sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3d54b3c8b17c98223f558d3a99710f62ece8ce701fbb2f8ce18c9c454002d1f1 | Perl | 2,801 | 111 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:t:q:n", \%opt);
$threads = 1;
$minq = 10;
$die = "
sciMET_rmdup.pl (options) [namesort bam file]
Performs barcode-aware duplicate read removal.
Duplicate reads will be chosen based on the longest
aligned read.
Options:
-O [STR] Output prefix (def = in... |
a5808e906758c673739380da5186cabcf09290c7e22aa5744e27999d0e077480 | Perl | 2,862 | 120 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:t:q:pr:N", \%opt);
$threads = 1;
$minq = 10;
$die = "
sciMET_rmdup_pe.pl (options) [namesort bam file]
Performs barcode-aware duplicate read removal.
Paired end alignment mode only.
Outputs a name-sorted bam.
Options:
-O [STR] Output prefix (def = in... |
96d0c7577ea14b2664f952bf2c697a7fd6f92b15ee4ea867c9aa8661c78aa4c0 | Perl | 3,011 | 195 | #! /usr/bin/perl -w
use strict;
use warnings;
use List::Util qw(sum);
my @line;
my $nm1 = 0;
my $nm2 = 0;
my $snp1;
my $snp2;
my $score1 = 0;
my $score2 = 0;
my @snps1 = ();
my @snps2 = ();
my @tags1 = ();
my @tags2 = ();
my @tagname1 = ();
my @tagid1 = ();
my @tagname2 = ();
my @tagid2 = ();
my $preread = "";
my $pr... |
7eb22266c11ab09558b785362d52a9a1e1348625c070923e972eda4208fae5a7 | Perl | 3,031 | 110 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("F:O:", \%opt);
#defaults
$die = "
Usage:
sciMET_pairwise.pl -F [chroms] -O [output file] 2> [logfile of progress]
Produces all-by-all cell overlap and shared cytosine methylation.
Options:
-F [DIR] Directory with methylation by cell for each chromosome (... |
f9f85f7892f80b07ea200b698608d481302d7a9ed541404da6b5152f9f7de6d3 | Perl | 3,037 | 88 | #!/usr/bin/perl
#chr10 101288606 66.67 1 2
use Getopt::Std; %opt = ();
getopts("O:F:A:C:R:f:v", \%opt);
$die = "
sciMET_aggregateClusterCov.pl -O [output folder] -A [annot for cells to clusters] -F [cov file folder]
Optional: -C [context] - def = CG
-R [chrom] - only run this chromo... |
9e37faada45671016f038f8bfe5604989cffce9b658a156f93bde7aa9e041ba9 | Perl | 3,066 | 149 | #!/usr/bin/perl -w
# smoothpred
# Jens Erik Pontoppidan Larsen
# 2004.05.17
# Applies a running averaging window to prediction data.
# New version with asymmetric windows in the beginning and the end of the file
# jepl 2004.10.21
#
# Import libraries
#
use Getopt::Std;
use strict;
use English;
use vars qw... |
5a039496f113e85778090454c1c84246ad98f84f5b4ca241fe6b4840061e649d | Perl | 3,260 | 84 | #!/usr/bin/env perl
# Convert primer design file from illumina manifest format to BEDPE format
# Usage: manifest2bedpe.pl < TruSight-Myeloid-Manifest.txt > trusight_myeloid.bedpe
use strict;
use warnings;
use Tie::IxHash;
my $debug = 0;
my $current_block;
my @column_headers;
my %required_column_headers = ("Probes" => ... |
7b6879712505e421019a73f474d28d454ec8deaa9e4d95cf83fdfe8e7241dfc8 | Perl | 3,378 | 144 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("C:W:M:O:w:L:F:", \%opt);
#defaults
$minCells = 0.75;
$minCov = 20;
$minFrac = 0.75;
$die = "
sciMET_filtMtx.pl (options) -C [coverage matrix] -M [methylation or ratio matrix] -O [output prefix]
Options:
-C [STR] Coverage matrix (req)
-M [STR] Methylati... |
cd8d2cf7dfb1bae05d4e0769b180f4daf220d3409790b780823589de51be2dca | Perl | 3,439 | 122 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:B:1:2:", \%opt);
$die = "
sciMET_speciesSplit.pl -B [barnyard_compare cell stats file] -1 [trimmed read 1] -2 [trimmed read 2] -O [out prefix]
All options required - will split fastq files by species.
";
if (!defined $opt{'O'} ||
!defined $opt{'1'} ||
!def... |
b4cee80c030ff9e312ec3bae8d5db7c221337ddb38818eb573700e13868a9073 | Perl | 3,579 | 129 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e469daa1819132ad5535dc6a05498d2ce346710d4464169e594bfbb641c66b21 | Perl | 3,803 | 211 | #! /usr/bin/perl -w
# assign reads and also tabulate methylated base versus non-methylated base
# ============================================================
# z unmethylated C in CpG context
# Z methylated C in CpG context
# x unmethylated C in CHG context
# X methylated C in CHG context
# h unmet... |
1363630bf21cd09a2dc537c1e2365f22db4399eeee4a952e13c06ff0fb16f024 | Perl | 3,815 | 128 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("w:h:O:A:G:HS:", \%opt);
$width = 5;
$height = 4;
$die = "
sciMET_plotGeneByAnnot.pl (options) geneByAnnot.meth.txt
Will make a dotplot of targets x annotations from the file
produced by sciMET_getGeneMeth.pl
If 1 or more gene/target names are provided it will ... |
ce6a5ec2cf0848ab74bbc19e997871c710e0ec1586a680f2a8aa0422d95694d6 | Perl | 3,839 | 127 | #!/usr/bin/perl
=head1 Name
svg2xxx.pl -- convert SVG figure to other formats
=head1 Description
This program convert SVG files by invoking batik-rasterizer.jar, its advantage
is caculating the fiure pixel width and pixel height automatically.
The png format is a popular format which has excellent performance on... |
d9c4c78540dbeccce12c9312c4ea55cf059e5c0667a33119866af4be442f97ea | Perl | 3,863 | 123 | #!/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
# (... |
f5995fd52862e30d282ae56da2bf7e4f96c5e14ae14b77391b4fe093117ee09d | Perl | 3,888 | 144 | #!/usr/bin/perl
#defaults
$featureWin = 100;
$minSize = 1000;
$maxSize = 50000;
$upstreamSize = 0;
$upstreamWin = 0;
$downstreamSize = 0;
$downstreamWin = 0;
use Getopt::Std; %opt = ();
getopts("N:m:M:S:s:E:e:", \%opt);
$die = "
sciMET_featuresToScanBed.pl (options) [Bed of peaks or features] [output bed file]
De... |
491ab8ef55ba6f73eaee992d21f65bae4010bda38469ea0fe1a58dd54b688d27 | Perl | 4,082 | 143 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:X:N:B:C:o:d", \%opt);
$die = "
sciMET_cellCall_contextExtract.pl (options) [folder with cellcall files]
Options:
-O [DIR] Output directory for new cellcall files (def = input directory)
-C [CG/CH] Context that will be searched. Can also search custom... |
80152b66b4c0b00075f482f6374e10568b5f935b540acb3ba6cb74928b78b0a9 | Perl | 4,378 | 150 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
05eeb718c05a2b1b0deb2dd875ef664cb68007f772a0f8fc3fd06b81b516f0aa | Perl | 4,458 | 230 | #!/usr/bin/perl -w
# #
# Script ASTA-Seq2.pl #
# #
# #
# Input : List of reads with gene,SNP,CG (COMPACT)#
# Output... |
053ca9fc6ff8bcf111ba39a8938d4cb30c61644a1c5b91fce2fd20f1eebfbd5e | Perl | 4,591 | 140 | #!/usr/bin/perl
#
# tophat_bam_xsA_tag_fix.pl
# xwei 03/24/2014
# reads a bam file generated by tophat and fix the XS:A:+ or XS:A:- tags for tophat version 2.0.8
# check the flag field to decide "+" or "-"
#for cases where the mate is unmapped (flag 8) if the read is the first in the pair (flag 64), and maps ... |
1381bcd6f51d8ffe412c997fba8da1aac5c6e2eeba2dd70ba773e59daa6f68dd | Perl | 4,594 | 142 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("F:B:A:a:O:m:", \%opt);
# defaults
$minCov=10;
$die = "
Usage:
sciMET_getWindowMeth.pl -F [chromosome meth call folder(s)] -O [output prefix / folder] [gene1] -B [Bed of targets]
Required options:
-F [STR] Folder with chromosome-split methylation calls for... |
91e6b8387bd264ad5f34bb816dc10f03338c338b6e0fdf86ecdba43ff3bfc296 | Perl | 4,800 | 131 | #!/usr/bin/perl
use strict;
use warnings;
use 5.010;
use List::Util qw[min max];
my $col1;
my $col2;
my $col3;
my $col4;
my $col5;
my $col6;
my $col7;
my $col8;
my $strand;
my $name = "Veno";
my $col11;
my $read_start;
my $read_end;
my $chr;
my $col15;
my $start;
my $end;
my @rest;
my $first_strand;
my $first_name = ... |
122c984761fef33340a434c184a488dd72143015bf765212d84a48514a9cace1 | Perl | 4,914 | 134 | #!/usr/bin/perl
$die = "
sciMET_aggAlign.pl [alignment_stats_file] [file for separate run] ...
Each file must only include reports from iterations
of a single run, not multiple. (ie all iterations of
reads 1 and 2 from the same sequencing run)
";
if (!defined $ARGV[0]) {die $die};
$r1_total = 0; $r2_total = 0;
$r1... |
5115c4dd752a773b8e78f09745e4863c4648f59b630bcbff68e9f4d7d3090a4d | Perl | 5,045 | 168 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e365af65254a6db361e057b9f9ba4df3b606609bf91b5a735d7b4bd6c5101c6f | Perl | 5,486 | 185 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("A:F:O:G:S:s:E:Vm:", \%opt);
# defaults
$refGene = "/home/groups/oroaklab/refs/hg38/hg38.refGene.txt";
$startPad = 20000;
$endPad = 20000;
$minCov = 50;
$die = "
Usage:
getGeneMeth.pl -F [chromosome meth call folder] -O [output prefix] [gene1] ... [chrN:#-#] ...... |
f3e4c49e82e365d8df7f3d06b14bdc5248594f74756fc29afb81704a9459a920 | Perl | 5,507 | 178 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
my %data = ();
my %opts = ();
my $version = 0.0.23;
$opts{reference} = "hs37d5.fa";
$opts{samtools} = "samtools";
my $optResult = GetOptions(
"reference=s" => \$opts{reference},
"samtools=s" => \$opts{samtools}
);
checkOptions... |
448992de50171c268ec42312beeaee7f462e9b6b8345f1f01312f749e1136ed4 | Perl | 5,551 | 178 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e3ba8e8f7ba2ecc12f413e3421927529ec215c15abedfde875ea45e6002049df | Perl | 5,631 | 178 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
my %data = ();
my %opts = ();
my $version = 0.0.23;
$opts{reference} = "/home/arthurz/scratch_arthur/20.04.07.Numt.1kg/ref.GRCh38_full_analysis_set_plus_decoy_hla/GRCh38_full_analysis_set_plus_decoy_hla.fa";
$opts{samtools} = "samtools"... |
1f2947bc145605fa920f8afd0be7a23c859d7bf1c86d910b32e5add098a84a79 | Perl | 5,854 | 199 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e6bf4fb80532f2888b257af177c9ed1834381ca318d744d3f824f8132f65c9d4 | Perl | 5,952 | 212 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use GD::Simple;
use cworld::dekker;
my $tool=(spli... |
1b5ea1233c2b2bb18bb31d26c71d4fc6d2c9b66cdff55cd73d9474ff4207e176 | Perl | 5,976 | 248 | #! /usr/bin/perl -w
# process VCF file to perform
# 1) call consensus
# 2) remove clusters of snps that overlap with deletions
# 3) imputation of missing genotypes based on consensus
use Getopt::Long;
use strict;
use warnings;
use List::Util qw(first sum);
my $vcf;
my $geno = 0.8; # non-missing rate
my $freq = 0.8; #... |
34ed239a8ab71233fde5e28f9df2e359a3f59d63fbe023ee0d7fa221ca1d9788 | Perl | 6,103 | 198 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e1d339d816790965936526b5da5dd078a45fe27fd50d55626b25e06a5cce4eab | Perl | 6,164 | 193 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
582b4c1cdaae2afd7d3f4b8f4e866899a0421188c894f6133de0ee25019ab881 | Perl | 6,290 | 164 | #!D:/perl/bin/perl.exe
use strict;
use lib "E:\2.study\01.program-language\04.SVG\SVG-ÂÛ̳·¢²¼\perl-SVG";
use SVG;
use FontSize;
my $svg = SVG->new('width',640,'height',480);
my $font = FontSize->new();
##header notes
$svg->title('id','document-title','-cdata','This is the title');
$svg->desc('id','document-desc', '... |
af594205fd240d3cc4deacccb95b10760afda87944d658d61c66c6f575fec74c | Perl | 6,427 | 307 | #! /usr/bin/perl -w
use strict;
use warnings;
use List::Util qw(sum);
my @line;
my $read = 0;
my $strand;
my $nm = 0;
my $thismd;
my $thiscigar;
my $chr;
my $thisstart;
my @parse;
my $blocksum;
my @var;
while (<>) {
chomp $_;
@line = split /\t/, $_;
if ($line[1] & 0x40) {
$read = 1;
} else {
$re... |
1bbb66d06a60779c9af012af11cb7bb3df5e30f2775fa70475aaf6b157f02ef0 | Perl | 7,145 | 251 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("F:C:O:B:", \%opt);
#defaults
$die = "
Usage:
sciMET_meth2mtx.pl [options] -B [window bed file] -O [output prefix] -F [methylation chrom folder] ...
Options:
-F [DIR] Directory with methylation by cell for each chromosome (req)
Can be a comma ... |
044dfe87986ee58cafa43c4d7d20f16fc3a3082edf56d66274bbb1997a1efe59 | Perl | 7,174 | 222 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e2a52339262428cf909305ff6f0807075f861c2c48e032e5fe28805b040e7d67 | Perl | 7,529 | 233 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
80645bfe3baeba2dfc5f1b03f25d10d383a0366d31361e4a01a587c96c068643 | Perl | 7,595 | 272 | #!/usr/bin/perl
BEGIN {
use FindBin '$RealBin';
push @INC, $RealBin;
}
use Getopt::Std; %opt = ();
getopts("O:t:sm:G:C:", \%opt);
# dfaults
$minSize = 10000000;
$die = "
sciMET_BSBolt2cellCalls.pl (options) [rmdup & filtered bam file, name-sorted]
Extracts methylation from a BSBolt bam and outputs bismark anno... |
98493682415856c9f1bcbbaf680569691497bcd055392d97d34b56b00f63b71b | Perl | 7,596 | 271 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("f:c:F:L:", \%opt);
#defaults
$minCalled = 10;
$qualFrac = 0.75;
$die = "
Usage:
CGmeth2mtx.pl [options] [window bed file] [output prefix] [extracted_CG_methtylaiton.txt.gz] ...
Extracted methylaiton files should be from the Bismark output.
Options:
-c [INT]... |
889e5250a630f5f9b2e820d5f4bd811ad33ac7992796ccc2c2c4d93e8fc9eaba | Perl | 8,231 | 280 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)))[-1];
sub c... |
8c668b1a9293aeca97221652165609e51ab3ba1438734436e7249a482b0b0649 | Perl | 8,289 | 278 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("f:c:F:L:", \%opt);
#defaults
$minCalled = 100;
$qualFrac = 0.9;
$die = "
Usage:
CHmeth2mtx.pl [options] [window bed file] [output prefix] [extracted_CH_methtylaiton.txt.gz] ...
Extracted methylaiton files should be fromt he Bismark output.
All CH contexts must ... |
5acb03a2f48b6f171de4435e907400cd77d34e3833ec64e3f2e910d592501ab1 | Perl | 8,416 | 220 | #!/usr/bin/perl
BEGIN {
use FindBin '$RealBin';
push @INC, $RealBin;
}
use Getopt::Std; %opt = ();
# defaults
$adapters = "$RealBin/sciMETv2_adapters.fa";
$trimmomatic = "/home/users/oconneru/bin/Trimmomatic-0.38/trimmomatic-0.38.jar";
$min_RL = 30;
$threads = 1;
$r2_trim = 0;
$a1 = "CTATCTCTTATA";
$a2 = "AGATCGGA... |
86756e74b1b9ba0b3b51cea25cf4e551e3bb8aabdac8bfd67bce70890f1c5835 | Perl | 8,499 | 180 | #!/usr/bin/perl
#
# encode_tophat_pipeline.pl
# xwei 09/15/2014
## NOTE:: using tophat version -- tophat/2.0.8
## bowtie2/2.1.0
## samtools/0.1.17
## Modification 09/15/2014
# 1. for single-end and unstranded data
# - remove "--no-discordant" and "--... |
e9cca138c53a4a74289ef619fbf5dac381f5eca128f5fae39c89e7e9f400feb6 | Perl | 8,542 | 254 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
80f7326737bd21e1fde512ed2dbdc164da00f2fa5cde832def3679d45fc60257 | Perl | 8,544 | 328 | #!/usr/bin/perl
BEGIN {
use FindBin '$RealBin';
push @INC, $RealBin;
}
use Getopt::Std; %opt = ();
getopts("O:t:sm:G:C:", \%opt);
# dfaults
$minSize = 10000000;
$die = "
sciMET_BSBolt_extract.pl (options) [rmdup & filtered bam file, name-sorted]
Extracts methylation from a BSBolt bam and outputs bismark annota... |
5f6dc027cce38df9f13fb787b38f3d5eb60f800964b5507949e59e89c64e9f7e | Perl | 8,614 | 270 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
c41e4f609c3b4c0723afcc3181c186dc838aa3a073f8cc5695c89e6ee776547e | Perl | 9,077 | 290 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("A:F:O:G:S:s:E:Vm:rL:xpC:a:", \%opt);
# defaults
$refGene = "/home/groups/ravnica/refs/hg38/hg38.refGene.txt";
$startPad = 20000;
$endPad = 20000;
$minCov = 50;
$die = "
Usage:
sciMET_getGeneMeth.pl -F [chromosome meth call folder] -O [output prefix / folder] [g... |
ee72298b3c26a87f9592279659f8f862eff0c544d835f0089b8cad56507ec2ce | Perl | 9,784 | 266 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
07e3f0d05c192840a3932cb90f2c825a08b1d44a52fcafd82682772b06da10fd | Perl | 9,869 | 179 | #!/usr/bin/perl
#
# encode_tophat_pipeline.pl
# xwei 04/25/2014
## NOTE:: using tophat version -- tophat/2.0.8
## bowtie2/2.1.0
## samtools/0.1.17
## Modification 04/25/2014
# 1. using the agreed tophat parameters
# --min-intron-length 20... |
ad7dc04c6addc019463d3fd4d2597b8128224c232f00a00cc045e9e6fc5d04f2 | Perl | 9,896 | 146 | #!/usr/bin/perl
#
# encode_bam_to_bigwig.pl
#
# xwei 09/24/2013
### modification 9/24/2013
# 1. can generate unstranded wig files
### using Georgi's script (makewigglefromBAM-NH.py) to split accepted_hits.bam to plus or minus strand. and generate unique or multi mapped files
### usage: /home/CAM/xwei/tg... |
c9cedeaa27b65b704a9cfb9f94282eefbbd928f2af85733af2ade0bfbb2ccdfb | Perl | 9,927 | 356 | #! /usr/bin/perl -w
use Getopt::Long;
use strict;
use warnings;
my $fasta;
my $gtf;
my $bed;
my $gtf_out;
my $fasta_out;
my $var_out;
GetOptions("gtf=s" => \$gtf,
"bed=s" => \$bed,
"fasta=s" => \$fasta,
"gtfout=s" => \$gtf_out,
"varout=s" => \$var_out,
"fastaout... |
711d715e31240e46f22d0286a8e0a699404e310153754728d68cb7e01a63f3d6 | Perl | 10,158 | 271 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
aab632ceeedced3f090ff344e021dc6f13fa0086584b5729fd7dcaa44c78a7b1 | Perl | 10,434 | 509 | #!/usr/bin/perl -w
# #
# Script ASTA-Seq1 #
# #
# #
# Input : Configuration file,FASTQ file #
# O... |
9b582f747032d21dde7c6632ff8233af63d4334138c55369290dc1995e274014 | Perl | 10,544 | 287 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
b0c8defc326d7bbcf185e5c99a4a417cd5a575f7d2a44da3282a8e017147eab5 | Perl | 10,626 | 417 | #! /usr/bin/perl -w
# modify sam2bed.pl to process at the same time the XM tag
# which specifies the methylation status of the read
# ============================================================
use strict;
use warnings;
use List::Util qw(sum);
my @line;
my $read = 0;
my $strand;
my $nm = 0;
my $thismd;
my $thisxm;
m... |
be70787cce533b8efc7ccd7e332567d631628cda322d43aee9f75fdf16de726e | Perl | 10,865 | 323 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
b394deb4c3139e463872d0ca9cd394a0b4338104ac77f7e708a8ab02e6cb9918 | Perl | 11,157 | 305 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
b151fecff132e1e4fe1ecc2ec123cbdc83a99dd4a4f3365c4bd09f5efa1d078e | Perl | 11,346 | 294 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("O:1:2:t:w:R:sXA:a:B:b:mk:l:", \%opt);
$hg38na = "/home/groups/oroaklab/refs/hg38/hs38d1_noalt_bismark/";
$mm10 = "/home/groups/oroaklab/refs/mm10/bismark/";
$hybrid = "/home/groups/oroaklab/refs/bismark_hybrid.hg19.mm10/";
$bowtie = "/home/groups/oroaklab/src/bowt... |
f55125ef8304ed14671d7261cf446af5341cbb4e77efe7292937e10b514e0ea6 | Perl | 11,439 | 352 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
2482f94833112c9f136e3ee61e2c05977da7ca264040f6bf070d552b3f1f8c73 | Perl | 11,462 | 318 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e0298701eca117bbe8c63b66e9cade02b742860db061f1e59956409d612ac3ce | Perl | 12,206 | 316 | #!/usr/bin/env perl
# clipprimer.pl - the workhorse of BAMClipper
use strict;
use warnings;
use Getopt::Long;
use Data::Dumper;
use IO::File;
##
# internal logic below
my $phredoffset = 33;
my $bedpe;
my $debug = 0;
my $window_upstream = 1;
my $window_downstream = 5;
my $sam_header_block_seen = 0;
GetOptions ("in=s" =... |
e6de511c6c346254d93195dac144c9049ab5dd57385babd0a2334cb0ba056994 | Perl | 12,251 | 344 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)))[-1];
sub c... |
f7a9f4a6c5f9cdd2f18195eca65f39f7dd39fde2da53206ac109ea7f0c20a187 | Perl | 12,755 | 371 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
bead536926c8cf188c884744fa7d023298039f9549b0bdbb98351982e1177b64 | Perl | 12,774 | 349 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
43a9fdc5da82f3427f81c515bb009764221c06222c1f31a36aac32f7d30baeff | Perl | 12,874 | 333 | #! /usr/bin/perl --
#Copyright (c) 2009-2019, Jean-Francois Flot <http://dx.doi.org/10.1111/j.1755-0998.2009.02732.x>
#
#Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is
#hereby granted, provided that the above copyright notice and this permission notice appear in... |
c985b92d9f3d19810802af3f09b3aaafa86a49da9c76de15cbca13a2c1b93936 | Perl | 14,100 | 374 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
3059d415559cc0a29873ed9bfe5e2f61053c147e92b38d5da462d55b346209a6 | Perl | 14,192 | 372 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
a7fc2d9bdcdbb2e44312c0b8f500085eb07640ddf4a8c0b7de64b7fdfa5f3112 | Perl | 15,223 | 422 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw(:config no_ignore_case no_auto_abbrev pass_through);
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path(... |
72851a13debc0f07dccc47a7e90dbc8514c4472adb3bdfd625161c00e73aaf21 | Perl | 16,304 | 463 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
fa65922e02c096d21ff79d21f743d0dce362d572a821d67c6910e70b918440c3 | Perl | 16,337 | 427 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)))[-1];
sub c... |
e06330207ef15a7f0f9bec791c2015cb304f53b6985ae73e809bdb7ed9e0e182 | Perl | 16,508 | 417 | #!/usr/bin/perl
use threads;
use strict;
use Getopt::Long;
##############################
##
## This program filters the lines that contain (or not) certain words from a list
##
##############################
##############################
# Copyright (c) 2024, David Valle Garcia
#
# Permission is hereby granted, f... |
da01c2eee0ba03f011f16bb6bd77603cb06f0b604b1bf29870e18d634a8f9110 | Perl | 16,794 | 443 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
b1c743a408a6eac0b71e8d65104cee4298dcf8a5bf0179b68f328cb3a06e6595 | Perl | 17,113 | 546 | #!/usr/bin/perl
use Getopt::Std; %opt = ();
getopts("L:O:m:Xt:C:H:bN:G:", \%opt);
#defaults
$minSize = 10000000;
$threads = 1;
$mCH_max = 10;
$cells_per_folder = 100;
$die = "
Usage:
sciMET_extract.pl (options) [rmdup & filtered bam file]
Extracts methylation calls and produces a 'chroms' folder for
subsequent an... |
cefd57d45f00c7edfadd9a014c81fa0216f68fd426c5df311be5daffa89993c1 | Perl | 17,502 | 448 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use Data::Dumper;
use cworld::dekker;
my $tool=(spli... |
cd9dd38659e85052c6546832db46b26184dcbe76fe4ec07cc30aed44c98f0307 | Perl | 17,987 | 441 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
4fb3b87468842bf5dfae5122fa76387b8f41f4b3aa234b7af6936d808c264d0f | Perl | 18,290 | 495 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e7d8b2d5fca96c32dc07d2803e70357e2088845198991d2a41e5f343b85fa164 | Perl | 18,322 | 500 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
0c9e552c37348d143c63274dbc53789d49315082bdf6f4fbce6ff3e0f048196e | Perl | 19,055 | 481 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
ecc29c3c861f4c22a82e00bc993dc34aae669a7a3593d43069925150076d3ace | Perl | 19,314 | 478 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
c199f72a733f0d4d770cdcc2bbec3ec7265c1bdbe1c347e64b553d68abfcaed9 | Perl | 20,261 | 510 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
1a3c1472b2745c7c39d32d781c6421ca035622b74d20066022f27cc5e008abc6 | Perl | 20,484 | 507 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
87745c02184180c438570c4f46937e16f7a067fbccaa85add6f32cc1700cd1ac | Perl | 20,701 | 529 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
1d79fe0293da9e52a69c8a8d27c26d62b7f3b7d1c4f6609bc26d95eff6647d97 | Perl | 21,737 | 580 | #! /usr/bin/perl --
#Copyright (c) 2009-2019, Jean-Francois Flot <http://dx.doi.org/10.1111/j.1755-0998.2009.02732.x>
#
#Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is
#hereby granted, provided that the above copyright notice and this permission notice appear in... |
f4b3c81a7c791f4e880752a3b5cb16bd444688bb9c6bf30ddfabe5c921d09a34 | Perl | 21,935 | 586 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
19829343ad9a4580dbab7251f27b965ba82762e4634d00a055a66d917a81e7cd | Perl | 23,563 | 624 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)))[-1];
sub c... |
f3f466a9ba1193062a8635c3d9b2c24985e5a2deabb98821c737cd93d5c30fda | Perl | 25,549 | 621 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use GD::Simple;
use cworld::dekker;
my $tool=(split(/\//,abs_path(... |
5df706b07f24b25cc6df7312901c69b6d55de3e94384534f8dad8c248b7df10e | Perl | 28,167 | 676 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
5fe968ad54cf2f6aaaed7b8a202a682204a97aaffaaa5d40d574de21913ab07d | Perl | 34,671 | 778 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use cworld::dekker;
my $tool=(split(/\//,abs_path($0)... |
e3939f203a0a9f870598bb1f85eaaf2b7082c7468acc3b90b41441d2976a3d70 | Perl | 41,437 | 975 | #!/usr/bin/perl -w
use English;
use warnings;
use strict;
use Carp qw(carp cluck croak confess);
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use POSIX qw(ceil floor);
use List::Util qw[min max];
use Cwd 'abs_path';
use Cwd;
use GD::Simple;
my $tool=(split(/\//,abs_path($0)))[-... |
56d255e14c23b3cd9b78b1255fa3416c9301ae3d672c763bcf68ecd96d5d1dbf | Perl | 49,426 | 1,199 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $version = "0.0.23";
#version update
# 0.0.23
# -fixed oversight on mask overlap to consider all possible overlaps of reference numt
#
# 0.0.22
# -changed name to "dinumt" (dynumite!)
# -added option --mt_names for discrete MT identifiers
#
# 0.0.2... |
912cdd5d041d783e7022b01e0b0d64fce039dea118ff3de1925962dc570dc5ee | Perl | 49,676 | 1,197 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $version = "0.0.23";
#version update
# 0.0.23
# -fixed oversight on mask overlap to consider all possible overlaps of reference numt
#
# 0.0.22
# -changed name to "dinumt" (dynumite!)
# -added option --mt_names for discrete MT identifiers
#
# 0.0.2... |
09511530aa87bc0152ab2a24eb6f8dfd3f5827cb752e34bbe34b2c39f8ceebf5 | Perl | 57,456 | 1,218 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $version = "0.0.23";
# version update
# 0.0.23
# -added option to require a minimum level of evidence for sample level genotyping
#
# 0.0.22
# -updated version to be consistent with dinumt package
#
# 0.0.16
# -fixed program with too many supportin... |
71f3479d7f4253ad85a634310911414dcd4e793eaf51d8320ec94fe39826f7fe | Perl | 200,000 | 3,192 | #!/usr/bin/perl -w
#Author:Li Shengting
#E-mail:lishengting@genomics.org.cn
#Program Date:2002-12-2015:53
#Last Update:2006-11-14 0:19
#Describe:add fonts defs to svg for batik
my $ver=1.00; #
use strict;
#use diagnostics;
#use Getopt::Long;
#############################################################################... |
83b4a70691f6d2bed97783db0b958a189459c89f7582be5152147d3c948c731a | Perl | 200,000 | 4,131 | #!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
my $version = "0.0.23";
# version update
# 0.0.23
# -added option to require a minimum level of evidence for sample level genotyping
#
# 0.0.22
# -updated version to be consistent with dinumt package
#
# 0.0.16
# -fixed program with too many supportin... |
83c07b1b80388baa828b6983f13096b6b8a641532a75d491af9ab92289bce866 | Python | 18 | 1 | from .src import * |
2cec87e5f8b9609e21e0fe0dd7e40d90293db59d2f0d480258dd86a1fb9be894 | Python | 19 | 1 | from . import lack
|
9fbccdbebe87f7502207fff59c20285d35ae9aa4af93b3876a028ac58bb323fe | Python | 19 | 1 | VERSION = "2.80.1"
|
d875da6870bd5e5f41a9390c0b31752ab9d588165bb9e78ef339d94b0c161b87 | Python | 19 | 1 | __version__ = "1.0" |
332ba97e9d7c11565a704e13a7ba98a98a62984f1358926bfb3423ac1c082620 | Python | 20 | 1 | __version__ = "0.2"
|
4cbd57d075e5a9812f8056b2cfae69f20d6b75f145df4eab4a26d469678e66fb | Python | 21 | 1 | __version__ = '0.6.1' |
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