sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
444a23c2dc4098068a0581f46ee3fc32644038ede2d33978472e76b51b6e5c85 | NEURON | 200,000 | 5,950 | //Defining CA1 PC morphology including: 3D shape, creating section lists, cutting into segments
load_file("subiter.hoc")
load_file("stdrun.hoc")
create soma, dendrite[158], axon[5]
proc topol() { local i
connect dendrite[0](0), soma(1)
for i = 1, 3 connect dendrite[i](0), soma(0)
for i = 4, 5 c... |
565003bb5ffa90f959855421fd17081848aeb4c3ffd400aebcadf5a70c5cb238 | NEURON | 200,000 | 5,353 | proc celldef() {
topol()
subsets()
geom()
geom_nseg()
biophys()
}
create soma, axon[5], dend[22], apic[116]
proc topol() { local i
connect axon(0), soma(0.5)
for i = 1, 2 connect axon[i](0), axon(1)
for i = 3, 4 connect axon[i](0), axon[2](1)
connect dend(0), soma(0.5)
for i = 1, 2 ... |
770bb70b966454bb342a041eca0b7d676d8f82c45c57b41049fc4f2508574171 | NEURON | 200,000 | 3,615 | begintemplate PVDL
public init, topol, basic_shape, subsets, geom, memb
public x, y, z, position
// Some methods for referencing the cells
public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
// Section: Soma, id: Soma, parent: $s.parent
create Soma
public Soma
// Section: Axon, id: Axon,... |
9efb28ef228932282f9c1b862383e3a0d4c431bc40159fa7f5222bb056eea303 | NEURON | 200,000 | 3,590 | begintemplate PVDR
public init, topol, basic_shape, subsets, geom, memb
public x, y, z, position
// Some methods for referencing the cells
public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
// Section: Soma, id: Soma, parent: $s.parent
create Soma
public Soma
// Section: Axon, id: Axon,... |
acf3a564c419abf87399d814b4fd1e831af7adec2d0c2acda5870f051d1861ed | NEURON | 200,000 | 4,846 | proc celldef() {
topol()
subsets()
geom()
biophys()
geom_nseg()
}
create soma, apic[55], dend[101]
proc topol() { local i
connect apic(0), soma(0.5)
for i = 1, 2 connect apic[i](0), apic(1)
for i = 3, 4 connect apic[i](0), apic[1](1)
for i = 5, 6 connect apic[i](0), apic[2](1)
for i = 7, 8 connect... |
d8c3c5f2014ec3892e5b9f885c9f6af5f5ace53d80f9644e8eb3aab9287f128d | NEURON | 200,000 | 5,489 | proc celldef() {
topol()
subsets()
geom()
geom_nseg()
biophys()
}
create soma, axon[5], dend[22], apic[116]
proc topol() { local i
connect axon(0), soma(0.5)
for i = 1, 2 connect axon[i](0), axon(1)
for i = 3, 4 connect axon[i](0), axon[2](1)
connect dend(0), soma(0.5)
for i = 1, 2 connect dend[i]... |
3416187a5b5dd65fbf801c0bd601305f47b4830a6302ebab9dd45436403a1788 | Perl | 77 | 3 | #!/usr/bin/perl
# simple script used to test if perl is installed.
print 1 |
ffd8e9f7533aaefe15f10a7e2ef70837e21eb466c10971001cd2984e29ad7218 | Perl | 184 | 12 | #!/usr/bin/perl
# download a file from the web
# status = fetchfile source dest
use LWP::Simple;
my $status = getstore($ARGV[0], $ARGV[1]);
print is_success($status)
|
1976ee45568fa242744cebceca26e351c4e6d7b729792ae71660e26f1e911299 | Perl | 336 | 16 | #!/usr/bin/perl
use Env qw(TESTDATADIR);
if (defined $TESTDATADIR) {
system("./aromatic $TESTDATADIR/aromatics.smi");
} else {
system("./aromatic files/aromatics.smi");
}
# If the program failed to execute, ignore the test
if ($? == -1) {
print "1..0 skip because program would not run";
}
# Otherwise exi... |
7caa6a8d586e815c808d8b61925827d7d5aeef06c56f7f85ba4b0a19bd3d6c37 | Perl | 378 | 18 | #!/usr/bin/perl
use Env qw(TESTDATADIR);
if (defined $TESTDATADIR) {
$INCHIDIR="$TESTDATADIR/../inchi";
} else {
$INCHIDIR="./inchi";
}
system("./inchiwrite $INCHIDIR/Samples.sdf $INCHIDIR/Samples.txt 2>/dev/null");
# If the program failed to execute, ignore the test
if ($? == -1) {
print "1..0 skip because ... |
6d9bbc7171015e2472f07d69fe03af97ad3f38fb777661497570af5eed6aefcf | Perl | 392 | 18 | #!/usr/bin/perl
use Env qw(TESTDATADIR);
if (defined $TESTDATADIR) {
$INCHIDIR="$TESTDATADIR/../inchi";
} else {
$INCHIDIR="./inchi";
}
system("./inchiwrite $INCHIDIR/SamplesTechMan.sdf $INCHIDIR/SamplesTechMan.txt 2>/dev/null");
# If the program failed to execute, ignore the test
if ($? == -1) {
print "1..0... |
82b02dac7a7bd8a27a0b0b58dadfaabf5f37b17a4d74993c70553e395da5cc9d | Perl | 457 | 21 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
for(my $i = $MIN_REP; $i <= $MAX_REP; $i++) {
my $line = sprintf("./discoal %d... |
d1863b30b82838ec6e2215377080359564723188607bde30b8ca8600bf2fcf2e | Perl | 464 | 30 | #!/usr/bin/env perl
# collapseFA.pl
sub descSort;
sub version;
my $option = $ARGV[0];
version if $option eq "-v" or $option eq "--version";
while(<STDIN>) {
chomp;
chop($_) if ($_ =~ m/\r$/);
chomp;
if( not /^>/ and /\w/ ) { $count{$_}++; }
}
$counter = 0;
foreach my $seq ( sort descSort(keys(%count)) ) {
$coun... |
94d76d730bf700ed501f0d2ff0313e95be5ff01ee66d1ba513b5bc191da189aa | Perl | 506 | 19 | #!/usr/bin/perl
$species = shift;
if ($species eq "human"){ open IN, "zcat Roadmap_FantomAnnotations.InputData.pM10Kb.txt.gz | cut -f 1,11 | "; }
else{ open IN, "zcat Mouse_FantomAnnotations.InputData.pM10Kb.txt.gz | cut -f 1,11 | "; }
while(<IN>){
($id, $seq) = split /\t/, $_;
$id2seq{$id} = $seq;
}
close IN... |
8f097d67da97a9a94b31dcb9bcc288f40e4816b6333e48277478e115c4d63da3 | Perl | 519 | 29 | #!/usr/bin/perl -w
use strict;
my $TAG="CB:Z:";
while (<>)
{
my @fields = split /\s+/;
my $chr = $fields[2];
my $s = $fields[3];
my $e = $s + length($fields[9]);
my $name = $fields[0];
my $mq = $fields[4];
my $dir = "+";
my $tag = undef;
for (my $idx = 11; $idx < scalar @fields; $idx++)... |
2217004c070f71df1a6825158c3eefd004743b330c757342bbd1f64040d51a14 | Perl | 547 | 19 | #!/usr/bin/perl
open IN, "<hg19_promoters_cage_corrected_withChr.bed";
while(<IN>){
($id) = ($_ =~ /(ENSG\d+)/);
$seen{$id}=1;
print $_;
}
close IN;
open IN, "zgrep -P '\tgene\t' gencode.v27lift37.basic.annotation.gtf.gz | grep protein_coding | ";
while(<IN>){ chomp;
@a = split /\t/;
($id) = ($a[-1] =~ /(ENSG\d+... |
59d88c3292bc55ec02c0c7dd37523980fe9cc182968e370bd8f6a2e8ddc32c0d | Perl | 588 | 25 | #!/usr/bin/perl
use Chemistry::OpenBabel;
my $obMol = new Chemistry::OpenBabel::OBMol;
$obMol->NewAtom();
$numAtoms = $obMol->NumAtoms(); # now 1 atom
$obMol->NewAtom();
$obMol->AddBond(1, 2, 1);
$numBonds = $obMol->NumBonds(); # now 1 bond
$obMol->Clear();
my $obConversion = new Chemistry::OpenBabel::OBConversio... |
118520407697badf642b2712c70fb8315e905d2643c6f56dd943544db017f5a8 | Perl | 601 | 43 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin");
use GO_DAG;
my $go_dag = new GO_DAG();
#$go_dag->dump_DAG();
#die;
my @go_ids = @ARGV;
unless (@go_ids) {
for my $id (1..100) {
my $go_id = sprintf("GO:%07d", $id);
push (@go_ids, $go_id);
... |
9db5716ce88bf80762a640146fbd1ea294007dbcc7b6d929c93b65e937fe8f22 | Perl | 626 | 32 | #!/usr/bin/env perl
use strict;
use warnings;
unless (-s "gene_ontology_ext.obo") {
&process_cmd("wget http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo");
}
unless (-s "gene_ontology_ext.obo.tab") {
&process_cmd("./obo_to_tab.pl gene_ontology_ext.obo > gene_ontology_ext.obo.tab");
}
... |
e8523836ecaf5cbc978d956c687c6ea9636fda69231c1d79104edfc34ce878fe | Perl | 651 | 27 | #!/usr/bin/perl -w
use strict;
my $NREPS = $ARGV[0];
my $lambda = $ARGV[1];
my $mr = 1.25e-8;
my $sel = $ARGV[2]; # Either 0.1 or 0.5 for wearker or strong BGS
my $chr = 1100000;
my $mean_rr = 1e-8;
my $samp = 200;
my $size = 1e4;
my $tsamp = 12*$size;
for(my $i = 1; $i <= $NREPS; $i++) {
my $rr = -$mean_rr * log( ... |
8aa0c7a08647c518079cbf9646b120b8478056cf34ccb1f553973495882c9b58 | Perl | 683 | 43 | #!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Carp;
my $usage = "usage: $0 /path/to/target.pep\n\n";
my $target_pep = $ARGV[0] or die $usage;
my $workdir = dirname($target_pep);
chdir $workdir or die "Error, cannot cd to $workdir";
if (-e "biolib.ok") {
print STDERR "-skipping $target... |
035c46482a89c591ed633e53cb97977722cbca17445081b74121c24ddd84ebf3 | Perl | 698 | 30 | #!/usr/bin/perl
use strict;
use warnings;
my $use = <<"END";
converts parameters files
param,value
param2,value2
to
param,param2
value,value2
for molgenis
supports the removal of comments (lines starting with #) and empty lines for notes
use: $0 parameters.csv > parameters.molgenis.csv
END
die $use if(scal... |
e93beebe2d344dfce046062abc9f89cde3f8b1ffa1b679624bc473b65192a246 | Perl | 797 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
## cleaning up:
my @tmpfiles = qw(go-basic.obo
pfam2go
pfam2go.1
NOG.annotations.tsv.gz
NOG.annotations.tsv.gz.bulk_load
go-basic.obo.tab
... |
f604d304f87d9f89feecb82d356a48f036dd66a4071e749a33fbaca28cb9e907 | Perl | 846 | 33 | #!/usr/bin/perl
open IN, "<ensembl2geneName_v90.txt";
while(<IN>){ chomp;
@a = split /\t/, $_;
$id2parent{$a[1]} = $a[0] if $a[2] =~ /^\d+|^X/; #remove haplotypes when considering Ensembl ID
}
close IN;
open IN, "<HGNC2Ensembl.txt";
while(<IN>){ chomp;
@a = split /\t/, $_;
@b = split /, /, $a[1];
@c = split /, /... |
4e885659937835578b7bdf6dd588d93e2d43b092f4d257ae1063adf2fd12d464 | Perl | 865 | 34 | #!/usr/bin/env perl
use strict;
use warnings;
# orig contrib from Brian Couger
my $usage = "usage: pfamtoGo\n";
my $PFAMtoGO_file = $ARGV[0] or die $usage;
main: {
open (my $fh, "<", $PFAMtoGO_file) or die $!;
while (<$fh>)
{
chomp;
unless (/\w/) { next; }
if (/^\!/) { next; } # c... |
45f185cf03157faefeb9239058f280a5d99558e328cdea3424c22c6fcf8b1504 | Perl | 867 | 50 | #!/usr/bin/env perl
unless (@params = @ARGV) {
die "usage: $0 [-t|-s] <number list | range>\n";
}
$delimeter = pop @params;
if ($delimeter eq '-s' || $delimeter eq '-t') {
if ($delimeter eq '-s') {
$delimeter = '\s+';
} elsif ($delimeter eq '-t') {
$delimeter = '\t';
}
pop @ARGV;
} else {
$... |
2dd59f84cf77c2aec497af03dacdea94f6608b08d1299d7f00c3d8e6980c7802 | Perl | 898 | 31 | #!/usr/bin/perl
## The FASTA input should be your reference FASTA used in the MPRAMatch.wdl pipeline
## The FASTA should be broken into groups for each "project" i.e. negative controls, positive controls, experimental
## Any oligos which belong to more than one group should processed separately, and the two projects s... |
ca08c1e6c6ebaedd9a723c3975dbd74286265a4ed5b5c97ae70959c0f9e36589 | Perl | 916 | 48 | #!/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::RealBin or die "error, cannot cd to $FindBin::RealBin";
my @files_to_keep = qw (
cleanme.pl
runMe.sh
runMe.... |
e3ece490b5315b4e72d27b9760f3741b422306f39b622d0bb65e211a7b98e83c | Perl | 941 | 32 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
my $infreq_lower_log10 = log(0.001) / log(10);
my $infreq_upper_log10 = log... |
3656d2f0303d68e7df8fc40d1b1cbc1ac1e5b365dbb4856e455487c866d5ee98 | Perl | 968 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
use Data::Dumper;
my $usage = "usage: gene_ontology_ext.obo\n\n";
my $gene_ontology_file = $ARGV[0] or die $usage;
main: {
my %dat;
open (my $fh, $gene_ontology_file) or die $!;
while (<$fh>) {
unless (/\w/) { next; }
chomp;
if ... |
296c0d5b42ec264f2b1d922b522afcd77992b2ca91365129c11ff68be2c376c4 | Perl | 986 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Piechart;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Piechart",
-onLoad => "load_plots();");
my $piechart_tester = ... |
b53e51ca53e5c62c75223dfeec97ccd9618a2308401761c54ef66d48e67a5084 | Perl | 1,022 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Barplot;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Barplot",
-onLoad => "load_plots();");
my $barplot_tester = new... |
ad9efbded99a2b0dc10af2af2603f8c29535eb05d95a5916793c8572cefc8bbb | Perl | 1,055 | 35 | #!/usr/bin/perl -w
use strict;
my $MIN_REP = $ARGV[0];
my $MAX_REP = $ARGV[1];
my $n = 200;
my $L = 1.1e6;
my $N = 1e4;
my $mu = 1.25e-8;
my $meanR = 1e-8;
my $theta = 4 * $N * $mu * $L;
my $meanRho = 4 * $N * $meanR * $L;
my $infreq_lower_log10 = log(0.001) / log(10);
my $infreq_upper_log10 = log... |
ab22af1846deb925b28e6c8054195e43be8f2902c8a68b89ccecfb6aa2f4c665 | Perl | 1,063 | 54 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 Trinotate.xls\n\n";
my $trinotate_file = $ARGV[0] or die $usage;
main: {
open (my $fh, $trinotate_file) or die $!;
my $header = <$fh>;
chomp $header;
my @fields = split(/\t/, $header);
my %column_counter;
m... |
20c024d291bac20c68d733f7363cd793d1219512cb83302763ab714290fd8dde | Perl | 1,102 | 51 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = "usage: $0 sqlite.db transcripts.fasta\n\n";
my $sqlite_db = $ARGV[0] or die $usage;
m... |
6b2014691819c9e296f86bea33ab8fa4c5ac3a4a15ee9e7f3868d36af5dfa7c2 | Perl | 1,151 | 38 | #!/usr/bin/perl
$file = shift;
$spec = shift;
$dist = 10000;
open IN, "zgrep -P '\texon\t' $file | ";
while(<IN>){
($chr, $region, $start, $stop, $str, $last) = (split /\t/)[0,2,3,4,6,-1];
($parent) = ($last =~ /(ENS\w*G\d+)/);
$has5pUTR{$id} = 1;
if($str eq '+'){
$allregions{$parent} = $start if (! exists $al... |
1963c21f2c3268cca5c745def7f99fe1d200fab7008a5bb5f938157bf729ad9d | Perl | 1,177 | 63 | #!/usr/bin/perl
use strict;
my $tftb_root = "tests";
@ARGV = "$tftb_root";
my $dir = $ARGV[0];
ListRep($dir);
sub ListRep {
my ($dir) = @_;
if (! -e $dir ) {
print "Unknown directory ($dir).";
return undef;
}
if (! -d $dir ) {
print "$dir is not a directory";
return unde... |
f49b637f401899b26427a089bcf124822be28aab9dfdbe0e49a1fd5b65e75948 | Perl | 1,178 | 59 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../../PerlLib");
use Fasta_reader;
my $usage = "usage: $0 fasta_file output_prefix gapLength\n\n";
my $fasta_file = $ARGV[0] or die $usage;
my $output_prefix = $ARGV[1] or die $usage;
my $gapLength = $ARGV[2] or die $usage;
... |
fbbc36bf252c581fa10b8c02230cc09636c470518e50595bbf1c94ac7dd627ca | Perl | 1,178 | 63 | #!/usr/bin/perl
use strict;
my $tftb_root = "demos";
@ARGV = "$tftb_root";
my $dir = $ARGV[0];
ListRep($dir);
sub ListRep {
my ($dir) = @_;
if (! -e $dir ) {
print "Unknown directory ($dir).";
return undef;
}
if (! -d $dir ) {
print "$dir is not a directory";
return unde... |
4e27553a5daf101ec91ba3957113455a85ae0b14652b399d8b6ffbd6486f7543 | Perl | 1,183 | 38 | #!/usr/bin/perl
$file = shift;
open IN, "zgrep -P '\tUTR|CDS\t' $file | ";
while(<IN>){
($region, $start, $stop, $last) = (split /\t/)[2,3,4,-1];
($parent, $id) = ($last =~ /gene_id "(ENS\w*GR?[\d|\.]+.*)"; transcript_id "(ENS\w*TR?[\d|\.]+.*)"; gene_type/);
$lengths{$id}{$region} += ($stop-$start);
}
close IN;
o... |
f4619a6e14dd4340f0fa705e9c720b9bb6d18c2233a3519a3665142857c22e12 | Perl | 1,192 | 63 | #!/usr/bin/perl
use strict;
my $tftb_root = "refguide";
@ARGV = "$tftb_root";
my $dir = $ARGV[0];
ListRep($dir);
sub ListRep {
my ($dir) = @_;
if (! -e $dir ) {
print "Unknown directory ($dir).";
return undef;
}
if (! -d $dir ) {
print "$dir is not a directory";
return u... |
72bf46d35c1b6a624dc132862cb024f5a62e2805768f74f5e50be93fb8f0786b | Perl | 1,247 | 57 | #!/usr/bin/env perl
use warnings;
use strict;
my @temp=();
open(FH, "< ../All_ModelSEED_Structures.txt");
my %MS_Structures=();
while(<FH>){
chomp;
@temp=split(/\t/);
next unless $temp[1] eq "InChIKey";
$temp[7] =~ s/-\w$//;
$MS_Structures{$temp[7]}=1;
}
close(FH);
close(OUT);
#Downloaded from:
#... |
6a467eec11233c9482ced9ababfd3a5d04bb454722b65f6df96c342e5bd67bf0 | Perl | 1,286 | 62 | #!/usr/bin/env perl
use strict;
use warnings;
use DBI;
my $usage = "usage: $0 sqlite.db [go|go_slim] obo.tab\n\n";
my $sqlite_db = $ARGV[0] or die $usage;
my $tablename = $ARGV[1] or die $usage;
my $obo_tab_file = $ARGV[2] or die $usage;
unless ($tablename eq "go" || $tablename eq "go_slim") {
die "Error, tabl... |
dd33b5f80769a92ef34c93e0f653ab0bc7c9f5b1ceab3b7db9d88d6e3dc65748 | Perl | 1,316 | 43 | #!/usr/bin/perl -w
# Some sample GMP module operations
# Copyright 2001, 2004 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the F... |
dff0475cd5851a60a791020abeaacff762f0857c398c52d61ece90c701c07cb1 | Perl | 1,369 | 71 | #!/usr/bin/perl
# genoCheck.pl
use warnings;
use strict;
die(qq/
genoCheck.pl <vcf>
OR
cat <vcf> | genoCheck.pl
Quickly checks whether every line contains the expected number of individual entries.
\n/) if (!@ARGV && -t STDIN);
my $vcf = pop @ARGV if (@ARGV);
my $vcffh;
if ($vcf) {
open($vcffh, '<', $vcf) or die(... |
671aaa610260754d44da1ca085070f5ba06fa378ed9b2b21a67f8ee8fb8ad15a | Perl | 1,395 | 62 | #!/usr/bin/perl
## Create attributes file based on count data, and a list of controls
## Oligo example: chr:pos:ref:alt_allele_window_strand
## output columns: id snp allele window strand haplotype project
use strict;
use warnings;
my $oligo_project=$ARGV[0];
my $out=$ARGV[1];
open (PROJ, "$oligo_project") or d... |
284c71f3c553c32aebbafe5cb1ef8744b6b7ddf05aa8ba0d68c0108ad9e815ff | Perl | 1,407 | 69 | #!/usr/bin/perl
#-------------------------------------------------
#
# The script execute the tests under octave and
# sent the errors in error.log
#
#-------------------------------------------------
use strict;
my $tftb_root = "../tests";
@ARGV = "$tftb_root";
my $dir = $ARGV[0];
ListRep($dir);
sub ListRep {
... |
84f7606a7db51825422ca3e70ea5a3d3615d406485771a1392fb7232849ce4cc | Perl | 1,423 | 70 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Sqlite_connect;
use Trinotate;
my $usage = "usage: $0 sqlite.db annotations_file.txt\n\n"
. " Note: annotations file should have format: \n"
. " gene_id (tab) transcript_id (tab) annotation text till... |
07eec38942d3dc8d69d71b28a061dac8a79340e978a36d815747e814bd0daad4 | Perl | 1,441 | 61 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::GenomeBrowser;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing GenomeBrowser",
-onLoad => "load_plots();");
my $plot_loa... |
bcb8da9645194a0adc03369022f2be7d94c721fe1d5d467adfc5e603c3c3d34e | Perl | 1,467 | 41 | use ExtUtils::MakeMaker;
use lib 'inc';
use Devel::CheckLib;
$CC = 'g++';
$cmakesrcdir = @ENV{"SRC_DIR"};
$cmakebindir = @ENV{"OBJ_DIR"};
# Look for libopenbabel.so
if (-e "$cmakebindir/lib/libopenbabel.so" || -e "$cmakebindir/lib/libopenbabel.dylib") {
check_lib_or_exit( lib => 'openbabel' , libpath => "$cmakebi... |
7ee02d966b00691526ab7d97ed40d584596dbe5bdca0c3bb454f881b3639a822 | Perl | 1,484 | 68 | #!/usr/bin/perl
#usage: perl freq_calculator.pl -I <infile> -M <mean|median>
use strict;
use warnings;
use Getopt::Long;
use List::Util qw/sum/;
use File::Basename;
my ($infile,$method);
GetOptions(
"infile|I=s" => \$infile,
"method|M=s" => \$method,
);
if (defined($infile) and defined($method)) {
my ($fn,... |
920f915f48c99ee854dba9a049c7e1b16d4c27b5386863bbdde043e6acdde9e6 | Perl | 1,519 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = "usage: $0 --gene_accs gene_list.txt --suffix <string> matrix1 [matrix2 ...]\n\n";
my $help_flag;
my $gene_accs_file;
my $suffix = "selected";
&GetOptions ( 'h' => \$help_flag,
... |
d5188cd49b0beb992804cfbf6a91e37d1e48405f4d0af6861123aad3d50630fd | Perl | 1,604 | 78 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Carp;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###########################################################################
#
#... |
a6eaf718a90d10760eaaf7ca2947a8cc59b1d6c8c60073692bcff708ae860f63 | Perl | 1,608 | 76 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Sqlite_connect;
use Trinotate;
my $usage = "usage: $0 sqlite.db Trinotate_report.xls [purge_old_annots_flag]\n\n";
my $sqlite_db = $ARGV[0] or die $usage;
my $annot_file = $ARGV[1] or die $usage;
my $purge_... |
4aca3dbd99a6576ba31af89577b4a9d18a1b63c5ba2887d6d02e793716464c06 | Perl | 1,613 | 64 | # GMP perl module tests (part 2)
# Copyright 2001 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; eith... |
754a47f21f23672d3e7b365c653c34882532297545490833e00203d44f05443b | Perl | 1,640 | 65 | #!/usr/bin/perl
open IN, "<ensembl2geneName_v90_mm10.txt";
while(<IN>){ chomp;
@a = split /\t/, $_;
$id2parent{$a[1]} = $a[0] if $a[2] =~ /^\d+|^X/; #remove haplotypes when considering Ensembl ID
}
close IN;
open IN, "cut -f 2,10 MGI_EntrezGene.rpt | ";
while(<IN>){ chomp;
@a = split /\t/, $_;
$mgi2synonym{$a[0]}... |
bdf28e4363c9bf3216aa8128f6acabb06a9b3606fb3dc090fb3866ef41df329a | Perl | 1,642 | 75 | #!/usr/bin/perl -w
use strict;
use FileHandle;
my $USAGE = "splitbarcodes.pl validbarcodes all.bed directory >& split.log\n";
my $validfile = shift @ARGV or die $USAGE;
my $allfile = shift @ARGV or die $USAGE;
my $outdir = shift @ARGV or die $USAGE;
my %valid;
my %invalid;
my $invalidfh = FileHandle->new("> $ou... |
f309c983c9b1c20895e0eb3d8dd18607eecc55ef83cb764a8cac219854574a84 | Perl | 1,662 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Line;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Line plot",
-onLoad => "load_plots();");
my $tester = new CanvasXp... |
e7540a647980307a72f06f1de82d10440debb814e052e72602d51a07d96080c6 | Perl | 1,732 | 64 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Scatter2D;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Scatter2D",
-onLoad => "load_plots();");
my $scatter_2D_teste... |
3c1e5e29b2e3ff7132c046f005206b4604d9504df9da4f7c8e52812b214da6a3 | Perl | 1,761 | 40 | #!/usr/bin/perl
$file = shift;
open IN, "zgrep -P '\tfive_prime_utr|three_prime_utr|CDS\t' $file | ";
while(<IN>){
($region, $start, $stop, $last) = (split /\t/)[2,3,4,-1];
($parent, $id) = ($last =~ /gene_id "(ENS\w*GR?[\d|\.]+)"; gene_version "\d+"; transcript_id "(ENS\w*TR?[\d|\.]+)";/);
$lengths{$id}{$region} ... |
923f6834303223c05c8b5b5c7bae39fe02b99339b95da387b1c0997a35b6687a | Perl | 1,772 | 90 | #!/usr/bin/perl
#-------------------------------------------------
#the script changes the confidential text by
#that of the license CeCILL .
#
#-------------------------------------------------
use strict;
my $tftb_root = "mfiles";
@ARGV = "$tftb_root";
my $dir = $ARGV[0];
ListRep($dir);
sub ListRep {
my (... |
475ae7075b323ea94284d35f376a40b117482f1800e73e80c6e79a1f3bf24af6 | Perl | 1,800 | 69 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Heatmap;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Heatmap",
-onLoad => "load_plots();");
my $heatmap_tester = new... |
ff3a859d1b97f766cd2f8153c55bf3f31cd68b258c2211e03ab8a46e2c50d19d | Perl | 1,861 | 79 | #!/usr/bin/env perl
## Pombert JF, Illinois tech - 2019
my $version = '1.2a';
my $name = 'count_SNPs.pl';
my $updated = '2021-03-13';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
#########################################################################
### Command line options
#########################... |
dba1692cf581398311b9402b2079db7d7d1c5c9d037847d3b85b5ae35ae4a002 | Perl | 1,954 | 66 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 [port_no=8080]\n\n";
my $port_no = $ARGV[0] or die $usage;
## if the port comes up as already being used, check what's using it like so:
## sudo fuser -v 3000/tcp
## and kill it or choose a different port to use.
##
## other useful... |
9ddfda98bbe1b33bd5e2595a78041daa72c03c829ca86b78d1bebaa69ac4b568 | Perl | 1,960 | 71 | # Makefile for GMP perl module.
# Copyright 2001, 2003, 2004 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Found... |
2366a414853b4425a829a36081effebf262b9e6723de846b17c1843d1a085098 | Perl | 1,965 | 90 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
d96e208dbff5fc088dad1c1e0a4cbda2da257681b666480cfe3c0b78026c610c | Perl | 2,082 | 95 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################... |
c4520b34a1cf2999aba9ce52d7d1eef5e7c5337f7e6272064308361e78af8a1a | Perl | 2,116 | 98 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################... |
d06433d53bb9ce5eb5ff474a772e531231eb7e6862a51c0f19bde7daf20c2242 | Perl | 2,158 | 95 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../PerlLib");
use Data::Dumper;
use Sqlite_connect;
my $usage = "usage: $0 Trinotate_db.sqlite\n\n";
my $sqlite_db = $ARGV[0] or die $usage;
# truncate the UniprotIndex table:
=ladeda
delete from UniprotIndex where not exist... |
08e1a07eb213992eb9bdc9231529ba02270f8a30b7c863b42601410d278001cf | Perl | 2,200 | 59 | #/usr/bin/perl
while ($arg = shift) {
if ($arg =~ s/^-//) { $opt{$arg} = 1 ; }
else { last ; }
}
$chr = $arg ;
($pos = shift) || die "usage: perl looksite.pl [-ref] <chr> <pos> [<field>] where field is simple_id, genus, species, clade\n need to set HEADER, METADATA, VCFDIR\n" ;
$feat = shift ;
($chr >= 1 &... |
36edc5645cacd651b9ecded2c5cea5e6cec4d4fdabde62c78bc536017b73584d | Perl | 2,222 | 95 | #!/usr/bin/perl
## Create attributes file based on count data, and a list of controls
## Oligo example: chr:pos:ref:alt_allele_window_strand
## output columns: id snp chromosome snp_pos ref_allele alt_allele allele window strand start stop project
use strict;
use warnings;
my $oligo_project=$ARGV[0];
my $ou... |
a316ba6717396f828f7176267d710c2480f797884044412616d6958863bd12c4 | Perl | 2,359 | 108 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
e980656842c6a391508201e30f92010e9c59f735b148bf309042c3a683bfef3e | Perl | 2,413 | 80 | #! /usr/bin/perl -w
# Copyright 2001, 2003 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation; either vers... |
6721e0175d847ede474515c34da252ba215c119236f03cfb515a720ea0e2fc24 | Perl | 2,432 | 92 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use DBI;
my $usage = "usage: $0 sqlite.db\n\n";
my $sqlite_db = $ARGV[0] or die $usage;
$|++;
main: {
my $dbproc = DBI->connect("DBI:SQLite:$sqlite_db");
unless (ref $dbproc) {
croak "Cannot connect to $sqlite_db: $DBI::errstr";
}
... |
fee502910acb15ae18b00d4cef9a21709a58971ca00dfeedbddd8073dad6198a | Perl | 2,576 | 112 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################... |
244813cfa28a513c7568a6b7876c88c3c7f8e02721bdf8b38bb9d5336082219c | Perl | 2,578 | 109 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use DBI;
use Sqlite_connect;
use Data::Dumper;
my $usage = <<__EOUSAGE__;
###########################################################################... |
3f773a89817c14d4a4d0851c929ad8c40f933b65951b3c25d9f6b8528de994a0 | Perl | 2,579 | 103 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use File::Basename;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
################################################################################
#
# --transcriptome <string> Transcriptome assembly fas... |
da45732d614c66b996ed132aaf67136827a8a5336666c49f088c3e887f2ddd5f | Perl | 2,622 | 96 | #!/usr/bin/perl
## Create attributes file based on a project file containing the oligo ID and the project(s) to which it belongs
## Oligo example: chr:pos:ref:alt:allele:window(:haplotype)
## output columns: id snp chromosome snp_pos ref_allele alt_allele allele window strand project haplotype
use strict;
use war... |
e6e3a99ce355ec0bb547b571ca16d38eeb09b8fd341a4e71990c918e3d7c1518 | Perl | 2,671 | 117 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Fasta_reader;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
######################################################################... |
95b27648ef8769e9f83ed14dc5f9c105f7ab5a779e090fbc874713ba7e333e89 | Perl | 2,698 | 119 | #!/usr/bin/perl
# maskStarGeno.pl
# masked individuals have the following genotype information:
# GT set to missing, "./.", and all other FORMAT subfields to zero
# each PL value becomes 0, e.g. "0,0,0"
# encodes GQ for masked individuals as 0
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $version='0... |
efd4544d5ee3bbf7443228b00e40617032af577f8d9fecfa3a17be78f4c3f67a | Perl | 2,721 | 158 | #!/usr/bin/perl
#
# Program to reformat the TOPMed vcf to a format for pre-imputation checking.
# W.Rayner 2020
# william.rayner@helmholtz-muenchen.de
# wrayner@well.ox.ac.uk
#
# v1.0.0 Created
#
#
#
#
#
#
#
#
#
use strict;
use warnings;
use File::Basename;
use File::Spec;
use Getopt::Long;
use Cwd;
use IO::Uncompres... |
8a890e541fcd158786cbd9aa673d634203aa89427205bc9e74beef8430be3177 | Perl | 2,792 | 96 | #!/usr/bin/env perl
## Pombert JF, Illinois Tech - 2019
my $version = '1.1c';
my $name = 'run_Mash.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Path qw(make_path);
#########################################################################
### Command line optio... |
1b3202ead7d8a061627b5dac1b6371b486e05b0ac58df7ddd3796a8af348cf93 | Perl | 2,808 | 105 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
my $usage = "usage: $0 file.eggnog_counts\n\n";
my $inputfile = $ARGV[0] or die $usage;
my $funcat_file = "$FindBin::Bin/../../../resources/eggnog/3.0/COG_KOG_NOG.funccat.txt";
my $descr_file = "$FindBin::Bin/../../../resources/eggnog/3.0/fun.txt";
main: ... |
c53f0154700c51185db3d26bba23e256fd948af9bf2931f5b4ce8c90b8f8765c | Perl | 2,832 | 113 | #!/usr/bin/perl
#
# Uploads MP3s from current directory, recursively.
# Optional arguments can be directories.
#
use File::Basename;
use MP3::Info qw(:DEFAULT :utf8);
if ($ENV{'LANG'} =~ /utf-8/i) {
use_mp3_utf8();
}
foreach $dir (@ARGV) {
push @dirs,`find $dir -type d`;
}
if ($#dirs < 0) {
@dirs = `find . -type ... |
dd2546f629caeecb887184b2243fbce49697e2f8aa4457c547fb67380282bd95 | Perl | 2,961 | 115 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use GO_DAG;
use DelimParser;
main: {
my $go_slim_file = "$FindBin::Bin/../../PerlLib/obo/goslim_generic.obo.gz";
unless (-... |
ffdbf7eb3213f574729276aad037bb129098cde07e1d733234a011d3296864b6 | Perl | 3,031 | 113 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use Data::Dumper;
my $usage = "usage: $0 pfam.dat\n\n";
my $pfam_dat_file = $ARGV[0] or die $usage;
=sqlite_structure
pfam_accession = PF08793.5
pfam_domainname = 2C_adapt
pfam_domaindescription = 2-cysteine
Sequence_GatheringCutOff ... |
2fa19880d1e86c913ad43405fcc8ad4565df0e4b35167cbe99e00c6cf224903b | Perl | 3,058 | 93 | #!/usr/bin/perl
use allfxns;
$exprMat = shift;
$spec = ($exprMat =~ /mouse/)? 1 : 0; #species is mouse or human?
sub readBed{
local $bed = shift;
local %bed = ();
open BEDENTRY, "<$bed" || die "Could not open bed file for $bed\n";
while ($line = <BEDENTRY>){
@a = split /\t/, $line;
$bed{$a[3]} = $line;
}
c... |
cdeba3bf1896c7c57edf49ea16bff3a24a452f1e2d695f6cc2f688f245b45fab | Perl | 3,095 | 120 | #!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#-----------------------------------------------------------------------------
my $usage = ... |
2beee576201f917ce75bee72c12c481242e881a59340b696854d29c3abecb340 | Perl | 3,119 | 89 | #!/usr/bin/perl
use warnings;
use strict;
use File::Copy::Recursive qw(fcopy rcopy dircopy fmove rmove dirmove);
use File::Copy "cp";
use File::Spec "catfile";
use File::Spec "splitpath";
my $dir = shift@ARGV;
die "Please provide a directory to copy files to!\n\n" unless ($dir);
unless (-d $dir){
warn "Specified d... |
268406844da3c483e0d689c9aeb9b06d683226b4f2c17779044000609a531b86 | Perl | 3,136 | 128 | #!/usr/bin/env perl
## Pombert JF, Illinois Tech - 2019
my $version = '0.5a';
my $name = 'get_SRA.pl';
my $updated = '2024-05-28';
use strict;
use warnings;
use Getopt::Long qw(GetOptions);
#########################################################################
### Command line options
############################... |
b945a53da3379b18ec2d39a3de0e105afef0391ca7c2d8a13ebbc3f1dd20b386 | Perl | 3,387 | 117 | #!/usr/bin/env perl
use strict;
use warnings;
use CGI;
use FindBin;
use lib ("$FindBin::RealBin/../../");
use CanvasXpress::Sunburst;
use CanvasXpress::PlotOnLoader;
my $cgi = new CGI();
print $cgi->start_html(-title => "Testing Sunburst",
-onLoad => "load_plots();");
my $sunburst_tester = ... |
0bd78ae51894d75ba82e98deff9837b8f44dcd01d2d21b133a578a98f8b22414 | Perl | 3,408 | 117 | use strict;
use warnings;
use constant pi => 4*atan2(1, 1);
sub Gamma { #gamma function using lanczos method
my $z = shift;
use constant g => 9;
$z < .5 ? pi / sin(pi * $z) / Gamma(1 - $z) :
sqrt(2* pi) * ($z + g - .5)**($z - .5) * exp(-($z + g - .5)) *
do {
my @coeff = qw{
... |
b6a20b6f0b181bc7fa98921a97bc1ef579162271506bf1dd129883d884021310 | Perl | 3,444 | 125 | #!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 Trinotate.xls\n\n";
my $trinotate_xls = $ARGV[0] or die $usage;
main: {
my %data;
open (my $fh, $trinotate_xls) or die $!;
my $header = <$fh>;
chomp $header;
my @fields = split(/\t/, $header);
my %col_no_to_field;
... |
2c98b82f00272b552daca869aad6fa75b2676a24b6992e11873ede76c4d318ee | Perl | 3,498 | 113 | #!/usr/bin/perl
# variant_summary.pl
use warnings;
use strict;
die(qq/
variant_summary.pl <log directory> <log file prefix, '_[1-20,22-25].err' appended>
\n/) if (!@ARGV && scalar(@ARGV) < 2);
my $dir = $ARGV[0];
$dir =~ s/\/$//;
my $prefix = $ARGV[1];
my $nfields = 10;
my @counts;
# 0: Number of VCF entries (lin... |
fbe95e104f813ed24638db1109c62b6cfdfa07af7c1fd34509435904852eb2ae | Perl | 3,636 | 189 | #!/usr/bin/perl
#
#by Ryan Tewhey
use strict;
use warnings;
use Getopt::Std;
my %options=();
getopts('SA:', \%options);
#####
#
#-S = Run in saturation mutagenesis mode
#-A = Atributes file
#####
my $sat_mut_mode;
my $attributes = "NA";
$attributes = $options{A} || "NA";
if(exists($options{S}))
{
print STDERR ... |
e7fd0bf788f2f261990175499bb8d25efcf168bcca9c8dd984bc2e5eda5cb3c3 | Perl | 3,646 | 147 | #!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::RealBin/../../PerlLib");
use Carp;
use DBI;
use Sqlite_connect;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###########################################################################
#
#... |
a81953ac92770cf8e88acb33ef3e29c2d2759a3842d4a65a15d03d38e0280197 | Perl | 3,756 | 145 | #!/usr/bin/perl
# bedmask.pl
use warnings;
use strict;
use Getopt::Long;
my $mindepth = 0;
my $maxdepth = "inf";
my $minmq = 35;
my $maxmq0 = 0.2;
my $minbq = 20;
my $maxbq0 = 1;
die(qq/
bedmask.pl [options] <input bamstats file> <output file prefix>
Options:
--mindepth INT Minimum total depth [$mindepth]
--ma... |
f7eb20ce236f797beaec9eda33697127ecee6a58a53fb819f61f1d28863b4e3a | Perl | 3,758 | 136 | #!/usr/bin/perl -w
#
# Copyright 2001, 2002 Free Software Foundation, Inc.
#
# This file is part of the GNU MP Library.
#
# The GNU MP Library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either vers... |
a663b2764e4ff89cfcabbbc79e6c3ba85fd9e7b8c05d11c48ac60fe7fd14aad7 | Perl | 3,801 | 165 | #!/usr/bin/perl
# standardizeMissingGeno.pl
# expects FORMAT = GT:AD:DP:GQ:PL
use warnings;
use strict;
use IO::Zlib;
use Getopt::Long;
my $version = '1.0.0';
my $noheader = undef;
die(qq/
standardizeMissingGeno.pl v$version
standardizeMissingGeno.pl <input vcf> [options]
OR
cat VCF | standardizeMissingGeno.pl [... |
888995d829e8b1e30781ffbcb22e8832a06aa678c9a49c293864a694ecb472a5 | Perl | 3,838 | 168 | #!/usr/bin/perl
##################
#
#052314 - Updated to account for multimapping oligos
#
####
# FLAGS
##################
use strict;
use warnings;
my $tags = $ARGV[0]; #matched tag file
my $enhancers = $ARGV[1];
my $out = $ARGV[2];
my $read = $ARGV[3];
if ($enhancers =~ /.gz$/) {
open(ENHANCERS, "gunzip -c $enh... |
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