sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2f22d4e8324f53db998d31e833654e1d197679409fc2b5d0618b319ae0c3b475 | NEURON | 193 | 7 | module github.com/google/yggdrasil-decision-forests/yggdrasil_decision_forests/port/go
go 1.18
require github.com/google/go-cmp v0.5.8 // indirect
require google.golang.org/protobuf v1.33.0
|
e33fed3046f8967c114be804fabdab838d0681b8356a40197cb512a007d0c5eb | NEURON | 431 | 13 | ALPHABET: A C G T
ORDER: 0
SUBST_MOD: REV
NRATECATS: 4
ALPHA: 64.273037
TRAINING_LNL: -787.881056
BACKGROUND: 0.271893 0.251877 0.266889 0.209341
RATE_MAT:
-1.088889 0.259303 0.622319 0.207267
0.279910 -0.897589 0.138191 0.479487
0.633987 0.130418 -0.945603 0.181198
0.269200 ... |
c541d71e1f0c8d6d3c032be77cc737ce25ef287877602268212b649f939b5e85 | NEURON | 1,308 | 85 | TITLE The hyperpolarization-activated (Ih)
:
: Added three more ionic channehls to the modehl from Kameneva 2011 to distinguish the difference between ON and OFF RGCs.
: Written by Javad Paknahad July 5, 2018
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
NEURON {
SUFFIX Ih
NONSPECIFIC_CURRENT ih
RANGE ghbar, eh
RANGE ... |
138f79134d4cddc487fbf7e04ae9fb0c245ff0228fcc7a0dc3a30aa2b05f8abd | NEURON | 1,368 | 54 | {load_file("nrngui.hoc")}
{load_file("import3d.hoc")}
//////////////////////////////////////////////////////////////////
// Template for making a cell
begintemplate Cell
public soma, axon, dend, apic, nclist, dend_5, dend_6, dend_7
create soma, axon, dend, apic, dend_5, dend_6, dend_7
public all, somatic, axonal... |
1bf6977a0480633e56c98dcc2b81e870919288a32d68959abbb0c5f0ae7fe53f | NEURON | 1,988 | 84 | COMMENT
Javad Paknahad 4/4/2018
This T-type calcium current was originally reported in Wang XJ et al 1991
ENDCOMMENT
NEURON {
SUFFIX IT
: NONSPECIFIC_CURRENT i
USEION ca WRITE ica
RANGE Erev,g, gTbar, i
RANGE k, taum, minf, alpha_1, alpha_2, beta_1, beta_2, V_s
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(m... |
f74eb0ad4effd5d9db5a8a5f9f3b26e88d1d63f22ab42bca9693d5d8d1af761e | NEURON | 3,174 | 158 | TITLE HH style channels for spiking retinal ganglion cells
:
: Modified from Fohlmeister et al, 1990, Brain Res 510, 343-345
: by TJ Velte March 17, 1995
: must be used with calcium pump mechanism, i.e. capump.mod
:
:
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
NEURON {
SUFFIX spike
USEION na READ ena WRITE ina
USEION... |
c89b08f58db957cdb71d536c26ae3098d621ce541e02c980f266cdc1dba09df6 | NEURON | 3,847 | 251 | PCBNEW-LibModule-V1
# encoding utf-8
Units mm
$INDEX
LGA28R50P4X10_380X520X100
$EndINDEX
$MODULE LGA28R50P4X10_380X520X100
Po 0 0 0 15 00000000 00000000 ~~
Li LGA28R50P4X10_380X520X100
Cd
Sc 00000000
At SMD
Op 0 0 0
.SolderMask 0
.SolderPaste 0
T0 1.04105 -2.83785 1.00101 1.00101 0 0.05 N V 21 "LGA28R50P4X10_380X520... |
b4d0410756f5fc519b93096cc4c32fcc84c91c62ecc0a5ebd18fbf9c30593cb2 | Perl | 121 | 5 | #!/usr/bin/perl
while(<>){
s@http://ontology.neuinfo.org/NIF/\S+#@http://uri.neuinfo.org/nif/nifstd/@g;
print;
}
|
fe3e64372208677ae76247e640190cd3b442a4984925c3e37ddf9526fd408e91 | Perl | 284 | 9 | @files = <*.bam>;
foreach $file (@files) {
print "mv ".$file." ";
$file=~s/.sort.mdup.bam.sc_pre_mono_sort_for_mark_uniq.bam//;
print " ".$file.".sort.mdup.sc_pre_mono_sort_for_mark_uniq.bam\n\n";
print "samtools index ".$file.".sort.mdup.sc_pre_mono_sort_for_mark_uniq.bam\n\n";
}
|
6d7d7ff3ab998926a5d1eb9d3230bf9bee60b5a6142d9ad1f53a77b9d8ff0fbb | Perl | 306 | 9 | @files = <*uniq.bam>;
print "`multiBamSummary BED-file --BED /g/korbel2/StrandSeq/Test_HJ/reference/bin_Genes_for_CNN_sort.txt --bamfiles ";
foreach $file (@files)
{
print "$file ";
}
print "--extendReads --outRawCounts Deeptool_Genes_for_CNN_HG00512.tab -out Deeptool_Genes_for_CNN_HG00512.npz`;\n\n";
|
6c6df4ef007f73cd953903cc1ca00d1fad5680549accd2058861b869dacd8a25 | Perl | 313 | 19 | #!/usr/bin/perl
my @x=();
my $last='';
while(<>) {
if (/^s\S+def:\s+(\S+)\s+\"(.*)\"/) {
if ($last eq $1) {
my $pop = pop(@x);
printf STDERR "pop: $pop";
}
$last = $1;
}
else {
$last = '';
}
push(@x,$_);
}
foreach (@x) {
print $_;
}
|
cb08842e198dbf1211cdb019d7f6947b16460ef71d5b573dc451293f2f3b68a6 | Perl | 564 | 39 | #!/usr/bin/env perl
use strict;
use warnings;
my $seen_header = 0;
while(my $line = <>) {
unless ($seen_header) {
unless ($line =~ /^\@/) {
die "Error, no header observed ";
}
$seen_header = 1;
}
if ($line =~ /^\@/) {
print $line;
next;
}
my ... |
874ec716bfbc94dc6fbabcd4c5710deae7eef44a96be717cf7006709ad0c6a80 | Perl | 616 | 25 | #!/usr/bin/perl -w
$name = "PMF";
$nbin = 144;
$temp = 298;
$kB = 0.008314472;
$kT = $temp*$kB;
$kcal = 4.1868;
$kcaltokT = $kT/$kcal;
$outfile = "$name"."_"."$nbin";
$randn = 12323;
$sys = "../../../pymbar/wham-grossfield/wham/wham P360.0 -180 180 $nbin 0.0000000001 $temp 0 metadata.dat $outfile 100 $randn";
`$sys`;
... |
11d303258ba5c23d47939aa6ded3c81521ebca324edba072be2a2cdaab138afa | Perl | 715 | 21 | #!/usr/bin/perl
my $OBO="http://purl.obolibrary.org/obo";
my $ont = shift @ARGV;
my $import_ont = "imports/$ont"."_import.owl";
my $import_ont_staged = "imports/$ont"."_import-staged.owl";
my $owl = "$OBO/$ont.owl";
#my $cmd = "owltools $import_ont $owl --extract-module -s $owl @ARGV --merge-support-ontologies --extra... |
e817b4a773d830dfc1642439c8726e1f8a13b154a84a4546dce685117823ac39 | Perl | 783 | 37 | #!/usr/bin/perl -wd
$pi = 3.141592674;
# Grossfield's code uses this conversion
$kJpkcal = 4.1868;
@datafiles = <../data/p*dihed.xvg>;
# make new datafiles
@locations = ();
foreach $f (@datafiles) {
open(IN,"$f");@lines =<IN>;close(IN);
@v = split(/\//,$f);
$fl = $v[$#v];
push(@locations,$fl);
op... |
9d7e512f7879c859dca1b74ef1645a222dd5608256fa3488c93570b91be41d4e | Perl | 882 | 37 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
# pipe in a fastq file to check for "diagnostic" base quality score to determine whether it's... |
205795dd1b507921adff6d002d90f25cf15a54d99b7df3ecdaf6ad8ba200bd8e | Perl | 937 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use IO::File;
use Text::CSV;
my $tlxfile = shift;
my $bedfile = shift;
my $extsize = shift;
$extsize = 500 unless defined $extsize;
system("perl -pi -e 's/\r/\n/g' $tlxfile");
my $tlxfh = IO::File->new("<$tlxfile") or croak "Error: could not read file $tlxfil... |
38c102c3bbd192ca51d11a884d18649e244f53b281888ee5fab80985a7c4e58f | Perl | 981 | 18 | @files = <../bam/*.bam>;
foreach $file (@files) {
`samtools view -H $file > ../bam_haplo/header_test.sam`;
`samtools view -f 99 $file | cat ../bam_haplo/header_test.sam - | samtools view -Sb - > ../bam_haplo/$file.C1.bam`;
`samtools view -f 147 $file | cat ../bam_haplo/header_test.sam - | samtools view -Sb - > ../bam_... |
77e28a68d35154ea51c08a410d49eb1c53e8b900f79a901c8c10c7637835f63a | Perl | 1,007 | 46 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/PerlLib");
use Gene_obj;
use Gene_obj_indexer;
use GTF_utils;
use Carp;
my $usage = "usage: $0 file.GTF > file.GFF3\n\n";
my $gtf_file = $ARGV[0] or die $usage;
main: {
my $gene_obj_indexer = {};
print STDERR... |
6dd6640430d3b8ed2f4b31ccc95f5e25e3c68a17e44174b9add02bf7bdc2be91 | Perl | 1,214 | 47 | #!/usr/bin/perl
# generates an xfm file for a provided grid file
use strict;
use warnings;
use File::Spec;
use MNI::Startup;
use Getopt::Tabular;
use MNI::Spawn;
use MNI::FileUtilities qw(test_file check_output_dirs);
my $usage = "
$0 [options] deformation_grid.mnc output_xfm_for_grid.xfm\n";
# handle arguments
... |
baa2db21ba9fcc5290fa5c6eb40567072eb5c76914ebb093bacdfb8c128e1fd5 | Perl | 1,496 | 55 | #!/usr/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
# pipe in a fastq file to discard "Illumina chastity filter failed reads"
# this is a normal rea... |
a8a4ea798a3b133353ff4e884ec15703e41cce422d66d0b351de4b35b42d9af8 | Perl | 1,716 | 87 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
if (@ARGV < 2)
{
die "1.read bins file (use - for reading from STDIN) - 2.file with chromosom... |
3fa14afe7b54120b5689957e077729d505c56d6f9bee5c069908040b031b3dc9 | Perl | 1,800 | 75 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 paired_reads_aligned.bam\n\n";
my $paired_bam_filename = $ARGV[0] or die $usage;
main: {
## flags we care about for identifying and cleansing pair info.
my $IS_PAIRED_MASK = 0x0001;
my $IS_PROPPER_PAIR_MASK = 0x0002;
my $IS_MATE... |
97d77b83b6eeefeeddc4a7249ad5dbe23b81e227d45b9440edf91edab2d9d876 | Perl | 1,801 | 81 | #!/usr/bin/perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Barbara Hutter 2011, see http://seqanswers.com/forums/showthread.php?t=8164
use strict;
use warnings;
if (@ARGV < 1)
{
... |
a835af3fde0c2d70e9b3b83f07e1e406d15d7c696245db923585a4037c90d385 | Perl | 1,832 | 101 | #!/usr/bin/perl -w
# this is a copy of the script in obo-grep.pl
use strict;
my %tag_h=();
my $regexp = '';
my $noheader;
my $negate;
my $count;
while ($ARGV[0] =~ /^\-.+/) {
my $opt = shift @ARGV;
if ($opt eq '-h' || $opt eq '--help') {
print usage();
exit 0;
}
if ($opt eq '-r' || $opt... |
7b6707d1487b23234bb27a7a873611144c96cef6fe41e04e416470817bba8ba5 | Perl | 2,017 | 61 | #!/usr/bin/perl
$input_subclonality=$ARGV[0];
$subclonality_colnames=$ARGV[1];
$line=$ARGV[2];
my $prefix = (split "scNOVA_input_user", $input_subclonality)[0];
chop($prefix);
if ( length($prefix) == 0 ){
$prefix = ".";
}
print +($prefix)[0], "\n";
`mkdir -p $prefix/scNOVA_bam_merge`;
# `sed -n '1p' input_user/... |
bed9bb2587772b4c9caddd890747399b64f93f6ca995d327fc59bf402c542c67 | Perl | 2,645 | 148 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::File;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use IPC::System::Simple qw(system capture);
use Cwd qw(abs_path);
use FindBin;
use lib abs_path("$FindBin::Bin/../lib");
re... |
f5ac0d1544adc93fa01ef0647e73f295d084102296bdad4c871064d67027aa14 | Perl | 2,763 | 60 | #!/usr/bin/env perl
use strict;
use warnings;
use MNI::Startup;
use MNI::Spawn;
use File::Basename;
my $usage = "$0 source_atlas target_atlas\n";
my $outputdir = undef;
my $source_atlas = shift or die $usage;
my $target_atlas = shift or die $usage;
$outputdir = shift;
if(defined($outputdir) and ! -d $outputdir)
{
... |
c983e8ad397ab33928a56d6011fbb4e5ae290d93a1faeeadaea6740660b1b7bf | Perl | 2,904 | 150 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::File;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use Cwd qw(abs_path);
use FindBin;
use lib abs_path("$FindBin::Bin/../lib");
require "TranslocSub.pl";
# Flush output afte... |
ce4d94640e50a06ac8c746a77e1b07669bb28c9520b0f7a34bd8c313cd22d439 | Perl | 2,911 | 160 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use Bio::SeqIO;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use IPC::System::Simple qw(system capture);
use Cwd qw(abs_path);
use FindBin;
use lib abs_path("$FindBin::Bin/../lib");
require "Transl... |
7de3d9da517126b7fa747f0d3282ff48e1520f5b0cdbcc06b5188709a92b3ea2 | Perl | 2,914 | 73 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
if (@ARGV < 4)
{
die "need 3 arguments: 1) String with : separated BAM paths, 2) strin... |
62f73dc744a951956e9264cfefd29129636d88c5264e3de84c539741acceca1a | Perl | 2,923 | 83 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/PerlLib");
use Gene_obj;
use Gene_obj_indexer;
use GTF_utils;
use Carp;
# gencode_gtf_to_splice_adjacent_regions.pl $CTAT_GENOME_LIB/ref_annot.gtf > ref_annot.splice_adj.bed
my $usage = "usage: $0 file.GTF > file.splice_adjacent.bed\... |
ec86bb2d095a1bfb33f8993db0af3cccb6bd3057f174688435c8144047f30967 | Perl | 2,936 | 153 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::File;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use IPC::System::Simple qw(system capture);
use Cwd qw(abs_path);
use FindBin;
use lib abs_path("$FindBin::Bin/../lib");
re... |
509005c9eee3d2394859024e3a2128b35951c3c38d2e0dc859fb5e0ced2ee2a9 | Perl | 2,966 | 110 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
if (@ARGV < 1)
{
die "Usage: $0 output of coverageBed -d\n";
}
my $file = shift;
open (FH, ... |
a7ffaaf23c0f21c5818937de84a915ad2a13a6663cc82a2b1eec84a441b2eae4 | Perl | 3,012 | 110 | #!/usr/bin/env perl
use strict;
use warnings;
main: {
open(my $ofh_37, ">GRCh37.RNAediting.vcf") or die $!;
print $ofh_37
"##fileformat=VCFv4.2\n"
. "##reference=GRCh37\n"
. "##source=Rediportal\n"
. "##INFO=<ID=RNAEDIT,Number=.,Type=String,Description=\"A known or predic... |
a2272129603d32a7e2b2756c854354df5a7b39c5a0c0086d83202fd1165c7878 | Perl | 3,032 | 87 | #!/usr/bin/perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
if (@ARGV < 2)
{
die "$0 needs two arguments: 1.sam file (if piped in from samtools view, ... |
150c3120f95c850db72247d4575f67b774219928daf92fa6232494669c857fbe | Perl | 3,489 | 189 | #!/usr/bin/perl -w
use strict;
my $show_context;
my %tag_h;
while ($ARGV[0] =~ /^\-.+/) {
my $opt = shift @ARGV;
if ($opt eq '-h' || $opt eq '--help') {
print usage();
exit 0;
}
elsif ($opt eq '-c') {
$show_context = 1;
}
elsif ($opt eq '-l') {
%tag_h =
... |
52980494ac43c78238f8d79ea5661a924734dda95e11b29daddebd69a92003e9 | Perl | 4,048 | 188 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::File;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use Cwd qw(abs_path);
use FindBin;
use lib abs_path("$FindBin::Bin/../lib");
my $ANNOT = $ENV{'ANNOT'};
my $BOWTIE_IDX = $E... |
409e8e7be58c9f02d2fb3780f9e2ebe456adb6e15e57a7a562bb3143498aa4af | Perl | 4,430 | 91 | #!/usr/bin/perl
$strandphaser_output=$ARGV[0];
$nucleosome_sampleA=$ARGV[1];
$nucleosome_sampleB=$ARGV[2];
$strandphaser_output_copy=$ARGV[3];
# WARNING : change input_user for strandphaser
my $prefix = (split "strandphaser", $strandphaser_output)[0];
chop($prefix);
if ( length($prefix) == 0 ){
$prefix = ".";
}
... |
5d4acb4469c6961affdfb4fbccd21b3f651a2d95e1a7940c124af29258a147b8 | Perl | 4,754 | 155 | #!/usr/local/bin/perl
# Get data for sleeping fish
# Output each kind of duration (burst, mid, freeze) to a separate file
# Call this file like
# sort_fish input_file.txt
# where the only argument needed is the file from the robot
# The input file must end in '.txt'
# $Revision: 1.6 $, checked in $Date:... |
b279ca39fcc67a4900e2037504c5bcd26c758d301419f96efd45ecd6696572b2 | Perl | 5,646 | 302 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::Handle;
use IO::File;
use Text::CSV;
use File::Basename;
use File::Which;
use List::Util qw(min max);
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use Cwd qw(abs_path);
use FindBin;
use lib a... |
edc2f103cb0f5191ae65a8a5673f619681ef79b9fc1a5e5c95848c32d43971d0 | Perl | 6,481 | 236 | #!/usr/bin/perl
#|
#| similarity-matrix.pl
#|
#| written by Connor Burbridge
#|
#| This script has been written to compare samples in a vcf file. In order to find
#| the differences and similarities this script will look through the vcf and
#| calculate the ratios of identical calls between all samples. It will then ... |
0496345c2f917c41e67b25c6937fbdb67b1a8cc9ed5c93502d4e097e0b03837a | Perl | 6,792 | 267 | #!/usr/bin/perl
if ($#ARGV != 0)
{
die "Argument must contain filename $#ARGV"
}
else
{
$fname=$ARGV[0];
}
# If we have a .m file inside a (@)-folder with the same name :
# we will read each file of this folder
if ($fname =~ /^(.*)\@([\d\w-_]*)[\/\\](\2)\.m/)
{
$name = $2;
$nameExt = $name.".m";
$dir = $1."@... |
be1c9853b38f37ac1333eb89161f7f7b414f89d5b42de6e42de463d1626900e5 | Perl | 8,500 | 417 | # Source for mostly smaller subroutines
use Switch::Plain;
### Program execution
sub debug_print ($$;$) {
my $msg = shift;
my $code = shift;
my $id = shift;
return if ! defined $main::debug_level || $main::debug_level < $code;
my $new_msg = $code . "|";
$new_msg = $new_msg . $id . "|" if defined $id;
... |
29e7653889f47ec0069a42ce70a7244f1928b0eedc76d0e488d9d43d8b1333a5 | Perl | 8,609 | 317 | # Source of subroutines that calculate and set filters on tlxs
sub filter_unaligned ($) {
my $read_obj = shift;
my $tlxs = $read_obj->{tlxs};
if (! defined $tlxs->[0]->{B_Rname}) {
# my $junctions = filter_entire_read($tlxs,"unaligned");
filter_entire_read($tlxs,"unaligned");
# return(1,$junctions)... |
fbe1f7dcc2bbc701b426e235ec18f04131fae4929fc436a57cc67fbfcc82d41a | Perl | 8,893 | 353 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use File::Basename;
use File::Copy;
use File::List;
use File::Spec;
use IO::Handle;
use IO::File;
use Bio::SeqIO;
use Bio::DB::Fasta;
use Bio::DB::Sam;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv... |
66ba6dcb8f247bada9cb83ccdc0d8352a83a398686adb0f49742b3147529572b | Perl | 10,277 | 213 | #!/usr/bin/perl -w
use strict;
my $min_AF_for_grouping =0.03;
my $AF_simiarity_threshold = 0.6;
my $input_file = $ARGV[0];
my $safe_llr_to_ref = 30;
if (!$ARGV[0]) {
print STDERR "inputfile missing\n";
print STDERR "-> cluster into groups by chromosome, if similar AF (relative threshold=$AF_simiarity_threshold), if... |
0594ba064e06ad0b647a9927bc73541edd85fd18c09a65c7a5c849b318b93ef9 | Perl | 10,475 | 464 | #!/usr/bin/perl
#####################################################################
# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp)
#
# Ver. Date Changelog
#####################################################################
# 1.0 07.26.13 Initial release
# 2.0 09.03.13 Added extensive warnings and error... |
472ac25b4eb75982db3aa9bd5b70cb845435b1e19b2087bc51d854856a28edd4 | Perl | 11,218 | 343 | #!/usr/bin/perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# extended flagstats with number of secondary and supplementary alignments,
# paired end reads mapping to different chromosom... |
76d1b8b136e15cd2e9f70ac5bcb874489228f95daaafe0c38ca39d930620646b | Perl | 11,744 | 459 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Carp;
use IO::Handle;
use IO::File;
use Text::CSV;
use Interpolation 'arg:@->$' => \&argument;
use POSIX qw(ceil floor);
use threads;
use threads::shared;
use Time::HiRes qw(gettimeofday tv_interval);
use IPC::System::Simple qw(system capture);
use... |
e3b8429c23a815a2a6e7f630cdfbcd966ef7d0b340e33d2978e993e1206daaa4 | Perl | 11,896 | 237 | #!/usr/bin/perl -w
use strict;
my $min_N_inv = 3;
my $min_WC = 1/3;
my $safe_llr_to_ref = 30;
# my $SegDup_file = "../../data/segdups/segDups_hg38_UCSCtrack.bed.gz";
my $SegDup_file = $ARGV[1];
my $MaxSegDup_overlap = 0.5;
#Use input file with format "chrom start end sample cell class scalar num_bins sv_call_name sv_... |
cc45ba08dd32d17cdb857de7172d9e49c657b8617f2a4f3f8ec4bcf5f829a49f | Perl | 11,898 | 309 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
use Getopt::Std;
my %opts = (p=>1000,n=>1);
getopts("c:d:f:i:l:m:p:r:s:t:w:h", \%opts);
my $c... |
3da83cb37895a3c25d30371c6dbeedfab7fd0dee81f92e3c8351c6eefbdf89c4 | Perl | 14,230 | 495 | #!/usr/bin/env perl
## original code is !/usr/bin/env perl.
use strict;
use warnings;
use Getopt::Long;
use Carp;
use File::Spec;
use IO::File;
use Text::CSV;
use Bio::DB::Fasta;
use threads;
use Interpolation 'arg:@->$' => \&argument;
use Time::HiRes qw(gettimeofday tv_interval);
use IPC::System::Simple qw(system c... |
bfe2f4cd579c3734ac9a4979c9a1b577bef8993f5242c342019df2c490d82fd3 | Perl | 15,541 | 600 | #!/usr/bin/perl
####################################################################################
# Author: KM Amada (kmamada@ifrec.osaka-u.ac.jp)
#
# Ver. Date Changelog
####################################################################################
# 1.0 11.01.13 Initial release
#
# **Skipped version... |
d640b340b8be977a4d8ea05ef253bee440358b4623cb9d30ec67501ab1f72b82 | Perl | 19,737 | 601 |
# sub manage_blast_options ($$) {
# my $defaultoptstr = shift;
# my $useroptstr = shift;
# return $defaultoptstr unless $useroptstr =~ /\S/;
# return $useroptstr unless $defaultoptstr =~ /\S/;
# my @defaultopt = split(/\s+-/,$defaultoptstr);
# my @useropt = split(/\s+-/,$useroptstr);
# my %opt_hash;
... |
600ece12f663f493ff7f1edcc2a9323a68dd6106918c8b259d565c5e44d7f448 | Perl | 21,208 | 601 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings;
use v5.10;
my %opts;
my @standardColnames;
BEGIN {
use Getopt::Long;
use Pod::Usage;
... |
bc9bcba67d8353b49a5af4a435e4694eb5fc1a44c6c622815fc42a2ed422de4d | Perl | 22,424 | 460 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
use strict;
use warnings FATAL => 'all';
use IO::File;
use Carp;
use Scalar::Util qw(looks_like_number);
use Pod::Usage;
... |
0b4d0d7f3f04d78fd7f1ba806d5bcec485599ace07e3d5f1c6b895977cb5b002 | Perl | 23,420 | 640 | #!/usr/bin/env perl
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Read in a number of statistics files and compile some of the content into a JSON file.
# The JSON file is required by OT... |
4c7939d578eee32f4257cf9c1f081225aee6f91bdb805d81b80c06a12d12fa4f | Perl | 38,011 | 1,302 | # Source for larger subroutines having to do with major program flow
use Switch::Plain;
sub wrap_alignment ($$) {
my $pe = shift;
my $aln = shift;
return undef unless defined $aln;
croak "Error: first argument to wrap_alignment must be either \"R1\" or \"R2\"" unless ($pe eq "R1" || $pe eq "R2");
# my %w... |
b123ce12a51295d66616ce9b15b92cfdebb43e52db71eb077a7bb30c999c33d1 | Perl | 39,914 | 1,147 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long;
use IO::Handle;
use IO::File;
use Text::CSV;
use File::Basename;
use File::Which;
use File::Copy;
use POSIX qw(floor ceil);
use List::Util qw(min max shuffle);
use List::MoreUtils qw(pairwise firstidx);
use Data::GUID;
use Bio::SeqIO;
use Bio::D... |
4bcf13fd8a777bb6e7472e814ce55630a9b17e542d1ea103336beab81045a378 | Python | 5 | 1 | # ..
|
75cbe3e42f44d85d8a0ac1993c10677107ff12f549002d6a4209f20fc3f8644c | Python | 6 | 1 | # ...
|
00ed1facc0b32574772870d058fbbe5a75055189ee2a240a41b1ef7cf45f8267 | Python | 8 | 3 | """
""" |
4f7d64017689437e6d93f5724f3f797054f3935d98a13148025b616b8db8fb2c | Python | 11 | 1 | Coming soon |
73a33b54007356201006ecbc38381003892098fa38f3ac46bd725337589a70c9 | Python | 11 | 5 | """"""
|
4b75630590f7168ce4e65602d4fe35475184a5813bdd26a288db4db196d3304d | Python | 15 | 1 | # whobpyt init
|
225e50f404dd5fcc97a95c6d3ff9d8a94844c73c4f0bfaa4fd65d0ff88747b18 | Python | 16 | 1 | from . import *
|
362b51bf5ae5601a17408a85a03f9b9dbc515ac437e942738d974d9dc45a5d83 | Python | 18 | 1 | #!/usr/bin/python
|
5a3ce0a07d5615aefdc1cf00ecee9432e25fa2890b7e072250d70231b2870104 | Python | 21 | 2 | def test():
pass
|
931a6d16f799dfbcdb3d298a53b28c100f0f8bb877fac335fa9d9a826d8fa422 | Python | 21 | 2 | __version__ = '3.1'
|
d02e91fe125b82e6e5f0642b897f7439094506d06f32771b40d00170deb8eae1 | Python | 21 | 1 | __author__ = 'tylin'
|
27e8febb48ada44153ea2add9969a2c50a9831a74d9755fdd53c549a888b1cc2 | Python | 22 | 1 | __version__ = "1.0.0"
|
df0544b36403ffb39c4e50fdedc65d09e8b37768546c927419e20ef304088eb9 | Python | 22 | 1 | __version__ = '0.3.0'
|
c52e4bd3361e308c63e32ab5d64dd0adbfee8c8d663ef0a700a2d5869f6a245e | Python | 23 | 1 | from .constant import * |
070b29bcdf29275ac69e70fc066f526616d5d8581c0f61f74d76905b4f100292 | Python | 24 | 1 | __version__ = "0.17.16"
|
c738bd2c18dc21fdac4bf3f0f673a9644eba743fa4298c170dc60cdb6f98fbee | Python | 24 | 1 | __author__ = 'shengdar'
|
88127b7d85448ddc4a31e4d99e17a94d9db625f3990994e5792d7a57b9cadb28 | Python | 25 | 1 | """MultiQC utilities."""
|
971629642afd14b5d8f68a34fd58c4b4450aa8f1e16c0fe9d82fe6815b086cda | Python | 25 | 1 | import voxelmorph as vxm
|
b7dce622f0d1946f0c91ab25940d17a036b61fbc6774d36fde15f1fbf3fe426e | Python | 26 | 1 | """Scripts for YAMMBS."""
|
22eef9fb0f7f9e53e69c1fea280ee761a69a1dfef1b53ac398af0de2fd96577e | Python | 27 | 1 | from .config import Config
|
18e1b69292f534e4851c409322aa4b0a71eefd4742f2f94166c9eaeb14904615 | Python | 28 | 1 | """Init core for ethopy."""
|
5df74ee6a5df4fac6dd5a0f48321c37baf60f4fc56c8063123b6c98091a4fdaf | Python | 29 | 2 | from .empirical import ecdf
|
1bacf116e96db8684140b0191d14a180b7b9adc753c18232e0e7e2f0ae7f638c | Python | 30 | 4 | """
WhoBPyt Data Classes
"""
|
79fadaa44ebbfe3732bdb5502b710b76ac5d0471b28738877f6731a64de3661a | Python | 31 | 1 | # Display module for TimeFlies
|
3f1bd25b88f486831b56cc6b2eaf08da012be6b99638853c17821ea2cf0e28b6 | Python | 32 | 1 | from . import check_ligand_prep
|
be0ec1ae8fcc91297d32c8941f0a96e4d0193b8df6cf1a2847aaaf28a594a98f | Python | 32 | 1 | """Cluster metadata helpers."""
|
114c68062bc80292702c0da13792f2aa501d4406e9c2af0a084d46620a1b6e67 | Python | 33 | 1 | """Test module for Draw Agent.""" |
4bc008e8529a0f24fa12bf7482198160e0bdd1874c929c88119e18ef13547064 | Python | 33 | 1 | from .base import ImmutableModel
|
5120717bef4c21ce830d816f18a8581d234c0ff50ff511c25982cb0e9c7ab4a5 | Python | 33 | 1 | """Neo4j integration helpers."""
|
05b53843fdb511f2101d4230dbac3133e41422b6041fb69714d2e7faa6c26a34 | Python | 34 | 1 | from .xenium import MultiqcModule
|
987cdb267eb8a8e7c0a44d1ccd87ae6031242bbd54eedca7db9e3463ab0e5a21 | Python | 35 | 1 | """Graph query service package."""
|
ebb347eeb4be4c203bc09374d4ffae0a74a515c9ecdc2475abbcda0acc630fc4 | Python | 35 | 3 | """
Options for training a GNN.
""" |
d8ab5cf605e73ce77a4aa0dcb2868a7dd22d09ba6073a556bfcd0dc748335d25 | Python | 39 | 1 | from .client import AlchemiscaleClient
|
5a3fabd45c16af5b6aca555f63abd07a9063ed1e2d64408f48099360c3572b26 | Python | 40 | 1 | """Test suite for TimeFlies project."""
|
0d4d75334d101bfce7ccc4eef1991feb1fcfda7fd609c0a830618c8310825877 | Python | 41 | 1 | # SAM Breast Ultrasound - Config module
|
4cbac1a49b316af424046ebb51f053bd7b1531888fc48eba3e6601e7bbd00d5b | Python | 41 | 1 | """Knowledge Agent evaluation modules.""" |
647222bee439c391895c1ee1c0ba74cdc91dfdbdb6ea4ebcc230614f493d032a | Python | 41 | 1 | """Algorithms implemented in Shapely."""
|
cfb8f2b453e0500fbbd28a56bca73a6229fe36b4eb85297800bf399b0122a0e7 | Python | 42 | 3 | from .cando import *
__version__ = '2.3'
|
3aad373b8b699c03223a2ffa2b63fa069f198c94964f66ef36f58473ad405345 | Python | 43 | 1 | # SAM Breast Ultrasound - Utility modules
|
6792ce903255fc3383f7bf7bd9a76b21dbc835961724913737b9749bf6496187 | Python | 43 | 1 | """Unit tests for TimeFlies components."""
|
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