sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ec7ac2443efa899a5037cbbbebec4a785f4d88a5a8c362140cff23dde77dd4fc | Perl | 5,418 | 137 | #!/usr/bin/perl
#to extract the intergenic sequences for a given genome.
print "print the name of the sequence file \n";
$filename=<>;
#chomp;
#open (o,"$file") || die "cant open $file \n ";
#while ($filename=<o>)
#{
$count,$count1,$k=0;
@interseq,@elements=0;
chomp$filename;
open (p,"$filename") || die "c... |
b7cce39a8c0527b4f9d333afdc83600d6c10d21abdd6acee0062bafde1688879 | Perl | 5,468 | 223 | # 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 ... |
fa2c94c6882f7e1af9752f75f61b7f2ac714b93998cd7725feaa3a9496176949 | Perl | 5,549 | 182 | #!/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:";
$file="test";
#$file=<>;
#chomp $file;
open(F,$file)||die "can't open";
#print "\nenter the output filename for position matrix\t:";
$dout="anid.txt";
#$dout=<>;
#... |
f6df75387dd34b2942f0f3d81232ef09d8ffa9957d490b77ca6c22fdbee071aa | Perl | 5,697 | 199 | # 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 ... |
47e35b1770b7c98b4112b32dee82aab36c1a0ed5d4e80cb9b85b0cb1047a67e3 | Perl | 5,713 | 200 | #!/usr/local/bin/perl
use strict;
use Cwd;
use Win32;
my %shortcuts = ('trev.exe' => 'Trev',
'pregap4.exe' => 'Pregap4',
'gap.exe' => 'Gap4',
'spin.exe' => 'Spin',
'sprun.exe' => 'Console'
);
my %extensions = ('trev.exe' => {'ztr' => ['ZTR trace file',
'"%1"',
'application/oc... |
3bd7cb8c9f8e02c965a877ced9d7be63f46132ca994e58ac2d2a377f7f876038 | Perl | 5,727 | 142 | #!/usr/bin/perl
#to extract the intergenic sequences for a given genome.
print "print the name of the sequence file \n";
$file=<>;
chomp$file;
open (o,"$file") || die "cant open $file \n ";
$filename=<o>;
while ($filename=<o>)
{
chomp$filename;
$count=0;$count1=0;$k=0;
@cdx=();@cdy=();@compcdx=();@compcdy=... |
1dec8a89d4a1cd7c0c8ea9bd6fca9f5a88438cb7fbfda7eb6eebd7e34f32797a | Perl | 5,785 | 224 | #!/usr/bin/perl
use strict;
my %kmers;
while (!eof(STDIN)){
my $count = <STDIN>; chomp $count;
my $kmer = <STDIN>; chomp $kmer;
$count =~ s/>//g;
$count = int($count);
$kmer =~ tr/acgt/ACGT/;
my $numbad = $kmer =~ tr/ACGT//c;
if ($numbad > 0){
die "$numbad nonacgtACGT characters in... |
f11a541261f8efb114d87405ad6e079bfb246807f33d652e736c008e1a281515 | Perl | 5,787 | 169 |
use lib 't';
use strict;
use warnings;
use bytes;
use Test::More ;
use CompTestUtils;
sub run
{
my $CompressClass = identify();
my $UncompressClass = getInverse($CompressClass);
my $Error = getErrorRef($CompressClass);
my $UnError = getErrorRef($UncompressClass);
... |
20d7193a4873c9aafe09ccb397b81eead0e78a2d8557cab72d554c25a8d080f0 | Perl | 5,801 | 204 | use strict;
use warnings;
use StatMsg;
my $tr_split_count = 0;
my $tr_translates_count = 0;
my $tr_partial_translates_count = 0;
my $tr_entire_translates_count = 0;
my $tr_no_sequence_left_count = 0;
my $tr_no_cds_left_count = 0;
my $tr_doesnt_translate_count = 0;
my $tr_partial_doesnt_translate_count = 0... |
065b13688f26525b58d57e8a5f2e9891a9e94950af664bb757f6de66089a424e | Perl | 5,802 | 168 | #!/usr/bin/perl
$|=1;
use strict;
my ($truth_file, $individual, $allele_file, $threshold_start, $threshold_step, $threshold_end, $output, $errors, $correct) = @ARGV;
if (not defined($errors)) { $errors = "/dev/null"; }
if (not defined($correct)) { $correct = "/dev/null"; }
my $temp_truth_file = "$output.temp_trut... |
ae6c69e75213b1625129a0fa9a5fbe330b4cd1236b7310268e79188fd08b1237 | Perl | 5,837 | 225 | # 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 ... |
18eaf4796ce9f3c5a68ba281e96c6c18718ff1006ea61c21807d55d7558d056c | Perl | 5,862 | 234 | #!/usr/bin/perl
$file = shift @ARGV;
open(F,$file)||die "no such file";
%t2o = (
'ALA' => 'A',
'VAL' => 'V',
'LEU' => 'L',
'ILE' => 'I',
'PRO' => 'P',
'TRP' => 'W',
'PHE' => 'F',
'MET' => 'M',
'GLY' => 'G',
'SER' => 'S',
'THR' => 'T',
... |
e7324d3537fd7f67067039a5ca3130a5afcd400e45519575adda0f8af7f84c4f | Perl | 5,901 | 208 | #!/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:";
$file="ys.txt";
#$file=<>;
#chomp $file;
open(F,$file)||die "can't open";
#print "\nenter the output filename for position matrix\t:";
$dout="anid.txt";
#$dout=<>;
... |
0ac5f53e71926823afd12027a7535f79953c727ef672a9df372c0ff2e26f7917 | Perl | 5,910 | 180 | #source http://en.wikibooks.org/wiki/Algorithm_implementation/Strings/Longest_common_substring#Perl
use strict;
use warnings;
my @reads;
{
my $f = $ARGV[0] // "-";
open my $fh,"<",$f or die "Cannot open $f: $!";
@reads = <$fh>;
close $fh;
}
my $min_ovl = $ARGV[1] // 1; # minimum overlap -- use >=4 for peptide... |
122caf758276dfe1e6fd3dfa04a2e402a9ad975793b756868506d01b13fea276 | Perl | 6,020 | 153 | #!/usr/local/bin/perl
# LOOCV U-test, weighted vote (2001)
open (IN, '*.csv') or die "$!"; # file name
@file = <IN>;
close (IN);
@miss = "";
for ($trao = 0; $trao <= 999; ++ $trao) { # outer
$miss = 0;
print "No.".$trao.": \n";
for ($minus =0; $minus <=7; ++$minus) { #... |
9b68052d3ea083f8978d0627e1bb424aca16d50b50ddb97c57ce13f61f898703 | Perl | 6,058 | 217 | #!/usr/bin/perl
$f1=shift;
open(F1,$f1);
while(<F1>)
{
if($_=~/^>/){
chomp;
$_=~s/^>//;
@tmp=split(/\s+/);
push(@name1,@tmp[0]);
push(@name2,@tmp[2]);
$n11{@tmp[0]}=@tmp[1];
$n12{@tmp[2]}=@tmp[1];
$namecord1{@tmp[0]}=@tmp[2];
$cordname1{@tmp[2]}=@tmp[0];
if ($seq ne ""){
$seq1{@tmp[... |
3097aaf0958b32020873a22f57e3f8da0a0b95516c67c320a7328fded6d74eb5 | Perl | 6,158 | 253 | # 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 ... |
6db9df9674022167bddbfd4d0b075021902b52153d0766488153635035286311 | Perl | 6,216 | 149 | #!/usr/bin/perl
#wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gbff.gz
#gunzip GCF_000001405.40_GRCh38.p14_genomic.gbff.gz
#perl gbkcds2fas.pl GCF_000001405.40_GRCh38.p14_genomic.gbff
#https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?to... |
4c96a0c9e73247680bf05d115d73270c4ca8937ecc2f22555b16fe45419a20d1 | Perl | 6,301 | 199 | # 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 ... |
4531210a2dd8b061d863d8f5e9d12e95ed99175e3ab9b4cf1f195f7db64757cc | Perl | 6,324 | 211 | #!/usr/bin/env perl
use File::Basename;
use Getopt::Long;
my $DCHIC = "../../dchicf.r";
chomp $DCHIC;
GetOptions(
'cpu=s' => \my $cpu,
'mem=s' => \my $mem,
'hrs=s' => \my $hrs,
'pfx=s' => \my $pfx,
'cmd=s' => \my $cmd,
'cen=s' => \my $cen,
'pexcl=s' => \my $pexcl,
'qexcl=s' => \my $qexcl
);
sub help {
p... |
71c8cf434d9ceb8a1871da99937310d6ca06d6925d1237213516a9d9518b4eee | Perl | 6,346 | 200 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
3737e54dabcba0764dbc7f4ac48fce5d316d073d13bebde1816d3572a9829525 | Perl | 6,419 | 209 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
23090e08b4662bab471eb74d1c1761317b614fd450e7c83f48323299bf5e7352 | Perl | 6,490 | 204 | #!/usr/bin/perl
# getorder.pl sharma.animesh@gmail.com 2009/03/09 10:01:28
#use warnings;
#use strict;
#$|=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 ... |
7e792849fa6e3c8dc00ecba56f6bc74ec2e29e14d9290ed6dd7e10b89ff65f19 | Perl | 6,612 | 218 | #!/usr/bin/perl
if( @ARGV ne 2){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>) {
... |
ed3faa8e2ce3c722cb306a8d8512c93063f077804f5fefbe7b9afb6298cdf486 | Perl | 6,615 | 155 | #!/user/local/bin/perl
# LOOCV t-test weighted vote (2001)
open (IN, '*.csv') or die "$!"; # file name
@file = <IN>;
close (IN);
@miss = "";
for ($trao = 0; $trao <= 999; ++ $trao) { # outer
$miss = 0;
print "No.".$trao.": ";
for ($minus =0; $minus <=7; ++$minus) { ... |
4242d0026e56ff88a270166602a1981aa85489cc02cfc332fa80c5e5017348ab | Perl | 6,642 | 161 | #!/user/local/bin/perl
# LOOCV-discrimination score (2001)
open (IN, '*.csv') or die "$!"; # file name
@file = <IN>;
close (IN);
@miss = "";
for ($trao = 0; $trao <= 999; ++ $trao) { # number of permutations (outer)
$miss = 0;
print "No.".$trao.": ";
for ($minus =0; $minus <=7... |
da58bdbd2e146d8d99f564965fa00f5876b43cfb269a87d72283658b60c858bf | Perl | 6,804 | 201 | #!/usr/bin/perl
use lib '.','../..','./blib/lib','../../blib/lib','../..';
use strict;
use Bio::Graphics::Panel;
use Bio::Graphics::Feature;
chomp (my $CLASS = shift);
$CLASS or die "\nUsage: lots_of_glyphs IMAGE_CLASS
\t- where IMAGE_CLASS is one of GD or GD::SVG
\t- GD generate png output; GD::SVG generat... |
574fb60cc348b79b2d6fa77854fccf3142acb2e31d6f24124f6cf5e1e2b27acf | Perl | 7,058 | 252 | # 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 will ... |
a2878082c24aa8e9c084dddd5673867db1b2fa7e2ebff185a2b8bf0a1cf78949 | Perl | 7,072 | 64 | #!/usr/bin/perl
#@remove=qw/13 49 51 54 58 3 4/;
#@remove=qw/13 49 51 54 58 3 4 33 60 46/;
#@remove=qw/13 49 51 54 58 3 4 33 60 46 55/;
#@remove=qw/13 49 51 54 58 3 4 33 60 46 55 68/;
#@remove=qw/58 51 62 4 52 15 37 46 65 17/;
#@remove=qw/58 51 62 4 52 15 37 46 65 17/;
@remove=qw/58 51 62 4 52 15 37/;
$appendi=join('',... |
6ce580076b5fe8ea29f389b9b5a06c87a0b7220d8af1c7f9926c02f9f1f0760b | Perl | 7,327 | 234 | #use strict;
# usage perl harness.pl [testNum]
# where testNum is an integer from 1 to 41
# testNum may also be a list of integers denoting tests to be run
# ommitting testNum will lead to all tests being run
#
# this harness outputs the results to the file results.html as well
# as reporting them to... |
622b34421eb31d328037132fb99b1401e178f729f24aecaf0a6ab3947fabb7c6 | Perl | 7,329 | 365 | #!usr/bin/perl
print "Enter the filename containing the first sequence: ";
$afile=<>;
open (FILENAME, "$afile") ||
die "can't open the file: $!";
while ($aname=<FILENAME>)
{
chomp $aname;
$an=$an.$aname;
}
close (FILENAME, "$afile");
@aa=split(//,$an);
$alen=@aa;
print "Enter the filname containing the sec... |
6c26f398e41e6566b5585160a4b1958b1f8aadc34b31bb994ef2a2ab02bf2d84 | Perl | 7,682 | 363 | #!/usr/bin/perl
# creatertf.pl - Quintiles Clinical Search
use CGI qw(:standard escapeHTML);
use Qui::QuiDB; #for database connection
use warnings;
use RTF::Writer;
my ($query) = new CGI;
my ($dbh) = Qui::QuiDB::connect();
my ($filepath) = Qui::QuiDB::get_file_path (); #returns file path with IP where ... |
fc9dc15643b4a3aeabe8573917881bca3b6404211277954538742d8171a25fd7 | Perl | 7,682 | 298 | #! /usr/bin/perl
if ($#ARGV < 0)
{
print "Useage: $0 file1.chains [file2.chains ...]\n";
print " Converts a sorted chains file into a file of insert lengths.\n";
print " The read-ids are assumed to be those generated by\n";
print " MakeRealInserts.cc or MakeFakeInserts.cc\n";
exit(0)... |
ffef48c3066cf5b78a2a7af18d81a9351e4a87f2cd87aaab33209170f9f87188 | Perl | 7,694 | 332 | #!/usr/bin/perl
#parameters, parameters n, m, η α, an limit on E and maximum number of epochs
#the window size
$n=shift @ARGV;
#hidden node size
$m=shift @ARGV;
#output
$o=3;
#slide of the window
$slide=1;
#number of iteration, maximum number of epochs
$iter=shift @ARGV;
#threshold, an limit on E
$threshold=shift @A... |
6897c01597999d38648d33c5246e9895f036875d803f1318386d132555213ac0 | Perl | 8,225 | 216 | use strict;
sub merOverlapper($) {
my $isTrim = shift @_;
return if (-d "$wrk/$asm.ovlStore");
caFailure("createOverlapJobs()-- Help! I have no frags!\n") if ($numFrags == 0);
caFailure("createOverlapJobs()-- I need to know if I'm trimming or assembling!\n") if (!defined($isTrim));
my... |
73fa085561bc26edcd39ca07469574827217853c7e7b21a10d953d1d5818ae83 | Perl | 8,431 | 241 | #!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use IO::Uncompress::Gunzip qw($GunzipError);
sub print_header
{
print "\n";
print "\@------------------------------------------------------------------@\n";
print "| Compute sum of each annotation |\n";
print "|... |
f7ffe18970ad47e84ca240651d7d288faa4119919dc817b57d080c9017ce59d2 | Perl | 8,708 | 270 | # 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 will ... |
71072e5e6c27b4b955856d0ed5fefc9af9c02a82998c15e048de50d97498b49f | Perl | 8,899 | 223 | use lib '/usit/titan/u1/ash022/Graph-0.94/lib';
use lib '/usit/titan/u1/ash022/IPC-Run-0.90/lib';
use lib '/usit/titan/u1/ash022/GraphViz-2.04/lib';
if((@ARGV)!=2){die "2 args needed\n";}
$file1=shift @ARGV;
$file2=shift @ARGV;
open(F1,$file1);
open(F2,$file2);
$length1=100;
$length2=$length1;
getgraph();
#readseqfil... |
5fcb5f6f02acd3cec8c59874d0755bb8a137636acc800f49ff9638edb6166f17 | Perl | 8,978 | 270 | # 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 ... |
86c61ef6e0ff5cd5e645343bc7828f891e70dd503aced3ea77025a39c387d5e9 | Perl | 9,015 | 323 | # 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 will ... |
d94410cab0ad6849538106a497a831f126517b1cd27252be09f033f95c82617c | Perl | 9,064 | 292 | #! /usr/bin/perl
if ($#ARGV != 1 && $#ARGV != 2 && $#ARGV != 3 )
{
print "Useage: $0 ref_size lengths_file inserts_file [ output_file ]\n";
print " Computes the estimates of the new genome size based on\n";
print " comparing the original lengths in lengths_file and the\n";
print " observ... |
fd996a394d733f2ca047f389418e6d3672d66600f5ad3c9d5ee735adafeecd0b | Perl | 9,125 | 273 | # 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 ... |
5d3c65f6485b56d539af83857c3b2d3f206fb51740a3eb7ada3da75fbd6fa52f | Perl | 9,138 | 279 | # 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 ... |
9e4288587fa5d8d4b4c1ff705078fe991c42224fff10356796c9f50a7c8974f7 | Perl | 10,667 | 277 | # 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 ... |
91335a2dad2b32e4989c0b5c6a4c3ebece277c92a85522e17cb7501dfe60afba | Perl | 11,241 | 309 | # 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 ... |
3bf880848929da135d27467ffa0e3c4b9ad019775d70520df86bcf40945f9706 | Perl | 11,324 | 386 | #under GPL from krishn.bhakt@gmail.com
#!/usr/bin/perl
if((@ARGV)!=3){die "3 args needed\n";}
$file1=shift @ARGV;
$file2=shift @ARGV;
open(F1,$file2);
open(F2,$file1);
$length1=25;
$length2=$length1;
$file4=shift @ARGV;
open(F4,$file4);
while ($line4=<F4>) {
chomp ($line4);
if ($... |
2a881daac6598d97b903fcd004a159d0816412b7099fcf7c21c62d1e4c2954af | Perl | 11,987 | 451 | # 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 ... |
40b9c462ed77580681e01dff6290b77f2926c3acec4f7cccda638558f7207282 | Perl | 12,790 | 460 | # 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 ... |
7e404efb38971c91780912095ee79008dc0d3a48dd3e12a508fcff8ee588c552 | Perl | 15,178 | 510 | # 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 ... |
d95de5afd85c42e66386b0aa3e465239a13564f49d29e4b888037f0c7b1a2301 | Perl | 17,341 | 518 | #https://github.com/HKU-BAL/Clair#quick-demo
Call whole-genome variants in parallel (using callVarBamParallel)
# variables
SAMPLE_NAME="NA12878"
OUTPUT_PREFIX="call/var" # please make sure the call/ directory exists
# create command.sh for run jobs in parallel
python $CLAIR callVarBamParallel \
... |
2cfdc78a16931cb6c573e253c9bd27327c41555e092f21ad3681f1eb5b6f1bf8 | Perl | 17,866 | 117 | use warnings;
use strict;
my $f1=shift;
my $f2=shift;
open(F1,$f1);
open(F2,$f2);
my $mc1=0;
my $mc2=1;
my $mc3=2;
my $mc4=14;
my @list=<F1>;
my @gop=<F2>;
@list = sort { uc($a) cmp uc($b) } @list;
@gop = sort { uc($a) cmp uc($b) } @gop;
my $cnt=0;
my %match;
my %mf;
my %mf1;
my %mf2;
my $title;
for... |
98619ae43fd2009b4398ac7fff5441fbc6fb31df7f33f32c015b72ce7372184d | Perl | 18,242 | 361 | ### GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
... |
43daf95ae213e8b2cf932b88eea139298ff86be85e08f238a967ab5de2fb6871 | Perl | 19,881 | 615 | # 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 ... |
05db5476a07058a6411b12deefb2eb2eacf9ad2bc2cac64f969bc6465df8baa1 | Perl | 23,664 | 781 | my %twoBit = ('T' => 0b00,'C' => 0b01,'G' => 0b10,'A' => 0b11, 0b00 => 'T',0b01 => 'C',0b10 => 'G',0b11 => 'A');
my $fasta='TATAA';
print $fasta. length( $fasta ) . "\n";
sub compress2bit{
my $fasta=shift;
my @bases = split //, $fasta;
my $bits = '';
for my $i ( 0 .. $#bases ) {vec( $bits, $i, 2 ) = $t... |
90006df5e6bd86c9df0b2d2e19e38e91ebbfa3a6f26777ba41937ff6168ed84a | Perl | 29,042 | 1,282 | # 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 ... |
b1ae770a12cc6987d81c1d0c99dc68573ffb6319acb955c6dca41f127fee3e2c | Perl | 31,354 | 1,334 | # 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 ... |
01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b | Python | 1 | 1 | |
eae315245e6270eddc03247f3f4eeec5ca59c6384de3993a0d4e739eaccfa109 | Python | 13 | 1 | # GUI module
|
4abb85c205d942a5e9295956a76afb92ccf286daefe5ac18dceb1a04d5f28c5c | Python | 16 | 1 | # Spines module
|
0c5e0ee87b7481c47df3647f0fc8138f90a9b4608f8ccb8fb0405569aca25040 | Python | 17 | 1 | # Imaging module
|
9e2ab3f8ee196219b8dd8ead72c62efa5bcf96dfa595e44ed5a61c59e171bf09 | Python | 19 | 1 | # Figure 4 scripts
|
022576e379190d976cfadc9281ee0fdcec98eceaa78f84d1d291e9abf2ebbd45 | Python | 20 | 1 | # Timeseries module
|
2b490dcb6e959ba03ed55e65493de2972eb256c34b51b8aa93a0190c59b69c92 | Python | 20 | 1 | from .core import *
|
6b903fb7762640ef94fe9351e98703146593d2bda588565f770109ca68341729 | Python | 20 | 1 | print "Hello world"
|
90ce79aaa852adce1bf92b4d4ee374dd2ae0d24c1f8351b805c9022a1532b5a1 | Python | 20 | 1 | __version__ = "1.0"
|
3ebbb4065141012142168ecc70776886d2a452d80c3c3c1b19fc94665136fd5c | Python | 21 | 1 | __version__ = "0.1.0" |
6a52031819f1587e09bcff945beecdf7db1e0418b4af5195d61f1fd4444505e7 | Python | 21 | 1 | from .utils import *
|
c32f5cb4a5bc20d877dfca71a61ec0902bd8fd192cdbca73bab0c0caae7e31f5 | Python | 21 | 1 | """init of tests."""
|
611b560782be83dcb2bd9a32116df5082d4ad72bc615ec5e4b98c12ceac97745 | Python | 22 | 1 | # Segmentation module
|
91c1df9dc66768111291971a0cc0abf7556988e1280917afd8e47960b5680fc7 | Python | 22 | 1 | """Export helpers."""
|
acf49f5a021eab661654fc8448e030081b7cbdfb6c4e9224b8b0060c4cf24507 | Python | 22 | 1 | __version__ = "0.1.5"
|
e0ce153c1e570ccfa448da45890512a152824b2cb70d4231ca6d3c0a14c9f0af | Python | 22 | 1 | from .logger import *
|
eb5dba5155c5a1f6cfb7cb5f23cc3b446e07086e97eeee026ae84486067eba7d | Python | 22 | 1 | """Shared helpers."""
|
1f71527949e924674d85f18a3a8f77451aca959416c44a2aeb3113b3a11a59d3 | Python | 24 | 1 | from .garnetff import *
|
c148862fbbe3494a69e52fe2543d23cbca5621b352439d0d9e4d91ede68c111c | Python | 24 | 1 | IDLE_VERSION = "1.1.2"
|
3bd093d41d85f9c541f1e953d04a0225b82471f7e3be59aab5ea9abece208838 | Python | 25 | 2 | # -*- coding: utf-8 -*-
|
9552f854fcf77389160a08cfb4be2eb902cd9a0c0af76ab57df02cbf9125d369 | Python | 25 | 1 | # -*- coding: utf-8 -*-
|
04de47ed28a02528b8116971f7e80df21375bfc69896226608c1fa86f0be6361 | Python | 26 | 1 | from .spatialnet import *
|
5130262ed842ea2d40b3bd099e65ae3fc00f843fabe3b5a33d6076738dc9f7a3 | Python | 26 | 1 | from models.NCGCN import * |
5356ed11e54a84c3eab32371f005dc3542d136a9bb4d19bcb9d215ec1b06a29a | Python | 26 | 1 | from .assertions import *
|
804fd1abf28327230e92e25a6b525eb41059610a8d676cd6c708dc71f413070d | Python | 26 | 1 | from .numpy_core import *
|
0fc469686af1dad6a7a43d7b6edaa597f4f1ee4ead4e51d44f9e8ffa1f80653c | Python | 27 | 1 | # Electrophysiology module
|
998f1625876c9cb0405b0e96e7f7ee940e9f043ee546089597ae46e534e7910e | Python | 27 | 1 | from .pandas_core import *
|
43130677c3c5d7137a9c4ff3a8ba7899ca7f17eefe1bee615cc203ff233fbcfa | Python | 28 | 1 | """Data source adapters."""
|
bf5a6672bc6dfd83b89b0aea08280b6651fa13a26047aaeff676476e05d2b38d | Python | 29 | 1 | """CASCADE tests - v0.8.0"""
|
29691e9028d2e7688bb29ba2aa6aa4557c9461a613dba3c1f1ea8f6c5f9df847 | Python | 30 | 1 | """SMILES2Docking package."""
|
715a7ad4a48ddb4d6bd3bd2bae6596d881e60c4cfa6fe2e13edc1099760ac33c | Python | 30 | 1 | from .does_not_exist import x
|
7444cb9541c32f7be780636e61db78f771f305a031d83b547ee28d5f4c2983a4 | Python | 30 | 1 | """Desktop user interface."""
|
654f2d39f5719f7a0ce515af1b76eb0a32f0d0c40afb1cf1279bd69a2e66f28a | Python | 31 | 1 | """3D structure generation."""
|
db3d9c3473ac74a9574546f1ba93c3ace24ad6b8edde0ade6e541bf68eff9870 | Python | 32 | 1 | from .progressnotifier import *
|
93d37ac6efcf3d452dbf157e9b7467582dbf2bb634ef8144d0b966f33e09e725 | Python | 33 | 1 | from PV2NIfTiConverter import *
|
f9048575489336c8f64ffe4f7febb9a68a4ab17ebc08de92036f9e63b5069e32 | Python | 33 | 1 | from nb_to_doc import convert_nb
|
9ced5c3fe2b03ead3d7d712413c0f736892ae72482c194dffa55398ba33f9df2 | Python | 34 | 1 | from .dataloader import LFPDataset |
305b8fd0959998960cc179ee5f2a345af51ef80b25a7017b58b8137031d4a716 | Python | 35 | 3 | import sys
sys.path.append('./') |
99eaac595c359937cfb56e607ce4df2cd9ad4249dcbbc92a1a0218e73dc6661c | Python | 35 | 1 | # Tests for neuroHarmonize package
|
d091529cfe095148a323f73500b2a1d11c83e5881196499a0d8dbaa0a0c8f6c5 | Python | 35 | 2 | # type: ignore
__submodules__ = []
|
5b0e146d973f8091110351f3f46badd5a905dacb6bb08279014a00dbd8c9921f | Python | 37 | 3 | from setuptools import setup
setup() |
b007afb20ed6481293f9e2ee329a0d27353bb88bee1ad483004b7984b3878171 | Python | 37 | 1 | """SMILES preprocessing routines."""
|
424c1cf393c24748234e5cffd29f6caf525cec65c3e3e087d36f87b7ad6a4dcf | Python | 38 | 1 | """Molecule visualization outputs."""
|
6aef53a6bdaa46977463d127b37455afe0f9bab14c5bb0b7ed14b70036c613c8 | Python | 38 | 1 | """Quantum chemistry integrations."""
|
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