32fca5a0413624a619991eac5fe9d8a32dfe08f9e12bec5755caa689595664cd | Perl | 18,214 | 425 | #!/usr/local/bin/perl -w
################################################################################
# runHydrophobicity.pl 1.0.0 #
# Authors: V. Laigle (Institut Curie) #
# Contact: myproms@curie.fr ... |
f420713fc19da94949a4b00806cc6f9411707ad5bdc313e6b178e865c31d4509 | Perl | 18,366 | 342 | #! /usr/bin/perl
# Test that programs accept and reject argument of '-' (for reading
# data from stdin, rather than from files) as they're supposed to.
#
# Usage: ./i17-stdin.pl <builddir> <srcdir> <tmpfile prefix>
# Example: ./i17-stdin.pl .. .. tmpfoo
#
# SRE, Wed Oct 27 13:05:10 2010 [Janelia]
BEG... |
f6e1447591136709893016733127bd6922cc5df0b03c993e8c4f92316612f5a5 | Perl | 18,408 | 354 | #! /usr/bin/perl
# Integrated test of the esl-alimanip miniapp.
#
# Usage: ./esl-alimanip.itest.pl <esl-alimanip binary> <tmpfile prefix>
# Example: ./esl-alimanip.itest.pl ./esl-alimanip foo
#
# EPN, Tue Feb 2 13:19:44 2010
$eslalimanip= shift;
$tmppfx = shift;
if (! -x "$eslalimanip") { die "FAIL... |
77d7f472f68536a828fe576b7380c1c12c5f8deddac47512197b0f4440191aea | Perl | 20,810 | 648 | #!/usr/bin/env perl
=head1 SYNOPSIS
This script is a very basic version of what is performed by the HMMER website
searches. The script will connet to a hmmpgmd client and take the input fasta file
(containing one or more sequences) and push each sequence down the socket
to be searched by the master. When the res... |
c4b5f16b70ab1910ea7a5dc2850ccafbbf511469c3bcf7ed44712142aecf30b9 | Perl | 21,889 | 512 | #!/usr/local/bin/perl -w
################################################################################
# runProtRulerQuantification.pl 1.0.6 #
# Authors: V. Laigle (Institut Curie) #
# Contact: myproms@curie.fr ... |
49f52f344a715f21916d575466adf1a01292f27a4a3e0686d66f80118aba9105 | Perl | 22,281 | 322 | #! /usr/bin/perl
# Integrated test of esl-alimask miniapp.
#
# Usage: ./esl-alimask.itest.pl <esl-alimask binary> <tmpfile prefix>
# Example: ./esl-alimask.itest.pl ./esl-alimask foo
#
# EPN, Wed Nov 25 11:23:55 2009
$eslalimask = shift;
$tmppfx = shift;
if (! -x "$eslalimask") { die "FAIL: didn't ... |
4b1f856cc0b387bd4cec49bb0f074ef32fe5fe7bfffe0aebe34d4e76649fd1fa | Perl | 23,951 | 548 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie K
# date : Jan 2013 = version 1.0
# version : 1.6
# email : 4urelie.k@gmail.com
# Pupose : Parse RepeatMasker output
# -> get big tables with % divergence breakdown in bins to have dynamic landscape of a give... |
c00467a8850415135cb4d2e1125da302067bff718d41b4be05efba3d4264ffb1 | Perl | 26,868 | 506 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
b83e294e70f39343b23ce4aba12f29df693b7405575a0178b27b7888c34c6c8b | Perl | 31,528 | 739 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie K
# date : 04 May 2011 = v1.0 [other script, updated until 1.9]
# version : 2.3
# email : 4urelie.k@gmail.com
# Pupose : Parse RepeatMasker outputs to get summary info for each repeat as well as masked amounts by c... |
c2eced2bc2fc19473ac317ddb73ba49f3d8df72a083aac89ad1372debecf6dc9 | Perl | 35,654 | 743 | #!/usr/local/bin/perl -w
################################################################################
# runSINQuantification.pl 1.2.1 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
b5cac8fcd39bc58b191738eb56d141f375f28d03bc45a098d71176b1dc55fd7c | Perl | 35,778 | 644 | #! /usr/bin/perl
# Integrated test of the esl-ssdraw miniapp.
#
# Usage: ./esl-ssdraw.itest.pl <esl-ssdraw binary> <postscript template file> <alignment file> <tmpfile prefix>
# Example: ./esl-ssdraw.itest.pl ./esl-ssdraw ../testsuite/trna-ssdraw.ps ../testsuite/trna-5.stk foo
#
# EPN, Tue Feb 9 12:22:29... |
2e22eaa015db54a568bdd4dba0b0dd4327d21790de1e30b23c38cd72972a2072 | Perl | 39,185 | 745 | #!/usr/bin/perl
#######################################################
# Author : Aurelie Kapusta (https://github.com/4ureliek), with the help of Edward Chuong
# email : 4urelie.k@gmail.com
# Purpose : Writen to test enrichment of TEs in a set of simple features (ChIP-seq for example)
########################... |
e235955a2adbe02dcd70eebff03f286533b5b7205144be483f19d9e6aaaf493f | Perl | 39,422 | 777 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie Kapusta
# version : see below / see changelog
# email : 4urelie.k@gmail.com
# github : https://github.com/4ureliek?tab=repositories
#######################################################
use strict;
use warnings;
us... |
f4c42196200040273c0a6fe5b5a1e48d6e6f59adbe64b05dfe2f56d535efb851 | Perl | 41,774 | 732 |
use Getopt::Std;
getopts("sxr");
$SEM = $opt_s;
$XTRA = $opt_x;
$REUN = $opt_r;
print( $SEM );
$SHORT = '(?!<[aeiou])(?:[aeiou])';
while ( <> ) {
# ## remove old -lI tag
# s/-lI[^\)]* //g;
# ## lowercase all words -- U (uppercase) category in gcg16 lets us reconstruct capitalization for proper names if we wan... |
14a285458483bba47f7901f139270a9425236b9ba72863774258486f2fc5b8a6 | Perl | 44,256 | 983 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie K
# version : 2.0 (see below)
# email : 4urelie.k@gmail.com
# Purpose : It reads a repeat masker output file and extracts sequences (all or subset based on filter and/or random)
# Check Usage for the many opt... |
018bb8e5ea7d3ba1d9417f408e59272fda48bc194402745bb6ef5db323b60776 | Perl | 47,148 | 1,371 | #!/usr/bin/perl
use Cwd;
$wd = cwd();
die "usage has changed, no arguments are needed, but \$us2 and \$us2sdev must be defined\n" if @ARGV;
$us2 = $ENV{'us2'} || die "can't find env variable us2\n";
$us2sdev = $ENV{'us2sdev'} || die "can't find env variable us2sdev\n";
print "us2 is $us2\n";
print "us2sdev is $us2... |
a545d65d63c378befa0230a45e66114ae69308954856f59bb2d89c9ab483c759 | Perl | 51,062 | 698 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie Kapusta
# - adapted from another script (Qi Wang, former student in C. Feschotte Lab)
# email : 4urelie.k@gmail.com
# version : 1.4 (see updates below)
#######################################################
# Date ... |
e40e7ff97134c1096520668db3b3b5e8e0024b845b6f9fdef36b962291f3676d | Perl | 53,905 | 1,026 | #!/usr/local/bin/perl -w
################################################################################
# launchQuantifications.pl 1.8.18 #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
91dcc3b8f369dfe39df39903015904c32c8c05a0e2df436421fc5252a630fb23 | Perl | 55,065 | 1,406 | #!/usr/bin/perl -w
#----------------------------------------------------------------------------
# Author : Aurelie Kapusta
# email : 4urelie.k@gmail.com
# PURPOSE : parsing Repeat Masker outputs, .out and/or .align
#----------------------------------------------------------------------------
use warnings;
use st... |
b2f4bb57d99ed9813130455596589f01274ea810f2fa9c34631f4d2444b10f1e | Perl | 64,141 | 1,380 | #!/usr/local/bin/perl -w
################################################################################
# runSSProtQuantification.pl 1.8.0 #
# Component of site myProMS Web Server #
# Authors: P. Poullet (Institut Curie) ... |
b57fc702032a15fede33e6a48e73877d698d18cc71985a8c3b32d1db022c11e5 | Perl | 64,631 | 1,220 | #!/usr/bin/perl
#######################################################
# Author : Zev Kronenberg (https://github.com/zeeev), for the v1.0
# Modifications by Aurelie Kapusta (https://github.com/4ureliek) after v2.0
# email : 4urelie.k@gmail.com
# Purpose : Originally writen to generate data (observed... |
272ad398a73dca8fd556b04a581a8cbca3d8b828822f405a0d266e844aff073e | Perl | 67,771 | 783 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
c3dd226dc54248d5d8c433ef91c20eea6c419fba40f9748a786cc58fe5b0c61a | Perl | 72,469 | 811 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
c38f285cd38c1c7a8de40ae88f3b8366d5185047e4668aeb934c1b863d8057a0 | Perl | 75,211 | 832 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
e4fb53f83c6714d1de0fd517d91ae21c627803da80b13c9103b7bb46117fd8b5 | Perl | 79,279 | 1,870 | #!/usr/local/bin/perl -w
################################################################################
# mapProteinIdentifiers.pl 1.5.7 #
# Authors: P. Poullet, G. Arras & F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
53d196ca2c6d5f9bc6bdb0701cf2bbeef4b5949a064a3185943cefd5de33a3b1 | Perl | 79,483 | 874 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
85f37f00a4b5c05bf8740d4f414fcc455c5d1dfffb1bbc3f0d327870920ae850 | Perl | 81,334 | 895 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
4aeb054bd29a88f980726abc6131cfef48ff2e85f5ad3620329551d4cb590b49 | Perl | 86,026 | 940 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
b6e1f3e17db6162513bf85b32fbe5e2b3c0a45939ffe23e6bbc26ddd216a7b3a | Perl | 87,509 | 966 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
5bb8e8e0bb00a6bf505b820db91688198281a79c0eaee8e0288b7d1f076b590d | Perl | 98,718 | 2,175 | #!/usr/local/bin/perl -w
################################################################################
# runMassChroQ.pl 1.9.15 #
# Authors: P. Poullet, V. Laigle, G. Arras, F. Yvon (Institut Curie) #
# Contact: myproms@curie.fr ... |
840ba96399d8132c6deabac786eee33bdbac54dba8c8aec9b1ddc88cc2b402b9 | Perl | 123,571 | 1,600 | ###############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
... |
55b4736b838273343388b89a1a29f4aa521b69012bbb73ddc8dda0ce55486969 | Perl | 128,408 | 2,662 | #!/usr/bin/perl -w
#######################################################
# Author : Aurelie Kapusta
# version : see below, $version
# email : 4urelie.k@gmail.com
# Purpose : Pipeline to analyse TE composition in features (exons of transcripts, coding or non coding, transcription factor binding sites, ChIP-seq ... |
0d7665fcc3532a24c5e4628737e3644de772b9137922cea6a184e4ba209ff1df | Perl | 143,496 | 2,895 | #!/usr/local/bin/perl -w
################################################################################
# runMaxquantImport.pl 2.0.9 #
# Component of site myProMS Web Server #
# Authors: P. Poullet, G. Arras, S. Liva (Institut ... |
1e20393a29b93fbbcb43fdb0e3012880c3196aacd5ec66510de74ddd55b8628d | Perl | 189,619 | 1,449 | #! /usr/bin/env perl
# Test that hmmpgmd is correctly applying bit score thresholds;
# in this case, the --cut_ga threshold, using an example that
# Rob Finn found as a bug in Jan 2011.
#
# This test creates its own small HMM database in $tmppfx.hmm
# create_test_hmmdb() writes three specific models to a file.
# Then... |
ebde1a8e0ccd59cf04dcd420b5e913ecf586bca3758df77643b57304ec708ea7 | Perl | 190,589 | 1,466 | #! /usr/bin/env perl
# Test that hmmpgmd is correctly applying bit score thresholds;
# in this case, the --cut_ga threshold, using an example that
# Rob Finn found as a bug in Jan 2011.
#
# This test creates its own small HMM database in $tmppfx.hmm
# create_test_hmmdb() writes three specific models to a file.
# Then... |
16857c16b2327a370b8d10f750c8fbd4d681fde6ea8e9987956f5c68ecec7c0f | Perl | 200,002 | 4,125 | #!/usr/local/bin/perl -w
################################################################################
# runXICProtQuantification.pl 2.19.10 #
# Component of site myProMS Web Server #
# Authors: P. Poullet, G. Arras, F. Yvon (Institut... |
49ca5d81054fdd20572294b9350b605d05e0df91da09a46fb8bde7fd6c1c172d | Python | 5 | 1 | 1111
|
584a3a1268c99ef99b39887515738eaf5c90b82fe81e2c18917fdda6af1ebba6 | Python | 8 | 2 | # TODO
|
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