sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d81fced294a29b55e9d7429dfe1d7f6b353a0aef788a07f01ca26a6808515b9f | NEURON | 15,839 | 364 | /* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ... |
fc7a71d4277122362aa454aaed62c0c98cec6d38d9023ea11ecb8e73c9853e39 | NEURON | 15,839 | 364 | /* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ... |
1a0c5b2b93991733d96bf396ee963cbb7ed9d60d7a07705d3acab01962a5aee5 | NEURON | 16,048 | 373 | /* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ... |
0f527f36ac18b359dc1b2ffe63f63b8f98b86fc8d2b731fd9373fcff2da28a5b | NEURON | 16,400 | 399 | /* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, ... |
fb7284ad9c5047e9d15960738ca5f442849dc7d1d68e2ebf1ae7675849d2b3bb | NEURON | 21,376 | 623 | COMMENT
/*
Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS'' ... |
683f03bdb97bcfc57c2d1b27e37b7e89fc9abb4bbf2c3c569521972616bcf83d | NEURON | 21,615 | 627 | COMMENT
/*
Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS'' ... |
0d629c0941cf33f334429d10138ed8f52b838be54761a72640c86028829a4343 | Perl | 116 | 12 | #!/usr/bin/env perl
use strict;
use warnings;
use URI::Escape;
while (<>) {
print uri_unescape($_);
}
exit(0);
|
0179e45a1f0fc9198efe1a425563d9444802615b9b06f5b13cc055483d9d2be1 | Perl | 153 | 8 | #! /usr/bin/env perl
use jellyfish;
my $mf = jellyfish::ReadMerFile->new($ARGV[0]);
while($mf->next_mer) {
print($mf->mer, " ", $mf->count, "\n");
}
|
8c6fb38acf6ea8fda39d707726c1fdcf8cc1c3c56da74e8acc436b8d56f9a55b | Perl | 174 | 8 | #! /usr/bin/env perl
use jellyfish;
my $qf = jellyfish::QueryMerFile->new(shift @ARGV);
for my $s (@ARGV) {
print($s, " ", $qf->get(jellyfish::MerDNA->new($s)), "\n");
}
|
5156544ceec1c88cf2b24d86c110c5b1dc54b8f2554c18d12b0f5b3418900b8d | Perl | 580 | 33 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;
my %opts = (n=>33088, s=>100);
getopts('n:', \%opts);
my $pseudo = .5;
my $tot = $pseudo;
my $err = $pseudo;
my $tot_last_out = -$opts{s};
my $state = 0;
my $mapq = 0;
while (<>) {
chomp;
if (/^Q\t(\d+)\t(\d+)\t(\d+)/) {
$tot += $2;
$err += $3;
if ($... |
ebdb9d9e6a29dbe84e7e929ce6146ea791bda1e6ef6eb895303b1fc2c5300a81 | Perl | 646 | 31 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 transcripts.fasta.transdecoder.gff3\n\n\n";
my $gff3_file = $ARGV[0] or die $usage;
main: {
open (my $fh, $gff3_file) or die $usage;
while (<$fh>) {
unless (/\w/) { next; }
my @x = split(/\t/);
my $type = $x... |
bba31d1aa826a77e141bf39bf9bbfcedd972575232aa818cff47e57508c4262e | Perl | 653 | 20 | #! /usr/bin/env perl
use strict;
use warnings;
use ExtUtils::MakeMaker;
mkdir('lib');
system('swig', '-c++', '-perl5', '-o', 'jellyfish_wrap.cxx', '../jellyfish.i');
my $jf_cflags = `pkg-config --cflags jellyfish-2.0`;
my $jf_libs = `pkg-config --libs jellyfish-2.0`;
my $jf_rpath = `pkg-config --libs-only-L jelly... |
49482a02fb9d0f5518f48cbcc4421ff21463ade8594ce2de61bb751dedb53856 | Perl | 781 | 38 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
my @files_to_keep = qw (cleanme.pl
... |
ce005f06178dbab089b77966c68a7f682a9bcf18c83edea313b4c83a68a28ef4 | Perl | 792 | 42 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
my @files_to_keep = qw (
cleanme.pl
runMe.sh
Trinity.fasta.g... |
a86ec6c5d68a54c4e8ad9f11da2da3630198f0d8755a9f3687f03dbcf7862d5b | Perl | 794 | 42 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
$|++;
my $usage = "\n\nusage: $0 gene_ID_list_file genes.gff3\n\n";
my $gene_ID_list = $ARGV[0] or die $usage;
my $gff3_file = $ARGV[1] or die $usage;
my $gene_obj_indexer_href... |
37253c323b053bde779555c8cd76d2ae514c455a90fe50f817061c0c9eff83c9 | Perl | 842 | 38 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
my @files_to_keep = qw (cleanme.pl
... |
455757cfac101b30f8cf4dd85799be82b48bfa806a834f2ceedf4f4ff029ec77 | Perl | 845 | 43 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
my @files_to_keep = qw (
cleanme.pl
genome.fasta.gz
pasa_ass... |
3684aa958055398053dee59a309dc820e184a3977ce565ba08dd88d05d6647c8 | Perl | 856 | 43 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
use Nuc_translator;
use File::Basename;
our $SEE = 0;
my $usage = "\n\nusage: $0 gff3_file\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my $gene_obj_indexer_href = {};
## asso... |
95a6e2bd161d25d9df5014c07d86eba651eeffe69ee3edc63eb157f7c4f02e21 | Perl | 925 | 41 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::Bin or die "error, cannot cd to $FindBin::Bin";
my @files_to_keep = qw (cleanme.pl
... |
1d4a7f98bf9fa766ea65a74057cc0c4792988ec5d7cf9fb966d361244d2d4bbd | Perl | 969 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 file.fasta numTopLongest [max_prot_length]\n\n";
my $file = $ARGV[0] or die $usage;
my $num_longest = $ARGV[1] or die $usage;
my $max_protein_length = $ARGV[2] || -1;
main: {
... |
1a74d4c97542a2c6a3ff166b975e081fac47ce2aa1098e983b1c7bf30ec87fce | Perl | 980 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use PWM;
my $usage = <<__EOUSAGE__;
#####################################################################
#
# --pwm <string> ... |
456253753efff2657a2cd3365aed9759e9c21d4faebafeda31bb65131513e61e | Perl | 993 | 31 | use strict;
use warnings;
# ===========================================================
# Author: Xiaokun Guo
# Date: 2023-11-27
# Description: Each line in the queryss.txt file contains a .queryss
# file generated for a protein using Foldseek.
# The output file isoform.foldseek.txt contains ... |
f6caddc618450a7a36e6cd0513e46e71976ce3c67178ca2fb9d97d43a2e8979e | Perl | 995 | 57 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 proteins.fa\n";
my $fasta_file = $ARGV[0];
unless ($fasta_file) {
die $usage;
}
my $fasta_reader = new Fasta_reader($fasta_file);
## make intervening stop codons fatal:
... |
0812bdf26e50f1d086de73c73b224941f7a1c4bded342d1492e5f02acc3028ea | Perl | 1,012 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
my $input_idx = shift;
my $done_input_idx = shift||die ("input IDX, basename of done IDX\n");
my $done_input = $done_input_idx;
$done_input =~s/\.idx$/.db/;
my $counter=int(0);
my (%hash_done,%hash_all);
open (IN,"$input_idx") ||die;
while (my $ln=<IN>){
$ln=~/^(... |
aac77a987f5012732e71028e308af592a53fa80c2e1ae82a575084c47af733fb | Perl | 1,028 | 52 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
my $usage = "usage: $0 transdecoder.gff3\n\n";
my $gff3_file = $ARGV[0] or die $usage;
main: {
my $indexer = {};
my $asmbl_id_to_gene_list_href = &GFF3_utils2::index_G... |
ea68d90e3e14f7119b5b56f7a5b9e43a6c9751bd8c5e6f9b4b3c045aef88fe9c | Perl | 1,152 | 65 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use PWM;
my $usage = <<__EOUSAGE__;
#####################################################################
#
# --features <string... |
66ed4eed8fcb8b57b72cd4e9595045992e837b523819fcf575bdaf824582d5e1 | Perl | 1,329 | 61 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
my $usage = "\n\n\tusage: $0 all_long_orfs.pep\n\n";
my $pep_file = $ARGV[0] or die $usage;
main: {
my %contig_to_longest_prot;
my $fasta_reader = new Fasta_reader($pep_file);
w... |
d93a1c43d2405b5f4edf2154df97081e1399592ed2a58b363e6b4d8f0b44bf1d | Perl | 1,373 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
my $usage = "usage: $0 transcripts_file [top_strand_only]\n\n";
my $transcripts_file = $ARGV[0] or die $usage;
my $top_strand_only_flag = $ARGV[1] || 0;
main: {
my %base_count... |
55db3e23f9fbfb7a794e9cd8b282c4796e1f222ac162538563d81d9f6365428e | Perl | 1,639 | 74 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
my $usage = "\n\nusage: $0 gff3_file\n\n";
my $gff3_file = $ARGV[0] or die $usage;
main: {
my $gene_obj_indexer_href = {};
my $asmbl_id_to_gene_list_href = &GFF3_u... |
773221e582c6f0de113f791633e2c05a04f2b3381322d328a0e56cba34d54450 | Perl | 1,836 | 65 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use Fasta_retriever;
use GFF3_utils2;
use Carp;
my $usage = "usage: $0 file.GFF3 genome.fasta > file.GTF\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my $genome_fasta = $ARGV[1] or die $usage;
main: {
... |
7684e4d07424b75236d78632fe93ecafdc4ddff15b33a3b597726908759da709 | Perl | 1,868 | 72 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 hexamer.scores\n\n";
my $hexamer_file = $ARGV[0] or die $usage;
open(my $fh, $hexamer_file) or die "Error, cannot open file $hexamer_file";
my $header = <$fh>;
my @hex_scores;
while (<$fh>) {
chomp;
my ($framed_kmer, $kmer_count, $prefix... |
2096b96f9771611cf2730b05a39ac135e7380c51c89f5c07e8c06f6ad7d2bef6 | Perl | 1,946 | 74 | #!/usr/bin/env perl
use strict;
my $nmeryl = "/work/meryl/FreeBSD-amd64/bin/meryl";
my $omeryl = "/work/canu/FreeBSD-amd64/bin/meryl";
sub makeSequence ($$$) {
my $name = shift @_;
my $seq = shift @_;
my $seqLen = length($seq);
my $lines = shift @_;
my $bases = 0;
if (-e $name) {
... |
69d1b334a1748deab23a16b6d7258adbaa234f90fd29638b55e98f444361ec06 | Perl | 2,023 | 99 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
my $usage = "usage: $0 cufflinks.gtf\n\n";
my $cufflinks_gtf = $ARGV[0] or die $usage;
main: {
my %genome_trans_to_coords;
open (my $fh, $cufflinks_gtf) or die "Error, cannot op... |
a3a7c9a61af33ffcbb5bdaeb21578fe215f36ff4a5a13369dbc3bcedcd8ea81f | Perl | 2,068 | 80 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 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
# (... |
e505c85e96cf2a328e5e50ed82d22994eb5a2b7f16db16a594b805d8fd1be2d2 | Perl | 2,104 | 84 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2022
# Convert SUPPA2 ioe file to EANMD AS_events input list. TransIOE2SEinput.pl v0.100 2024/02/27
# hukaining@gmail.com
#
use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use re 'eval';
our $opfn="";
our $exlen = 100;
GetOptions("o=s" => \$opfn,"l=i... |
3bc32fd223dd504370df716f4839bac1d8b063e9bd100b4bfdc8bf04727af72b | Perl | 2,178 | 100 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
my $usage = "usage: $0 cufflinks.gtf\n\n";
my $cufflinks_gtf = $ARGV[0] or die $usage;
main: {
my %genome_trans_to_coords;
open (my $fh, $cufflinks_gtf) or die "Error, cannot open file $cufflinks_g... |
0777bd7a520f580a79fd217ac0771138d996bae190cd082fb3b237b3c632e62c | Perl | 2,294 | 89 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2022
# Convert SUPPA2 ioe file to EANMD AS_events input list. TransIOE2IRinput.pl v0.100 2024/02/27
# hukaining@gmail.com
#
use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use re 'eval';
our $opfn="";
# our $exlen = 100;
# GetOptions("o=s" => \$opfn,... |
9f64287cc07c6b3bfb8e208bea033ba830476e45fdc618cadb228a3b176ff9f7 | Perl | 2,337 | 108 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 feature.scores [num_ROC_threshold_intervals=10]\n\n";
my $feature_score_file = $ARGV[0] or die $usage;
my $num_intervals = $ARGV[1] || 10;
main: {
my ($min_val, $max_val);
my %cat_type_to_scores;
print STDERR "-parsing scores\n";
... |
fdee5f8ac0ce7c8e74f09e91efa6e1fa03a4fb4b3ea1b4e12b4bc6e671355360 | Perl | 2,394 | 64 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2021
# FilterATG of EANMD outCombined file v1.01 2021/10/01
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use re 'eval';
our $opfn="filterATGOut";
my $verbose;
our $startcodon="ATG";
#GetOptions("i=s... |
eaa285859b73a627a42ab2ac432deb115e82b92744501d34aa6673e820403331 | Perl | 2,426 | 119 | #!/usr/bin/env perl
################################################################################
#
# This file is part of meryl, a genomic k-kmer counter with nice features.
#
# This software is based on:
# 'Canu' v2.0 (https://github.com/marbl/canu)
# which is based on:
# 'Celera Asse... |
6ced0f42e5830e46fa9225bd3125736924899821e19e30d10388c6a88796319a | Perl | 2,456 | 104 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2022
# Convert SUPPA2 ioe file to EANMD AS_events input list. TransIOE2A3SSinput.pl v0.100 2024/02/27
# hukaining@gmail.com
#
use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use re 'eval';
our $opfn="";
our $exlen = 100;
GetOptions("o=s" => \$opfn,"l... |
855cce2c7ea08f66ef717e7b5e22ac2ff9c996cbea06900d5bea597e9d97f1ea | Perl | 2,456 | 104 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2022
# Convert SUPPA2 ioe file to EANMD AS_events input list. TransIOE2A5SSinput.pl v0.100 2024/02/27
# hukaining@gmail.com
#
use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use re 'eval';
our $opfn="";
our $exlen = 100;
GetOptions("o=s" => \$opfn,"l... |
ae814c7d0c724643d8ebb3323ddeb8673b0b66f8aced1deada58ddd25a164fc9 | Perl | 2,511 | 93 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
$|++;
my $usage = "\n\nusage: $0 gff3_file\n\n";
my $gff3_file = $ARGV[0] or die $usage;
main: {
my $gene_obj_indexer_href = {};
my $asmbl_id_to_gene_list_href = ... |
d684151008f480ec4f7536907fcc6c6373cf49deee90585af4267819ca17cac2 | Perl | 2,515 | 113 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use Fasta_reader;
my $usage = "usage: $0 cufflinks.gtf genome.fasta\n\n";
my $cufflinks_gtf = $ARGV[0] or die $usage;
my $genome = $ARGV[1] or die $usage;
main: {
print STDERR "-parsing GTF: $cufflinks... |
de28f570b96c09b9bd05173073accac0749a251f5bc984151aa5aaed9c0961e3 | Perl | 2,689 | 79 | #!/usr/bin/perl
use strict;
use warnings;
my $input_file = shift or die "Usage: $0 input.gtf\n";
open my $fh, '<', $input_file or die "Cannot open file: $input_file\n";
my %transcripts;
# First pass: Collect exons and CDS by transcript
while (<$fh>) {
chomp;
my @fields = split /\t/;
next unless @fields ... |
8bda74a2ba4124964faef638a06bee326cde67de1df2c904f3f6efec053a46fb | Perl | 2,851 | 128 | #!/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 Fasta_reader;
use Nuc_translator;
use PWM;
my $usage = <<__EOUSAGE__;
#######################################################... |
7033abe1120799f143b7ea50efc5986f58f07986a1f6452c46e8be4359308e9a | Perl | 2,960 | 114 | #!/usr/bin/env perl
use strict;
use warnings;
use List::Util qw(min);
my $usage = "\n\n\tusage: $0 feature.scores.roc\n\n";
my $roc_file = $ARGV[0] or die $usage;
main: {
my $auc_outfile = "$roc_file.auc";
open (my $ofh, ">$auc_outfile") or die "Error, cannot write to $auc_outfile";
my %data... |
b0e1fedb14dd7bd801f4b2a76cece3e34a80bc4e2efea3bc3bca30d2b4a659ba | Perl | 3,038 | 106 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 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
# (... |
0506e3deba8c48755b49597b5038c692d80ac994110166e034f0937b7525f4e3 | Perl | 3,042 | 92 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2021
# Transformat NMD combined result to Fasta file. (Combo2Fa)v0.16 2021/06/07
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
# use Time::HiRes 'time';
#use Parallel::ForkManager;
#our $MAX_processes=2;
#my $pm=Parallel::For... |
61609a564f80093f067a02dcd622de37aab1a793203c31b40f7631155eee01e3 | Perl | 3,179 | 144 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
use List::Util qw(min);
my $usage = "usage: $0 CDS hexamerScores\n\n";
my $MAX_REPEAT_COUNT = 3;
my $cds_file = $ARGV[0] or die $usage;
my $kmer_scores_file = $ARGV[1] or die $usa... |
f8b0ff82506d56c02b6cd81ef0f7acb10710589b179d7617e6c47f7e3ff10175 | Perl | 3,205 | 76 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2022
# Filter EANMD SE outCombined file v1.21 2022/01/16
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use re 'eval';
our $opfn="filteredOut";
my $verbose;
our $startcodon="ATG";
#GetOptions("i=s"=>\... |
1e6c11a4cec76a830411e59019438d9150bbdafffe26fa5884971d5078678f6b | Perl | 3,378 | 133 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 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
# (... |
3b9ab327925dc2da25483bcb1a7a063b62494537cb4f15cc43b8da4dfeb09264 | Perl | 3,408 | 82 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2025
# Filter EANMD A3SS outCombined file v1.10 2025/03/07
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use re 'eval';
our $opfn="filteredOut";
my $verbose;
our $startcodon="ATG";
#GetOptions("i=s"=... |
db9212786d81f554c1f04e3c742f46eb2815cd6410becacf211254279a441a9d | Perl | 3,414 | 82 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2025
# Filter EANMD A5SS outCombined file v1.10 2025/03/07
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use re 'eval';
our $opfn="filteredOut";
my $verbose;
our $startcodon="ATG";
#GetOptions("i=s"=... |
2361b57c0fea8e827543802af5c9ae2c79a9a6837b7e530307b86b694462473c | Perl | 3,487 | 118 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Carp;
use Nuc_translator;
use Fasta_reader;
my $usage = "\n\nusage: $0 fasta_file [DEBUG]\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $DEBUG = $ARGV[1] || 0;
my $WMER_SIZE = 5;
my %CAPTURED_WMERS;
my $MAX_PER... |
90e1ac9759ae9565ff6554b8aac1a0397ad953a7a5264e3b91bf9d6bcf1d80dc | Perl | 3,807 | 99 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2022
# Filter EANMD SE outCombined file v1.30 2025/03/06
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use re 'eval';
our $opfn="filteredOut";
my $verbose;
our $startcodon="ATG";
#GetOptions("i=s"=>\... |
f6c525208d898b58d19df57d13f2c531d0b3051d579861d29073a50f4efa4ad5 | Perl | 3,857 | 133 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (... |
50016a982baeaabe7440577de0748bf402a2717d8c8a892184363aa233bf933a | Perl | 3,888 | 152 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
## hexamer stats
my %framed_kmers;
my %background_base_probs;
my $usage = "usage: $0 targetCDSs base_probs.dat\n\n";
my $target_CDS = $ARGV[0] or die $usage;
my $base_probs_dat_f... |
15cdf4202421ad50468c8bb3936032576004e3e223e7d0feb2ec5255d9a3fa75 | Perl | 4,008 | 183 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Fasta_reader;
use Nuc_translator;
use PWM;
my $usage = <<__EOUSAGE__;
#######################################################... |
61f4c0618efd3943ad683b19f6552c7427b75db32f61b05ddcfc6517bbe3a713 | Perl | 4,107 | 132 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (... |
9ebbcd377d0f16f52a4041a4b98ccb02b23a63a40d468d5924500fbf1f6cf6fe | Perl | 4,267 | 147 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib ("$FindBin::Bin/../PerlLib");
use Pipeliner;
my $utildir = "$FindBin::Bin/PWM";
my $help_flag;
my $pwm_left = 20;
my $pwm_right = 10;
my $usage = <<__EOUSAG... |
02e139c9cf1c8b96a132b5f7b9fca09444f11a11fa818cd13bf09f05c74e9b68 | Perl | 4,725 | 167 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use Fasta_reader;
use GFF3_utils2;
use Carp;
use Nuc_translator;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
################################... |
6eec1d4894c385ee236b0ccb84609d299dac3cf7e4387f079d0267c16277b5aa | Perl | 5,284 | 197 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use PWM;
use List::Util qw(shuffle);
my $pct_features_retain = 30;
my $usage = <<__EOUSAGE__;
#############################... |
a0c3132170c9739d791287e56efc6ca1a87b1df11ff460ccd6efa452831a4c7c | Perl | 5,629 | 248 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
use PWM;
my $pwm_left = 20;
my $pwm_right = 10;
my $usage = <<__EOUSAGE__;
###########... |
cc763f3b1602d2b9dbbddedcee0897d27ebb9c44fd0c593b2150850aef04cae1 | Perl | 6,137 | 222 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::Bin/../../PerlLib");
use Fasta_reader;
use Nuc_translator;
use PWM;
use Process_cmd;
my $num_rounds = 5;
my $fraction_train = 0.75;
my $atg_positio... |
166e7c29f50a4fb9a32bf80d371d968ac76044f72b7ca49f15ee90f0e5186d86 | Perl | 6,361 | 239 | #!/usr/bin/env perl
use strict;
use warnings;
use List::Util qw(sum);
use Getopt::Long;
use Pod::Usage;
use utf8;
# 版本信息
our $VERSION = '1.01 2025-03-06';
# 命令行选项处理
GetOptions(
'help|h' => \my $help,
'version|v' => \my $version,
'output|o=s' => \my $output_file,
'dj|d=i' => \my $dj_threshold
) or... |
2a110ceb507a40b0b1d110a1e08faee87452f8d692d1bde906e5e89c4aee1342 | Perl | 6,605 | 210 | #!/usr/bin/perl -w
use warnings;
use strict;
#use Data::Dumper;
print STDERR "\n\nUsage: MergeBigFiles.pl\n",
"1: FileRgx (single quoted perl rgx to match files)\n",
"2: FileDir (directory to parse files)\n",
"3: OutTag (file output tag)\n",
"4: Header_lineNumber (indicating whether files have header; default=1)\n",
... |
ea47b13edfb00b8b6389e80ee32dafadeddfadce2240c4bf3c1dbf83534ad1ac | Perl | 6,672 | 257 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (... |
cd7203534aaa55902a035272701a01e6e7ee25da35d7d0ce4bcc3adfe57291a7 | Perl | 7,042 | 251 | #!/usr/bin/env perl
###############################################################################
#
# This file is part of meryl-utility, a collection of miscellaneous code
# used by Meryl, Canu and others.
#
# This software is based on:
# 'Canu' v2.0 (https://github.com/marbl/canu)
# whic... |
e9b2112b41db83d1f3e0a43888c4469b1dfdf68ad0791ba883b047f7389d6fb4 | Perl | 7,138 | 212 | #/usr/bin/perl -w
use strict;
use Cwd 'realpath';
use Switch;
use File::Find;
use File::Basename;
use File::Path;
use File::Spec;
use FindBin qw($Bin);
my $baseDirectory = "/pub/ntustiso/Data/SRPB1600/";
my $t1Directory = "${baseDirectory}/data/";
my @suffixList = ( ".nii.gz" );
my @subjects = <${t1Directory}/sub... |
ab3fba7e5c7363ea64e0c8846873f3c5273e4ea89869abb17f5211457d4781c2 | Perl | 7,937 | 235 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2022
# EANMD Filter the rMATS results and output an EANMD AS_events input list. EANMD_fileterPSI v1.250 2023/01/10
# hukaining@gmail.com
#
#use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use List::Util qw/ min max sum /;
sub mean {
return sum(@_)/... |
d413b836445d7fbe4db582182d64ca32224d839de49bf478115783f9f41af7de | Perl | 8,194 | 239 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2026
# EANMD Filter the rMATS results and output an EANMD AS_events input list. GetSEinput.pl v1.310 2026/04/13
# hukaining@gmail.com
#
#use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use List::Util qw/ min max sum /;
sub mean {
return sum(@_)/@_;... |
a300b20d8b09cee0aee2422905d08b7c5007ba3d62078476876147e5ba49d664 | Perl | 8,549 | 270 | #!/usr/bin/env perl
###############################################################################
#
# This file is part of meryl-utility, a collection of miscellaneous code
# used by Meryl, Canu and others.
#
# This software is based on:
# 'Canu' v2.0 (https://github.com/marbl/canu)
# whic... |
d48082d7cc2cd7539e78610b1c3e7ff75b57d8b42813c42d41f11fddd98cd1d9 | Perl | 8,787 | 255 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2023
# EANMD convert rMATS results to an EANMD AS_events input list. GetA3SSinput v1.100 2023/02/06
# hukaining@gmail.com
#
#use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
# use List::Util qw/ min max sum /;
our $opfn = "";
# our $opnmdinput="";
our $... |
1c5e3eb25b4109f551a25d7d74eb190ec9ce30c579c6d9c4a7f497ea8b4e2dd7 | Perl | 9,248 | 309 | #!/usr/bin/env perl
use FindBin;
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Data::Dumper;
use List::Util qw (min max);
use File::Basename;
use lib ("$FindBin::RealBin/PerlLib");
use POSIX qw(ceil);
use Gene_obj;
use Nuc_translator;
use Fasta_reader;
use Longest_o... |
86221c84b18207b12e2fa57617aed6e6d476f0bb7ecdd02072eb8421ea3ae964 | Perl | 9,309 | 319 | #!/usr/bin/env perl
##
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 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
#... |
62011ddc35b8de67bed697f2f6f00b0fed915c0ad722c85ee636bfad8546d191 | Perl | 9,469 | 274 | #!/usr/bin/perl
#AUTHORS
# Kaining Hu (c) 2023
# EANMD convert rMATS results to an EANMD AS_events input list. GetA5SSinput v1.100 2023/02/06
# hukaining@gmail.com
#
#use 5.0100;
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
# use List::Util qw/ min max sum /;
our $opfn = "";
# our $opnmdinput="";
our $... |
43b788df9f242eafd26b81e6ab5a9d450de50f50ce82b99e211900e936b072d7 | Perl | 10,032 | 333 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Fasta_reader;
use Nuc_translator;
use Carp;
use Data::Dumper;
use List::Util qw (max);
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use PWM;
use File::... |
6c235df72a27eefce95a199d7f0fca682e5cf93f28378288946658d5afa7aeec | Perl | 10,149 | 372 | #!/usr/bin/env perl
use strict;
my $nmeryl = "/work/meryl/FreeBSD-amd64/bin/meryl";
my $omeryl = "/work/canu/FreeBSD-amd64/bin/meryl";
testBuild();
testUnion();
testIntersect();
exit(0);
sub testBuild {
system("mkdir new");
system("$nmeryl k=22 count n=5000000 DATA/ecoli-dh.fasta output new/ecoli-dh");
... |
2650656a5fa42b5ac8ba6e0a87cbd54b1c66cfeaaa101fa36803b0ef5c86f391 | Perl | 11,624 | 414 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Carp;
use Data::Dumper;
use DelimParser;
use List::Util qw (max);
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
require "overlapping_nucs.ph";
srand(12... |
6f5c5fdbcd5b8cac3fe4ae2bd86c50bfd790e8cbf80e0ad5118d822888f827c3 | Perl | 12,743 | 315 | #!/usr/bin/perl -w
# conlleval: evaluate result of processing CoNLL-2000 shared task
# usage: conlleval [-l] [-r] [-d delimiterTag] [-o oTag] < file
# README: http://www.clips.uantwerpen.be/conll2000/chunking/output.html
# options: l: generate LaTeX output for tables like in
# http://cnts... |
9177103887794aed0891dc4056f7948a7e1b3046453b9e723b2f4f9f69ac6ccb | Perl | 12,897 | 410 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils2;
use Data::Dumper;
use Fasta_reader;
my $usage = "\nusage: $0 cdna_orfs.genes.gff3 cdna_genome.alignments.gff3 cdna.fasta [DEBUG]\n\n";
my $cdna_orfs_gff3 = $ARGV[0] or die $usage... |
ff64173be706a34da9172571c5f6b077bf27bf899dc28d2f2ff9addf43ff4b69 | Perl | 14,881 | 359 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2022
# Transformation NMD unique flag results into GTF v1.200 2025/01/13
# hukaining@gmail.com
use strict;
use warnings;
#use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
#use Parallel::ForkManager;
#our $MAX_processes=2;
#my $pm=Parallel::ForkManager-... |
9bfe6115ea8352d6478acf1a7164625ab0053e0f0ad6de03b584b77fbe7b95b6 | Perl | 161,767 | 3,368 | #!/usr/bin/env perl
#AUTHORS
# Kaining Hu (c) 2021
# Get NMD transid from GTF and genome for MM10.EnsGene (Multiple Threads version)v1.354 2021/09/30
# hukaining@gmail.com
use strict;
use warnings;
use 5.010;
use Getopt::Long;
use Pod::Usage;
use Time::HiRes 'time';
use Parallel::ForkManager;
our $MAX_p... |
bdf6725b6241d393ffc02193dffec37f2943af6eeb498902ec55a00587924a1c | Perl | 200,000 | 3,193 | #!/usr/bin/perl -w
#
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
#
# This file is part of Bowtie 2.
#
# Bowtie 2 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
# (... |
334359b90efed75da5f0ada1d5e6b256f4a6bd0aee7eb39c0f90182a021ffc8b | Python | 1 | 1 | # |
0486028fa4d1cc658211b606e5935a4c74386a6e9cf5055b812f3484b1b46e57 | Python | 6 | 1 | # init |
0e73e2035f7c07ee8710896346b79fc949a1db4392ec0d9d81bd05104d316e69 | Python | 10 | 1 | # init.py
|
2645ab4e30113fac9efe3f617d658565844101badb5cd4f7ae16b9d7ed9a9c58 | Python | 11 | 1 | ROOT = '.'
|
e0a63b09a42a295b03b3360d694c515d6e00f5951281b20b81627456fb921756 | Python | 11 | 1 | eps = 1e-8
|
ab3f3cdd96b0de714abf67c354c9e0d93b18f45c58eee8ef918c37fd10d3b143 | Python | 15 | 1 | # flake8: noqa
|
eb524fbb292ded7e99ccc49499e59a72f09d78b9faea5d791e309906312669a2 | Python | 15 | 1 | # Test package
|
df69c4040d846aea388ea564b3b275030e5987130015c539890380cc43c824bd | Python | 16 | 3 |
import pytest
|
1785bca1275d94ce7e136f02c318e572f66484dea35ce934969a55c4a34f2a09 | Python | 18 | 1 | import deep_events |
10c333c417b01a93142b157a0ec8f3556be4cda1e6e616cb34d8e1b580f379fb | Python | 19 | 1 | #!/usr/bin/python
|
2afd8429f09b3e5866cb267154fd37ff527cec603c083da6fd19e039879456c6 | Python | 19 | 1 | VERSION = "2.77.1"
|
3f3e9977cda630d549df81605808756e9323e63da893a22b8bcae621f5c4e3f1 | Python | 19 | 1 | from ._vis import * |
71864a7a066e35207fa8fda1e43c8b56660329b6a388fb48615fd60f7fce90fc | Python | 19 | 1 | """__init__.py."""
|
d41ba769cf3e1a75f721a5ab65ffc04c7cb0e6b638ffeb386c6ecf04a8b6fdaa | Python | 19 | 1 | from ._cli import * |
838189060d61aad49e6f4f2c1eddb332ef81f5bef78ddbab9223df8f83954125 | Python | 20 | 2 | from .log import *
|
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