sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8fa654e0e50d96b5e9d846c861db3f11f40b5f43a7da11878c162e453dca9c6e | Perl | 2,600 | 75 | use strict;
use warnings;
my $f=shift @ARGV;
unless(-e $f){die "USAGE:perl fastaUniq.pl <fasta FILE>";}
die "$f.uniq.fasta exists, bailing out for $f!\n" if -e "$f.uniq.fasta";
my %seqh;
my $seqc;
my $f1=shift @ARGV;
open(F1,$f);
my $cnt=0;
my %seqns;
while(my $l1=<F1>){
chomp $l1;
$l1=~s/\r//g;
$l1=~s/\\t//g;
$l1... |
5a66a02df46651a6f14df8160601693f7f7e6dcfe6ceff4f0318a5955f57d485 | Perl | 2,602 | 94 | #!/usr/bin/perl
#programme for motif generation FASTER ALGO;
@base=qw/a t c g/;
print "\nenter the multiple seq. containing fasta file name\t:";
#$file="testy.txt";
$file=<>;
chomp $file;
open(F,$file)||die "can't open";
print "\nenter the output filename for position matrix\t:";
#$out="out.txt";
$dout=<>;
c... |
3bafda1db5634ba85a442d77ea40cc80323955bca63002706bc9e8378c0e0046 | Perl | 2,620 | 94 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
79d63a13657c95c797efed1af5d7976fc557d33d604fcb40d6da52bbe83d12cd | Perl | 2,620 | 107 | #!/usr/bin/perl
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName MultSeqFile\t\n\n\n";}
$file = shift @ARGV;
open (F, $file) || die "can't open \"$file\": $!";
$seq="";
while ($line = <F>) {
if ($line =~ /^>/){
$c++;
chomp $line;
#print "Reading\t\tseq no.$c\t$line\n";
$line=~s/\|/\-/g; $line=~s/\s+//g;#$lin... |
1d342579c80c4498e5e49c5fb96bfdf49ff647c5cf3d9e8fa57d38a59ca23587 | Perl | 2,622 | 97 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
dd33da88996392fc011cd2ec1282a741a89a19a0756aa78f59745841e16b89a9 | Perl | 2,651 | 94 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
15fce763955f9d816d702530d69709562d613298c620c59437b74a1cf7bc2787 | Perl | 2,659 | 106 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
d043d5990cfbb3ada80927fadd215d8d20358493208da31779ebb5ca01385913 | Perl | 2,687 | 68 | use lib '/Home/siv11/ash022/home/cbu/2010/JSON-2.17/lib';
use JSON;
use Data::Dumper;
use LWP::Simple;
# gene queries
my @geneQ = qw (
http://www.ebi.ac.uk/gxa/api?geneGotermIs=p53+binding&geneDisease=cancer&rows=5
http://www.ebi.ac.uk/gxa/api?geneIs=ASPM&rows=5
http://www.ebi.ac.uk/gxa/api?geneIsNot=cell+cycle&rows=... |
8c069c852e38c64fd241800e4d00a1a6f713a523914e13b30ad657d89540f360 | Perl | 2,704 | 109 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
edaf371aeb257a14df3bdc975ede1275c2fcd22b8a59eef7abd554da3056b526 | Perl | 2,713 | 84 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
12be278952a3f5ab2f85ca68fd1ea3ac8eab6202c1a3bb8696367ec1ffe928ea | Perl | 2,720 | 96 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
open(F,$file);
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0;
my %... |
42508aed7fcc658d80c493ae8c730a5db36a7911f3468f242fea631b6c5fe266 | Perl | 2,736 | 134 | #!/usr/bin/perl -w
#
# updates the contact list for everybuddy
#
# Ben Rigas <ben@everybuddy.com>
#
# * Now fixes empty group problem *
#
#############################################################################
if ( $ENV{"HOME"} ) {
$file = $ENV{"HOME"} . "/.everybuddy/contacts";
} else {
ch... |
bbde73f06b5893f10c0b5329e37b0bbdad8531d37712df670b16f21f025a7f57 | Perl | 2,744 | 114 | use strict;
use Text::ParseWords;
my $f1 = shift @ARGV;
my $f2 = shift @ARGV;
my $f3 = shift @ARGV;
my $f4 = shift @ARGV;
my $fa = shift @ARGV;
my @tmp;
my @name;
my @names;
my %pg1;
my %pg2;
my %pg3;
my %pg4;
my %pgfa;
my %nc;
#check P08729
open (F1, $f1) || die "can't open \"$f1\": $!";
while (my $line = <F1>) {
... |
6096afcaf07cf9cb3764cbb684d3c0c4678f881a850940ee3554caf4d83f4384 | Perl | 2,763 | 104 | use strict;
#use warnings;
#Simulate circular genome of length $seqlen
sub genseq{
my $seqlen=shift;
my $c=0;
my $seq;
my @b=qw/A T G C/;
#my @b=qw/A C A C/;
my $sn=">Seq$seqlen";
while($c<$seqlen){
$seq.=@b[int(rand(4))];
$c++;
}
print "Simulated Genome $seq\n";
return($sn,$seq);
}
#Split simulated se... |
d21923880e3e05f0a26ac570009a3ec720aa7493535bfd98100cce5eeb273e54 | Perl | 2,778 | 101 | #!/usr/bin/perl -w
use lib '/Home/siv11/ash022/home/cbu/2010/picr/SOAP-Lite-0.710.10/lib';
use SOAP::Lite;
#use SOAP::Lite +trace => 'debug';
use Data::Dumper;
my $accession = shift @ARGV;
#my $accession = 'P29375';
my $accession_version = '3';
my $nameSpace="http://www.ebi.ac.uk/picr/AccessionMappingService";
$soa... |
29cbaed224385c5933303f616e170d37f3fd74b3ed301389073b7ace3da413a8 | Perl | 2,788 | 119 | #!/usr/bin/perl
print "File containing sequence names? ";
chomp ($file = <STDIN>);
open (FILEIN,"$file");
open(FILEOUT,">blastn");
while (chomp ($seq = <FILEIN>) )
{$sout=$seq.".html";
print FILEOUT"/home/andrew/bic/blastcl3 -p blastn -d nr -i $seq -o $sout -T\n";
}
#!/usr/bin/perl
#parse blast results
$... |
7d27ef607fd5e9fa0616623c25907fabb3f34d5d0c7858c4ec3f2cb781903875 | Perl | 2,802 | 101 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
ae3f628d601a290a277364c17b1db783893ae1c2b6ea691b445e0b1383a8a76d | Perl | 2,802 | 101 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
3b40dde3d646893c53ca966f3f527efd26514ce734924749b56c007b7bfb9559 | Perl | 2,811 | 65 | $str="MDLQTLNETSVFLECVEAQGAASNGTPNSSLELTNITTCGNAYVVLKPQHVKQKEVDSLRILLYSVIFLLSVFGNLLIIVVLTVNKRMRTVTNSFLLSLAVSDLMMAIFCMPFTLIPNLLEDFIFGPAMCKIVAYLMGVSVSISTFSLVAIAIERYSAICNPLKSRAWQTRSHAYRVITATWLLSFMIMSPYPVFSHLVHVPLKDNITIARMCRHIWPHREVEQTWNMMLLLTLFVVPGVVMIVAYGLISRELYRGIQFELGQKTSSPGLKNGLTGTVSCGSDDGDGCYVQVSKRPHSMEMSTLTSSTASTSKV... |
e25a46636bf14d2e3eeee70fab1e1653edd65c0bf41be789327e37ac7c30d23d | Perl | 2,827 | 83 | #!/usr/bin/perl
if( @ARGV ne 3){die "\nUSAGE\t\"ProgName MultSeqFile N-basedPeriodicity\t\n\n\n";}
$file = shift @ARGV;$cp=0;$cnp=0;
$k = shift @ARGV;
#$ws = shift @ARGV;
use Math::Complex;
$pi=pi;
$i=sqrt(-1);
$f=(1/$k);
open (F, $file) || die "can't open \"$file\": $!";
$seq="";while ($line = <F>) {
... |
72d2ff43cd767a96d5d3d6df577870001ed5f32a39875cf6f6744d865ff47a85 | Perl | 2,867 | 100 | #!/usr/local/bin/perl -w
#
# Read a palette definition, create HTML to display those colors
# in a pattern so they can all be seen next to each other
# to determine if any of them are so similar they meld together
#
# The input palette definition file has lines defined as such:
#996600 1
# and yes, they do be... |
40ff042458c6ef11ec35eb8694f4a6e6db9c513e346eed5d8f2cb6914b909dd4 | Perl | 2,955 | 100 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
3d428f71fe3effce12f83f73f4a79dd6fc0831be3ac86c2dd001c51033b14bfb | Perl | 2,972 | 122 | #!/use/bin/env perl
use strict;
use warnings;
use DBI;
my $release = $ARGV[0] || die "Usage: $0 <release_num>\n";
my @servers = qw(ens-staging ens-staging2);
my $default_port = 3306;
my $aliases = {
"Homo_sapiens" => "human",
"Mus_musculus" => "mouse",
"Danio_rerio" ... |
c403146ebc1544716a16f93ca0704628670d05fe6116049f56babed58287801a | Perl | 2,988 | 104 | #!/usr/bin/perl -w
use Bio::Seq;
use Bio::Index::Fasta;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Tools::BPlite;
#$out = Bio::SeqIO->new(-file => ">>seq" , '-format' => 'Fasta');
my (@hits,@seqname,@repname);
print "File with list of contig_names? ";
$filename = <STDIN>;
open (FILENAME,$filename) || die... |
5287949f56f1de3550b970fbd3eba5ad0e09b027cd35bd04ee1b0bc802a44bc7 | Perl | 3,006 | 135 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
f1cb1ae074f6df2842f0faf61c9262efd6548360144806898a754659e10905d5 | Perl | 3,009 | 94 | #!/usr/bin/perl -w
use strict;
my $USAGE = "translate.pl file.fasta\n";
my %codon =
(
"TTT" => "F", "TTC" => "F", "TTA" => "L", "TTG" => "L",
"TCT" => "S", "TCC" => "S", "TCA" => "S", "TCG" => "S",
"TAT" => "Y", "TAC" => "Y", "TAA" => "*", "TAG" => "*",
"TGT" => "C", "TGC" => "C", "TGA" => "*", "TGG... |
de8e056216397552bd59d710657df8c350a09c2b57b4d8ee4709f50b9507136a | Perl | 3,014 | 96 | $file=shift @ARGV;chomp $file;
open (F,$file)||die "cant open :$!";
$seq="";
while ($line = <F>){
chomp ($line);
if ($line =~ /^>/){
$line =~ s/>//;
push(@seqname,$line);
if ($seq ne ""){
push(@seq,$seq);
$seq = "";
}
}... |
156fb17e3db75a68d0df4ff46e9a57af39d608fe9cb41065a260989c1229f283 | Perl | 3,026 | 103 | use strict;
use lib '/home/ash022/Desktop/bac2fish/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $file=shift @ARGV;
open(F,$file);
my $genome=shift @ARGV;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my $line... |
dd37087475c14bf2dd220244264466177a1fce904e8df08f2426abec58b14de4 | Perl | 3,034 | 98 | #!/usr/local/bin/perl -w
#
# Read a palette definition, create ImageMagick "convert"
# commands that will draw the color key png(/gif)
#
# The input palette definition file has lines defined as such:
#996600 1
# and yes, they do begin with the # character
# That is the hex value 996600 for chrom 1
use stric... |
e3e5728334a95c8a06336e2ac5886d51c9c3db47659dedb6b17dcbdc8fbf7151 | Perl | 3,053 | 108 | #!/usr/bin/perl
%t2o = (
'ALA' => 'A',
'VAL' => 'V',
'LEU' => 'L',
'ILE' => 'I',
'PRO' => 'P',
'TRP' => 'W',
'PHE' => 'F',
'MET' => 'M',
'GLY' => 'G',
'SER' => 'S',
'THR' => 'T',
'TYR' => 'Y',
'CYS' => 'C',
'ASN' => 'N',
... |
6f82d3236b1a24cdaf15bb0917819db8444cf1c5a6a227d6ff0e0b03ea39a744 | Perl | 3,072 | 96 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=100;
my %hitpos;
my %hitname;
my $max... |
e06b24ab9a87679ddf9784372aa3b16bbeb8413ac4e8709234be39ad69969150 | Perl | 3,076 | 112 | use strict;
use warnings;
use Text::ParseWords;
my $file1=shift @ARGV;
my $kmer=shift @ARGV;
my $kmerstart=shift @ARGV;
open F1, "$file1" or die "Can't open file : $file1 $!";
my %seqh;
my $seqc;
my %val;
my $cl=3;
my %kmergene;
my %kmerprot;
my %c2a = (
'TTT' => 'F','TTC' => 'F','TTA' => 'L','TTG' => 'L... |
4a717196faf55451f653db12f469075ae7cb4268eb17e01fb9038f32d0dfd3c8 | Perl | 3,091 | 102 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
a10aa5146e4184922a34b73f05699edff73c6f4e76d1d18bdc6cc928b7591182 | Perl | 3,092 | 118 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6fe2cc0847af7322115cc308508949e07f863b6e43921009bbdebfb13320b624 | Perl | 3,121 | 87 | use strict;
use Text::ParseWords;
my %bh;
my %bhn;
my $f1 = shift;
my $bp = shift;
my $gn = shift;
my $f2 = shift;
my $gnc = shift;
my $scc = shift;
my %score;
open (F1, $f1) || die "can't open \"$f1\": $!";
my $lc;
while (my $line = <F1>) {
$lc++;
$line =~ s/\r//g;
$line =~ s/\'//g;
chomp $line;
my @tmp1=parse... |
25977044891f8e544ba8b35d088498f7d7202c9a30ad3abe100c10539bfc550d | Perl | 3,124 | 152 | #!/usr/bin/perl
$linenew="";
open (FH,"AC109365.fas.2") || die "cant open file : $!";
while ($line1=<FH>){
chomp $line1;
$linenew=$linenew.$line1;
}
$linenew="0".$linenew;
#print "$linenew\n";
$count=0;
open (F, "AC109365.fas.2.glimmerR") || die "cant open file : $!";
while ($line=<F>){chomp$line;
if($line ... |
4f3d1df1f6dfef29d1da92738d4b72bee2edf7a75a2c474fca1052656bbc2ff3 | Perl | 3,125 | 129 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6b56d7db62ddc5c42ff40613ec5e4addc4090e763d3b5007158f0c6a9c2aa4eb | Perl | 3,146 | 137 | #!/usr/local/bin/perl
# makes GFF stuff for a contig.
BEGIN {
push(@INC,"../modules");
push(@INC,"../../../bioperl-live");
}
use CGI;
use Bio::EnsEMBL::DBSQL::Obj;
use Bio::EnsEMBL::Gene;
use strict;
my $q = new CGI;
print $q->header();
my $geneid = $q->param('gene');
my $gene;
my $db;
... |
8f9d70fc834c3b8652bc6920cff6b08964cbd65a1f76788acf8115a0862096bf | Perl | 3,153 | 153 | #!/usr/bin/perl
$linenew="";
open (FH,"AC109365.fas.2") || die "cant open file : $!";
while ($line1=<FH>){
chomp $line1;
$linenew=$linenew.$line1;
}
$linenew="0".$linenew;
#print "$linenew\n";
$count=0;
open (F, "AC109365.fas.2.glimmerR") || die "cant open file : $!";
while ($line=<F>){chomp$line;
if($line ... |
4faa5f3917c01d10ba5c52b7437f3d0b74fb338753d4c4a48179dc478360a273 | Perl | 3,154 | 96 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=100;
my %hitpos;
my %hitname;
my $max... |
ca4a688176dbe1396857ff0f41f050f78969ce1acb5f1789bcf1a7a64d148250 | Perl | 3,198 | 98 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0... |
abebdc64c4a1d1188572efebbf17a65bf7900159a04e0ad32f9a99fd53b52a6f | Perl | 3,199 | 115 | #!/usr/bin/perl
if(@ARGV != 4){print "usage:\tprogname c nc mm-model test\n";die;}
@base=qw/a t c g/;$bc=@base;
$file1=shift @ARGV;
$file2=shift @ARGV;
$co=shift @ARGV;$colo=$co+1;$jump=1;
$file3=shift @ARGV;
$total=$bc**$colo;#print $total;
(@sq1)=openfile($file1);undef @seqname;#print "sn\t\tsq @sq1\n";
(@... |
3c227d9ba77988ab503d1d7dbbb9e326589f22cc6eed8301ed6a37d649f2dcb2 | Perl | 3,226 | 112 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
399101360fb6dee1c8a15116d3dea1f413fd62d81bf31c4962670fb95c21bec1 | Perl | 3,230 | 108 | #!/usr/bin/perl
use strict;
# Compare trimmed reads against the untrimmed mapping to the reference.
my $gatekeeper = "wgs/FreeBSD-amd64/bin/gatekeeper";
my $snapper = "wgs/kmer/FreeBSD-amd64/bin/snapper2";
my $convert = "wgs/kmer/FreeBSD-amd64/bin/convertToExtent";
my $gkp = shift @ARGV;
my $ref = shift @ARG... |
5d5da77d4b354104f03a26da3227c79a4d3c2f6f7c95ef1c9dad477d9fffdc91 | Perl | 3,239 | 110 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
ac28976ad69493d31e850357ef010946456f26295a52dac2ed7ee92d84b08c92 | Perl | 3,261 | 97 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0... |
d6d3ca8f5d2da5951e1e17ed20d5781dac6699a6645023332caa755da8fde957 | Perl | 3,280 | 140 | #!/usr/bin/perl -w
use Bio::Seq;
use Bio::Index::Fasta;
print "File with list of genescan identified genes? ";
$filename = <STDIN>;
open (FILENAME,$filename) || die " cannot open $filename: $!";
$dir="/home/andrew/exhome";
$db="eh2x";
$dbobj = Bio::Index::Abstract->new("$dir/$db");
while ($gene_seq =<F... |
068325d7201a4245595149745da6aac700161b319d101c79013ea5e2b692d003 | Perl | 3,288 | 140 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
6ae2892e7cb96ea044408364ee06a5fe5565c8879ed44b74649dbd4d061087ad | Perl | 3,289 | 96 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0... |
b48720ec08e11bce3a93be185fd1ae0a008f5dc01396adeac7a9e96bd06dc99a | Perl | 3,319 | 65 | #for($c=1;$c<=10;$c++){
$tempvar=time;
print "File $c selected reads are being written to t1$tempvar\n";
system("head -n 150000 Ecoli.avgqual.sort > t15$tempvar");
system("/home/animesh/export/newblerv2/sfffile -i t15$tempvar -o ecol.rand757660.sel.sff Ecoli.sff");
system("/home/animesh/export/newblerv2/runAssembly -... |
b91866960591ea76f2e41db523a3850d0ccfd5490778c75b23c46cf0eb6e7ddd | Perl | 3,338 | 108 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
643e8aeafa247a4b5a62404baa6fe4ca2ed886f284412c0dd9e37bf06325ee9d | Perl | 3,355 | 132 | #!/usr/bin/perl
# This program 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
# (at your option) any later version.
#
# This program is distributed in ... |
c0961d6518a923d1e9921fe768d82db67354f4f9e6a27f9531470b3bfb568741 | Perl | 3,359 | 104 | use strict;
my @reads=<>;
my %ovlidx;
for(my $c1=0;$c1<=$#reads;$c1++){
my $str1=$reads[$c1];
chomp $str1;
my $len1=length($str1);
$str1=~s/\s+//g;
for(my $c2=$c1+1;$c2<=$#reads;$c2++){
my $str2=$reads[$c2];
chomp $str2;
my $len2=length($str2);
$str2=~s/\s+//g;
if($str2 ne $str1 and $str1 ne "" and $str... |
a21eb534ae6e957c02f84b40374a30c62984ef0c6c2d8088252f4975041fe3c2 | Perl | 3,367 | 122 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
edc41e512039600ce7f9baefc2f305cfc296ec09bc41c90502a01d22f1e7d3f3 | Perl | 3,377 | 84 | use strict;
use lib '/media/DATA/tariku/biomart/lib';
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = '/media/DATA/tariku/biomart/biomart.conf';
my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initi... |
9b951d9bad0941bbf64c1dc95ed94785865922cdc684c75b6fa08e01788f67d9 | Perl | 3,381 | 121 | use strict;
use lib '/home/ash022/Desktop/bac2fish/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $file=shift @ARGV;
open(F,$file);
my $genome=shift @ARGV;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my $line;
my $gn;
m... |
6639511f4e3f41aa71fe79ea6e520f8639eeee7c79f47da671b58652dc9137e5 | Perl | 3,465 | 135 | use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
open(F,$file);
my $perc=0.10;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my $cntseq;
my $totalbs;
my %us;
my $pit=0;
my $alt=0;
my $evt=1000;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0;
my $min=100000000000000;
my %hitscore;
my %compname;
my ... |
371cfdfb406d15e2614a04ed16471416831b2cdadfb173cad8a5710a21fc38d1 | Perl | 3,483 | 88 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
8cf001db8688f11a7ba5830093913da5490e9336263ed44c7b6c6128e3707e71 | Perl | 3,483 | 141 | #!/usr/bin/perl
# This program 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
# (at your option) any later version.
#
# This program is distributed in the ho... |
b3d92d5f3978e348f67efc9dced58e9007dd24b25b1a04d1db91f6142b6f8a2c | Perl | 3,489 | 141 | #!/usr/bin/perl
# This program 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
# (at your option) any later version.
#
# This program is distributed in the ho... |
d087b1d011cd4a8cb5ca58f0634bb05e2f5cf6473f2efdfa9e23b521607e83aa | Perl | 3,489 | 140 | #!/usr/local/bin/perl
# This program 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
# (at your option) any later version.
#
# This program is distributed in ... |
7b3c7ebee74c779718539cec0d1700be701afc2f8b5d0ea4d62282c5033b3828 | Perl | 3,504 | 102 | use strict;
use warnings;
my %seqh;
my %seqm;
my $seqc;
my $f1=shift @ARGV;
my %codon =
(
"TTT" => "F", "TTC" => "F", "TTA" => "L", "TTG" => "L",
"TCT" => "S", "TCC" => "S", "TCA" => "S", "TCG" => "S",
"TAT" => "Y", "TAC" => "Y", "TAA" => "*", "TAG" => "*",
"TGT" => "C", "TGC" => "C", "TGA" => "*", "TGG" => "... |
b575611c5f722a7a26d0f096e83a00b487399eb0aaf78e227dda45bafe9ba06e | Perl | 3,522 | 113 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
a744369e179dbb234d7d47f9424be52bdc6b4ae26e9dd7439203c928fb818be4 | Perl | 3,523 | 140 | #!/usr/bin/perl
# match_string.pl krishna_bhakt@BHAKTI-YOGA 2006/09/04 10:45:58
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $sim_thresh=90;
my $file1=shift @ARGV;my @seqname;my @seq;my $seq="";my $line;
open(F1,$file1)||die "can't open";
while ($line = <F1>) {
chomp ($line);
if ($line... |
3ba9c6ae13e2a6868df93124278ed5c04c5701ca19f6d7642928856bb6ceb757 | Perl | 3,588 | 127 | #!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
# Monoisotopic masses of amino acid residues
my %MONOISOTOPIC_MASS = (
'A' => 71.03711, 'R' => 156.10111, 'N' => 114.04293, 'D' => 115.02694, 'C' => 103.00919,
'E' => 129.04259, 'Q' => 128.05858, 'G' => 57.02146, 'H' => 137.05891, 'I' => 113.08406,
... |
e7a2cfcaf493e489e4073e6e1b63a19df8064ecf62803a4ee4ae84c520c5a177 | Perl | 3,607 | 111 | #!/usr/local/bin/perl
# TNoM, Infoscore (2001)
open (PREIN, '*.csv') or die "$!"; # initial raw data file
@prefile = <PREIN>;
close (PREIN);
open (OUT, '>rank.csv') or die "$!"; # convert to rank
foreach $preline (@prefile) {
$preline =~ s/\n//;
($name, $a, $b, $c, $d, $e, $f, $g, $h) = sp... |
ee7afc17925fbd9fdf93347551c8f6986a6499b8eb53b0260326952207fc6082 | Perl | 3,612 | 114 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
2c2bcc03f0c28f69c852110ee197e45304fd1039fafff0e880821219a8ac90f4 | Perl | 3,646 | 137 | #!/usr/local/bin/perl
$| = 1;
use strict;
use FindBin;
use lib "/home/walenzbp/projects/scripts";
use libBri;
my $tot = 0;
my $sma = 0;
my $big = 0;
my $smafirst = 0;
my $smalast = 0;
my $bigfirst = 0;
my $biglast = 0;
my $smaoneintronF = 0;
my $smaoneintronL = 0;
my $smaoneintronB = 0;
my $bigoneintron = 0;
my... |
f593636e17588015d2f2f2f83d175a8db2414daffb514e3e6a767f12dfcc995b | Perl | 3,658 | 138 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
873725417a917831b1f86c2f947edec8fece0861a4f881e67bc74bd4f2fb5cb8 | Perl | 3,675 | 88 | # An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >= 0.5
use strict;
use lib '/media/DATA/tariku/biomart/lib';
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = '/media/DATA/tariku/biomart/biomar... |
eafa460a9b4e156364ad4953259fb3825e57ea4258b2b6a32c0b66104668cc34 | Perl | 3,707 | 99 | #!/usr/bin/perl -w
use strict;
die "Usage: blast_parser.pl blast_output_file_name\n" unless @ARGV;
open INFILE, $ARGV[0] or die "Couldn't open infile: $!\n";
my %hits; # to store all data from this file;
my ($subject_ident, $comment_line, $subject_length);
my ($e_value, $identities, $gaps, $aligned_length,... |
bf5a83f708a45d39996a104c68f4641d36565a3ed1c67348546c6119d8095f7e | Perl | 3,823 | 124 | use strict;
use lib '/scratch/bac2fish/ensembl/modules';
use lib '/scratch/bac2fish/BioPerl-1.6.1';
use Bio::EnsEMBL::Registry;
my $file=shift @ARGV;
open(F,$file);
open(FO,">$file.genelist.txt");
my $cover=100000;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensemb... |
9f260eb0c49e66deadffc2ee30f7dfbfdb3129af2e1c956dd91c83529b2a72e0 | Perl | 3,855 | 138 | #!/usr/bin/perl
# match_string.pl krishna_bhakt@BHAKTI-YOGA 2006/09/04 10:45:58
use lib '/Home/siv11/ash022/bioperl';
use Bio::AlignIO;
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $sim_thresh=90;
my $file1=shift @ARGV;my @seqname;my @seq;my $seq="";my $line;
open(F1,$file1)||die "can't open";
while ($... |
68267b10f997bd7850c8b06d462a05863df493c004827ecf7626a2d59f33807b | Perl | 3,871 | 143 | #!/usr/local/bin/perl -w
use lib '/home/fimm/ii/ash022/bioperl';
use lib '/home/fimm/ii/ash022/bioperl/IO-String';
use Bio::DB::GenBank;
use Bio::SeqIO;
#use Bio::SeqIO;
use strict;
my $cnt;
my %seqhash;
while(<>){
chomp $_;
my @tmp=split(/\s+/,$_);
foreach my $n (@tmp){if($n=~/^NC/){$cnt++;co... |
6fd8b9d40d8e614d4becbde40300b72c0c8bd2d15876bb41eee5023ccae181da | Perl | 3,915 | 102 | use strict;
sub createOverlapCorrectionJobs {
my $ovlCorrBatchSize = getGlobal("ovlCorrBatchSize");
my $scratch = getGlobal("scratch");
return if (getGlobal("doFragmentCorrection") == 0);
return if (-e "$wrk/3-ovlcorr/jobsCreated.success");
system("mkdir $wrk/3-ovlcorr") if ... |
be1137cba82585ba7b34d6a63d86a6ae0199adb78cd27cb7fbf13b66b94610cf | Perl | 3,977 | 124 | #!/usr/bin/perl
use strict;
use lib '/home/ash022/Desktop/bac2fish/biomart-perl/lib';
my $fugufile="bacfugu.int.txt";
my $medakafile="bacmedaka.int.txt";
my $sticklefile="bacstickle.int.txt";
my $tetrafile="bactetraodon.int.txt";
my $zffile="baczf.int.txt";
#my $fugufile="t1";
#my $medakafile="t2";
#my $s... |
d806e3817cfb41ced958555119fd9ff0444957c94cb9276722de76a764f58ff6 | Perl | 4,013 | 135 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
d3048da0e88f02b2d1bf9e627e0b9be390ae247581270fe6485596c61a0bc823 | Perl | 4,099 | 154 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
fde980b9df602bab5982313b539f9c60c5c5a2a8c94be506d8fe2289dad7e898 | Perl | 4,218 | 113 | $file1=shift @ARGV;
#$file2=shift @ARGV;
$ftr=shift @ARGV;
chomp $ftr;
#$file4="$file1.$ftr.$file2.csv";
open(F1,$file1);
#open(F2,$file2);
#open(F4,">$file4");
while(<F1>){
$line++;
chomp;
@t=split(/,/);
if($line==1){for($c=0;$c<=$#t;$c++){
$label{@t[$c]}=$c;
}}
#else{
$id=@t[$label{"ID"}];
$fv... |
bb0bb170332217686668a9481c11c050453965992a5599eed95412cab599913b | Perl | 4,254 | 170 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
8549537e6aa3244da171d6ba5301455aed3591ad8ca256aa242b9a18a541fba7 | Perl | 4,328 | 186 | #!/usr/local/bin/perl
use Math::Complex;
use MIDI::Simple;
$pi=pi;
$i=sqrt(-1);
$file=shift @ARGV;
chomp $file;
@base=qw/G T A C/;
set_tempo 5000000;
patch_change 1, 8;
$thresh=450;
OPENFAS($file);
#new_score;
CRTDNAMUS();
#write_score("$wfile");
#exit;
sub OPENFAS{
$file = shift;
o... |
04a995e5b971f9d06c570e78ab99e525fa550ab93ed3da6cfb14e748e3053d76 | Perl | 4,397 | 187 | #!/usr/local/bin/perl
use lib '/Home/siv11/ash022/home/ysr/exp/ref/MIDI-Perl-0.81/lib/';
use Math::Complex;
use MIDI::Simple;
$pi=pi;
$i=sqrt(-1);
$file=shift @ARGV;
chomp $file;
@base=qw/G T A C/;
set_tempo 5000000;
patch_change 1, 8;
$thresh=450;
OPENFAS($file);
#new_score;
CRTDNAMUS();
#w... |
212e228d1b8e49b94548e97f14ae864661f521fc64bc8746daa91af5710965a6 | Perl | 4,445 | 157 | #!/usr/local/bin/perl -w
use lib '/home/fimm/ii/ash022/bioperl';
use lib '/home/fimm/ii/ash022/bioperl/IO-String';
use Bio::DB::GenBank;
use Bio::SeqIO;
#use Bio::SeqIO;
use strict;
my $cnt;
my %seqhash;
my $pattern="GATC";
my $fileo=time;
open(FO,">pattern.$fileo.csv");
while(<>){
chomp $_;
... |
230c7d7dc04fac4cb62cdcea3f97d62c8028b77dec8515f5431a0ab1dfe45be2 | Perl | 4,565 | 183 | use strict;
use lib '/home/animesh/export/biomart-perl/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $file=shift @ARGV;
open(F,$file);
my $genome=shift @ARGV;
my $slicename=shift @ARGV;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'ano... |
10dd43e16a462e0f42ffeafdb4148f69c09c336364d9d829c8703634f04a484f | Perl | 4,600 | 129 | #!/usr/local/bin/perl
# Extract WGS contig to accession mapping from Entrez Nucleotide summaries
# Outputs to STDOUT, one line per mapping, in the format:
# <contig>\t<accession>
# To get the summary file, access the Genbank page for the project by searching:
# genus[ORGN] AND WGS[KYWD]
# At the en... |
b9a9c996cabf825056be3af78ce173407f1e12cafdd2e82524baea700eb55369 | Perl | 4,665 | 127 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $max=0... |
e3cc71c5ef221e1805af2a6b451a9d21256802101a9b5c6c597af63ba7447094 | Perl | 4,673 | 183 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
use warnings;
use strict;
$|=1;
use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=100;
my %hitpos;
my %hitname;
my $max=0;
my %hitscore;
my ... |
304bd0f7ad29b7da9d497d2bdef7d2d067c02445c63e28d9aed7936edd565e32 | Perl | 4,756 | 192 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
0049cedc175a8579a0ec5e170cef114610ecc813782b9e2d0026e58ee4b61b9d | Perl | 4,784 | 195 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
5da70a4eb01e4671b47ce51783a710f7cc1d5d58389daffefc3fed1885fd713e | Perl | 4,790 | 129 | if((@ARGV)!=2){die "2 args needed\n";}
$file1=shift @ARGV;
$file2=shift @ARGV;
open(F1,$file1);
open(F2,$file2);
$length1=5;
$length2=$length1;
while ($line = <F2>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
push(@seqname,$snames);
... |
d530feca6b13a10247a7c49d90ea5e875f8ae83895212afe13c0ebb12e0d8e80 | Perl | 4,798 | 203 | #!/usr/bin/perl
print "enter name of multiple sequences containing file in FASTA format: \n(sequences must be of same length)--\t";
$file=<STDIN>;
chomp $file;
open (F,$file)||die "cant open :$!";
print "\nENTER-\n(1)For Hamming Distance Matrix calculation enter \t[1]\n";
print "(2)For J-K Distance Matrix calcul... |
e7b482aa7d871976ac4e07930119c5bdfb3e9bdd7043618f612eee2ee63d8d82 | Perl | 4,814 | 128 | #wget https://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS_nucleotide.20221027.fna.gz
#gunzip CCDS_nucleotide.20221027.fna.gz
#wget https://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS.20221027.txt
#perl codonusage.pl CCDS_nucleotide.20221027.fna CCDS.20221027.txt 2>0
# wc CCDS_nucleotide.20221027.fna.CCDS.... |
569433e32b2d6ae61a3efb99cceb3a36b327950b9c6be11b94623a7b1cf56c0f | Perl | 4,830 | 84 | use strict;
use warnings;
my $seq;
my $seqc;
my $seql;
my %seqh;
my %seqn;
my @st;
open(F2,$ARGV[0]);
while(my $l1=<F2>){
chomp $l1;
$l1=~s/\r//g;
$seql=$l1;
if($l1=~/^>/){
#print "$l1\t";
@st=split(/\s+/,$l1);
$seqn{$st[0]}=$l1;
#print "$st[0]\t";
}
else{
$seql=~s/\s+|[0-9]... |
10ae8727d0d906868ce16ebc16a8b30b287832e9156b7494f48f9643b0580e08 | Perl | 4,848 | 147 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
#use warnings;
#use strict;
#$|=1;
#use Data::Dumper;
my $file=shift @ARGV;
my $pia;
my $ala;
my $eva;
my $bsa;
my $cnt;
my %us;
my $pit=0;
my $alt=0;
my $evt=0.0000000001;
my $bst=0;
my %hitpos;
my %hitname;
my $m... |
498316a254932a3ab0eba1af506c47f2c3139e3fb9b2fe4a3d87445067d18725 | Perl | 4,904 | 103 | #!/usr/local/bin/perl
use warnings;
use strict;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db
( -host => 'ensembldb.ensembl.org',
-user => 'anonymous');
my $human_gene_adaptor = $reg->get_adaptor("Homo sapiens", "core", "Gene");
my $member_adaptor = $reg->get_adapt... |
a3e69bbf247b31304a229a07904aedaf961eda1909285f1e54cd91f4d659cda4 | Perl | 4,918 | 131 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
ab0613613e6650b2f0bad4be1ff9c0b1c3000baa575d093fbb6ae5612788b367 | Perl | 4,970 | 194 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
d69d5f1baebd8f7c51ee561b78e7c488183dafd4676655a0fc2bf6a022b1a03c | Perl | 5,124 | 141 | #!/usr/bin/perl
# Hack to read two qc files on the command line and report
# if they differ meaningfully.
use strict;
if (scalar(@ARGV) != 2) {
die "usage: $0 one.qc two.qc\n";
}
my %gainlossGood;
sub readOrder ($) {
my $qcname = shift @_;
my @order;
open(A, "< $qcname") or die "can't open $qc... |
a757f601c17d43f969c0a2830e12b9b20a19efec78a6623038f75f16395c595d | Perl | 5,134 | 146 | #!/usr/bin/perl
use strict;
use lib '/home/ash022/Desktop/bac2fish/biomart-perl/lib';
my $fugufile="bacfugu.int.txt";
my $medakafile="bacmedaka.int.txt";
my $sticklefile="bacstickle.int.txt";
my $tetrafile="bactetraodon.int.txt";
my $zffile="baczf.int.txt";
#my $fugufile="t1";
#my $medakafile="t2";
#my $s... |
86582da86bba3415db29bed6423e65f2c45b9af27cd76712460de0641532aa52 | Perl | 5,140 | 205 | # This program 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
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
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