sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
fa169aaa010669f40806822170be799a8dcc078357ad41fe45dde14f0d2d7d58 | Perl | 1,661 | 67 | # 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 ... |
5ceed23e426132513172c1d8151030e8e9026e7f52499d6eb741a1f5bfa18412 | Perl | 1,663 | 53 | # 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 ... |
e3503b12cc44242f6b653168d69cb5623e761d8ffb62d5608f537c249b0c43bc | Perl | 1,681 | 48 | # 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 ... |
5f3385e1399d30bd23d9d85c5dace02282879cd181736736c800a9f90c5021db | Perl | 1,696 | 40 | #!/usr/bin/perl
##################
#get the current hit count from the
# counter file.
open(FILE, "counter.txt");
$visits = <FILE>;
close(FILE);
# Incriment the hit count by 1
$visits++;
# Overwrite the old number with the new
# number which is 1 higher.
open(FILE, ">counter.txt");
print FILE ... |
050473938bf29f4f68a44cd88b957d9263b40925fe4c1bdf03f89e10a1926700 | Perl | 1,698 | 56 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
2487b837e09a830f4324220a712e7f202d5654cff261a19a2713bfb9534e1335 | Perl | 1,701 | 84 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
2e82f0a3ab1404d15bbebeefcf61b689fea99870a778cfb787f7aea5d4d14748 | Perl | 1,709 | 43 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
8bb41e20e31a2f9f7022505de6858b1eaf1189df1458cac4ebcab6ea296601c7 | Perl | 1,709 | 81 | use strict;
use Text::ParseWords;
open(F1,$ARGV[0]);
my %id;
my $lv=1;
my $lc=0;
my $pro=4;
my $mod=5;
my $pep=0;
my $tf=21;
my $nf=23;
my $rf=25;
my $conf="High";
my %pepos;
my %nmt;
my %mdt;
my %nmn;
my %mdn;
my %nmr;
my %mdr;
my %seqh;
my $seqc;
open(F2,$ARGV[1]);
while(my $l1=<F2>){
chomp... |
3ae7b55a14134d7652eaa260bdabebe9ec0ba04d11e473870b3d05d311e4e1a0 | Perl | 1,711 | 46 | use strict;
use Bio::EnsEMBL::Registry;
my $reg = 'Bio::EnsEMBL::Registry';
$reg->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
);
my $efg_db = $reg->get_DBAdaptor('Human', 'funcgen');
#Investigate the ResultSets for this Experiment
#Create a script which ret... |
9be97a89688f7969ff0ee264946846313318d33328f1867b4373526c089d18c3 | Perl | 1,712 | 56 | #!/usr/bin/perl
system("export CLASSPATH=/usit/titan/u1/ash022");
$file1="label.txt";
open(F1,$file1);
while($l1=<F1>){
$l1line++;
chomp $l1;
@t=split(//,$l1);
$len=$#t;
print "$len\t@t[0]\n";
if($len!=0||$l1line>66){die"label file incorrect or more labels"}
else{... |
f9ea6b8269a9ad777775b3eaeb074f2279723d839f0e832816db65ace25c0771 | Perl | 1,714 | 56 | # 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 ... |
6cb69e0199bb0185d3a384465286880750ab8f7d4e6f2350ee7b05dc4515fd6f | Perl | 1,724 | 59 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::Perl;
use Bio::SeqIO;
use strict;
my $coverage=50;
my $window=250;
my $socl=200;
my $eocl=300;
my $jump=5;
my $main_file=shift @ARGV;
my $fas_file=$main_file."_in.fasta";
open(FT,">$fas_file");
my ($wseqname,$wseq,$wseqlen)=get_other_source($main_file... |
0d693a3b6d89ae798bd4a58c95e9ae17737485aae90979554970295b643f604a | Perl | 1,726 | 79 | #!/usr/bin/perl
#Includes
use strict;
use warnings;
use IO::File;
use Getopt::Long;
use POSIX;
use List::Util qw[min max];
my %options = (
infile => undef,
constant => undef,
output => undef
);
&GetOptions(
'infile=s' => \$options{input},
'constant=s' => \$options{... |
04985c600f7a45d8912cef0b2abcbfeeccd4b338ec1b514e96bd4cf7e0fc108b | Perl | 1,728 | 105 | #! /usr/bin/perl -w
use strict;
use warnings;
# condenses all consecutive characters of one type
# convert_characters.pl [input] [character] [output]
die "Check arguments" unless @ARGV == 3;
my $inputfile = $ARGV[0];
my $character = $ARGV[1];
my $outputfile = $ARGV[2];
my $convert_from;
my $conver... |
0cb8e51989d1740230056da652092f8115cb925ad942ffaef4fbfc318a316248 | Perl | 1,737 | 52 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
dda0ee7a6e6ffc776456eb1c905fb46de0de7ef9f6b6bd3359fde99572b848fd | Perl | 1,753 | 43 | #!/usr/local/bin/perl
# Relation (2001)
open (IN1,'relation.csv') or die "$!"; @file1 = <IN1>;close (IN1);
open (IN2,'relation.csv') or die "$!";@file2 = <IN2>;close (IN2);
open (OUT,'>sampler2.csv');
# threshold value derived from rel_rand.pl
# $low = -0.978977408494646; $high = 0.996330902712367; ... |
f55bc003886eb845bf4981e600416d131de9340a4a306464080a84c02144cc5a | Perl | 1,757 | 73 | #usage: perl combineXlinkReports.pl 2>0 > combx.txt
use strict;
use warnings;
use Text::ParseWords;
my $path = "/mnt/f/20210118_8samples/QE/";
my $pat = "210114_Synnove_";
my $fpat = ".mgf.mq.txt";
my $idi = shift @ARGV;
my $idn = shift @ARGV;
my $i1 = shift @ARGV;
my $thr = shift @ARGV;
if(!$i1){$i1=2;}
if(!$idi){$... |
03a4f7c04ce793b4ea273e970e1fe10cfb662d2621723b1124100610fc7d7f5e | Perl | 1,766 | 71 | $file1=shift @ARGV;
$file2=shift @ARGV;
$file3=shift @ARGV;
$file4=shift @ARGV;
open(F1,$file1);
open(F2,$file2);
open(F3,$file3);
open(F4,$file4);
while(<F2>){
chomp;
@t=split(/,/);
#print "@t[0]\n";
$r=@t[0];
$r=~s/\s+//g;
if($r=~/^[0-9]/){$d1{$r}="D1-@t[5],D1-@t[6],D1-@t[7],D1-@t[8],D1-@t[9],D1-@t[10],D1-@t[11... |
4d40af1983ff2b572f7bfe21bd3d599e7b381a5cc274dbff3768a0d35433e9a7 | Perl | 1,781 | 49 | # 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 '/home/ash022/Desktop/bac2fish/biomart-perl/lib';
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile="/home/ash022... |
1e1a4d81c15c4f6bcefc1a28b2e851056b2a981583aa576972db9c1e286f64c6 | Perl | 1,786 | 48 | n example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >= 0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = "PATH TO YOUR REGISTRY FILE UNDER biomart-perl/conf/. For Biomart Central... |
49d5e37752d0efd7ba498a1945954a395db1ee693d51259318b1327822835860 | Perl | 1,787 | 63 | # 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 ... |
3efbd34c4d0bb81b2ebe52cf3a6788bfa9533756b66f3c5a03c5a7396a733dcb | Perl | 1,788 | 44 | # 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 ... |
b04927489a5783d656bdb68dad66e00fd71cf375074bd8b1ae2948aafa66ff94 | Perl | 1,798 | 66 | # 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 ... |
65f99074f06a0f73261b4922f60ec3d308ac0ef7477b9bf718ea4f0345fe07f8 | Perl | 1,801 | 52 | %Oblig3 - INF121 - Sondre Langeland Hisdal.
%Oppgave A
maxAlignment(Xs, Ys, Alignment) :- findall(N, alignment(Xs, Ys, N), L), maximum(L, Alignment).
alignment([], _, []).
alignment(_, [], []).
alignment([X|Xs], [X|Ys], [X|A]) :- alignment(Xs, Ys, A).
alignment(Xs, [_|Ys], A) :- alignment(Xs, Ys, A).
alignment([_|Xs]... |
ad35ca3c237fd2a5b9c4e172460b9a1de342b2ff108a749308531ba54a38b3e1 | Perl | 1,808 | 100 | #!/usr/bin/perl
# corseqcol1.pl krishn_bhakt@Bhakti-Yoga 2007/08/19 08:47:06
use warnings;
use strict;
$|=1;
use Data::Dumper;
use lib '/scratch/bioperl/';
use Bio::AlignIO;
my $fin=shift @ARGV;
my $fout=$fin.".aln2csv.txt";
my $str = Bio::AlignIO->new(-file=> $fin);
my $aln = $str->next_aln();
... |
dfbe7c39608f67bf0280a5fff0bdfc564756c047b031e63f0a29a01110c2cec6 | Perl | 1,809 | 64 | # subLineInFiles.pl : script to substitute a line with a specified string in param filespec and output new versions to param dir
use strict;
my $sString = "load\( \"ChemUtil\.lua\" \);";
my $sCheckString = "ChemUtil.lua";
my $sSubString = "\tload( \"ForceFieldUtil.lua\" );\n\tload( \"ForceObjectUtil.lua\" );\n"... |
b675290146cb7303572fa8abb49984d5b193ea5aff8b5f6c6d050d046a0d46c5 | Perl | 1,813 | 54 | # 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 ... |
8f5dff2eff994329fc3fc198c762889738621db3587e8511366fd86e120e7bb2 | Perl | 1,821 | 60 | #!/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... |
b9763460015353f59173c52e4bd98bf944cf8d74acab6d8fac8a40a17c0963f2 | Perl | 1,827 | 64 | # 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 ... |
aeb47617fe2dc34f580168da310c646a55ed8d07a2a30f65d74735a1bac5860e | Perl | 1,832 | 54 | # 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 ... |
5a0e5afad9f86780076dc127de46da0369ccb94955b4c72a418243cea6dab1da | Perl | 1,843 | 57 | # 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 ... |
2e449c2eccdf7e74ab3ae59252d29b4b41822b0cf7b4d4c9ad3825a378d7cdd8 | Perl | 1,848 | 55 | # 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 ... |
549a8c17ef6b9ec9170469b1f1ad6ae9f8568537e6f1dcefdef27264d1c841b4 | Perl | 1,848 | 74 | # we need tests with index shuffling once vaffines are fixed
sub ok {
my $no = shift ;
my $result = shift ;
print "not " unless $result ;
print "ok $no\n" ;
}
sub approx {
my($a,$b,$mdiff) = @_;
$mdiff = 0.01 unless defined($mdiff);
$c = abs($a-$b);
$d = max($c);
$d < $mdiff;
}
sub rpic_unl... |
dd46a93ebdb6b1a3daf6ffe0b5a24cbd9de4ab9d38d5378996afe3596f2664d9 | Perl | 1,848 | 61 | #!/usr/bin/perl
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName GenomeFile\n\n\n";}
$fileas = shift @ARGV;$cp=0;$cnp=0;
#open (F1, $filess) || die "can't open \"$filess\": $!";
open (F2, $fileas) || die "can't open \"$fileas\": $!";
#while ( $line = <F1> ) {
# chomp ($line);
# push(@name1,$line);
# ... |
8614e2323ea4bc67fea4bcc0a2d3290a83bbc67ad17d56cbdc046c3942509dd8 | Perl | 1,870 | 80 | if( @ARGV ne 2){die "\nUSAGE\t\"ProgName MultSeqFile1 MultSeqFile2\t\n\n\n";}
$thresh=90;
$file1 = shift @ARGV;
open (F, $file1) || die "can't open \"$file1\": $!";
$seq="";
while ($line = <F>) {
chomp $line;
if ($line =~ /^>/){
$c++;
push(@seqname1,$line);
if ($seq ne ""){
push(@seq1,$seq);
... |
7ece91b10096a535d2da5569ff3b8a1cc7d15d308d9ec988310ff77c6377a40d | Perl | 1,877 | 61 | #!/usr/local/bin/perl
use strict;
use Bio::EnsEMBL::Registry;
use Bio::TreeIO;
Bio::EnsEMBL::Registry->load_registry_from_db
(-host=>"ensembldb.ensembl.org",
-user=>"anonymous",
-db_version=>'48');
my $human_gene_adaptor =
Bio::EnsEMBL::Registry->get_adaptor
("Homo sapiens", "core", "Gene");
my $member... |
c3d0f3741ebf3b70cc23ff98b86559edcbb2475e287685d1e90ebf4a24ea6ddb | Perl | 1,879 | 33 | while(<>){chomp;@t=split(/\s+/);$c++;if($c>1){
$t[3]+=0;
if($t[3]<0){$pop{"0.00L"}++;$popl{"0.00"}.="$t[1],";}
if($t[3]>=0.0 && $t[3]<0.05){$pop{"0.05"}++;$popl{"0.05"}.="$t[1],";}
if($t[3]>=0.05 && $t[3]<0.1){$pop{"0.10"}++;$popl{"0.10"}.="$t[1],";}
if($t[3]>=0.1 && $t[3]<0.15){$pop{"0.15"}++;$popl{"0.15"}.="$t[1],";}... |
9bf8de8703eccd5df6be2a936bfb9877e93285d2fd1010904872909235c2cac3 | Perl | 1,907 | 66 | #!/usr/bin/perl
use strict;
my %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','GLN' => 'Q','LYS' => 'K','ARG' => 'R','HIS' => 'H','ASP' => 'D','GLU' => 'E',);
my $fasta_... |
3f95c66c604eef3d3b70daa0f82a4ff399f529702c442a8cdfb2a9ccb69aeb28 | Perl | 1,911 | 79 | use strict;
use warnings;
use Text::ParseWords;
my $path = shift @ARGV;
my $pat = "REP";
my $fpat = "proteinGroups.txt";
my $idi = shift @ARGV;
my $idn = shift @ARGV;
my $i1 = shift @ARGV;
my $thr = shift @ARGV;
if(!$i1){$i1=18;}
if(!$idi){$idi=0;}
if(!$idn){$idn=17;}
if(!$thr){$thr=1000;}
#my @files=<$path/*$pat/... |
05d811938853ec4a997c1674eb90dd671f5d0c10b7213a8fcb45d1ee7d3ab314 | Perl | 1,912 | 70 | # 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 ... |
0b5af460030fd721309f7809c8bd4df8198235d6704b2351ae69d96c036fac49 | Perl | 1,914 | 70 | #!/usr/bin/perl
$seq = "";
print "Enter the file containing sequence:";
$infile = <>;
open (INFILE, $infile) || die "can`t open $infile: $!";
while ($line = <INFILE>){
$line =~ s/-//g;
$seq = $seq.$line;
$seq =~ tr/[a-z]/[A-Z/;
$seq =~ s/\s//g;
$seq =~ s/[0-9]//g;
}
$len = length($seq);
#print "$se... |
c004c52f090b101a2638dc63b906808d6632d1dc3e04d62baeaebacd643dcc15 | Perl | 1,916 | 84 | if( @ARGV ne 2){die "\nUSAGE\t\"ProgName MultSeqFile1 MultSeqFile2\t\n\n\n";}
$thresh=90;
$file1 = shift @ARGV;
open (F, $file1) || die "can't open \"$file1\": $!";
$seq="";
while ($line = <F>) {
chomp $line;
if ($line =~ /^>/){
$c++;
push(@seqname1,$line);
if ($seq ne ""){
push(@seq1,$seq);
... |
ce7dc9c087a6c6144f09b6d3286a18e21dd5a49c461079ed15d123443b093c9d | Perl | 1,916 | 52 | # 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 ... |
b9c60b776702f0f552ce7b7a82e96c94d66bf3ea66e1fb36d9c0d64d568a43b4 | Perl | 1,934 | 62 | # 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 ... |
8e07f2f0515a2c56629870b637604a2dbe4c4df47b52028db8da28771a43b42e | Perl | 1,936 | 58 | # 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 ... |
790d89404d9485d31f83ad686e7c7e9a0803abd0a37552085c967f2d74c801cd | Perl | 1,944 | 60 | # 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 ... |
c0fa0b2eecb77b14c774691bf6b386b9a007d13d0b59eeeda3dcf18889b973f2 | Perl | 1,945 | 79 | # 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 ... |
7e4faa667d5923e5e43a18d9c466da322d4d40832a589a0555656a36847ddbd7 | Perl | 1,949 | 54 | # 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 ... |
10fe1671524f656a028bbb44e763bc3adcccb2aab96a76208fdfc5369e6441c9 | Perl | 1,953 | 100 | #!/usr/bin/perl -w
# diffs two files and writes an HTML output file.
use strict;
use CGI qw(:standard :html3);
use Algorithm::Diff 'traverse_sequences';
use Text::Tabs;
my ( @a, @b );
# Take care of whitespace.
sub preprocess
{
my $arrayRef = shift;
chomp(@$arrayRef);
@$arrayRef = expand(@$arrayRef);... |
2977ff79e5da2af8b4195ed69ae5d3dd395514e6b9a49e966e2dca6bd593e97d | Perl | 1,962 | 73 | # 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 ... |
cfbf9169f1d5c97aef5f6d3bf7d32b689b18cbf8f3a5e797f785fb711b7a5799 | Perl | 1,962 | 74 | use strict;
use Text::ParseWords;
my %vh;
my %nh;
my %gh;
my $cnt=0;
my $idcnt=0;
my $cntt;
my $category;
my $ID;
my $f1 = shift @ARGV;
my $id = shift @ARGV;
my $idg = shift @ARGV;
my $cat = shift @ARGV;
my $valchk = shift @ARGV;
my $thr = shift @ARGV;
open(F1,$f1);
while (my $line = <F1>) {
chomp $line;
$line =~ s/... |
82ab65f0f18e07d34027241e2af645329a2c2fb8ab7a7cb7039da546f307ba95 | Perl | 1,967 | 77 | use strict;
use warnings;
use Data::Dumper;
my $f=shift @ARGV;
unless(-e $f){die "USAGE:perl fastqUniq.pl <fastq with \@name followed by sequence, can also work with fasta if seqeuences are in single line after >name>";}
die "$f.uniq.fasta exists, bailing out for $f!\n" if -e "$f.uniq.fasta";
my $seqn="";
my %seq;
my ... |
3d559b1c3e12b85d1061cc19366e6e6bc0846aa515792c5f749f9ff4de325556 | Perl | 1,987 | 67 | # 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 ... |
34ab67afda16ae6e7782b55c356e2565d8355699f608c2f1aa52bfa2d16c4a72 | Perl | 1,999 | 86 | if( @ARGV ne 2){die "\nUSAGE\t\"ProgName MultSeqFile1 MultSeqFile2\t\n\n\n";}
$thresh=90;
$file1 = shift @ARGV;
open (F, $file1) || die "can't open \"$file1\": $!";
$seq="";
while ($line = <F>) {
chomp $line;
if ($line =~ /^>/){
$c++;
push(@seqname1,$line);
if ($seq ne ""){
push(@seq1,$seq);
... |
3a48a3f4cd71c2249c2fc357f30bffa189220dd5c5374c822fd34e9a9acc86a9 | Perl | 2,030 | 77 | $file1=shift @ARGV;
#$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... |
05eec7a8746b3aad326cfc4366dde55f9b46a7c5bcec8c5bfec1986afb44be98 | Perl | 2,038 | 54 | #!/usr/local/ensembl/bin/perl -w
use strict;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Exception qw(throw);
#
# Simple example to show how to get conservation scores for a slice.
# Works for ensembl release 51
#
my $reg = "Bio::EnsEMBL::Registry";
my $species = "Homo sapiens";
my $seq_region = "17";
my $s... |
923a0c9c4315b868f8a033d4fe437efbde71d6fbcc889ad90846ea0a5d770f61 | Perl | 2,064 | 67 | #!/usr/local/bin/perl
# Entropy (2001)
open (ENT,'*.csv') or die "$!"; # file name
@allfeat = <ENT>;
close (ENT);
open (ENTOUT,'>entropy.csv');
foreach $feat (@allfeat) {
$feat =~ s/\n//;
($name,$a,$b,$c,$d,$e,$f,$g,$h) = split(/,/,$feat);
@feature = ($a,$b,$c,$d,$e,$f,$g,$h);
@sor... |
c0d2b52a9f8b8ae573863cab599d5219f3cf283e61f053b5707e27d5917bdbf3 | Perl | 2,064 | 75 | #!/usr/bin/perl -w
use lib '/Home/siv11/ash022/home/cbu/2010/picr/SOAP-Lite-0.710.10/lib';
use SOAP::Lite +trace => 'debug';
use Data::Dumper;
my $ff= shift @ARGV;
open FASTA, $ff or die "Cannot open fasta file.";
my $fasta;
while (<FASTA>){
$fasta .= $_;
}
close FASTA;
my $nameSpace="http://www.ebi.ac.uk/picr/Acc... |
ff21d9d7ba4bb7aeeddbf44889652f0fc3816ae70089715f8be3669e6360c245 | Perl | 2,069 | 72 | # 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 ... |
348248bd03d37d927752e4f976b0d96f3698885ee785600d09ec69d69af27230 | Perl | 2,077 | 76 | #!/usr/bin/perl
print "program for picking up seqs with \>4 in particular periodicity \n";
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName MultSeqFile\"\t\n\n\n";}
$file = shift @ARGV;
#$n= shift @ARGV;
$n=3;
$f=1/$n;
use Math::Complex;
$pi=pi;
$i=sqrt(-1);
open (F, $file) || die "can't open \"$file\": $!";
$seq=""... |
492f7640b286d96b6f28e8e848b32c16134c507b78a806b2e9128f66bfb2d2dc | Perl | 2,102 | 103 | # 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 ... |
5229078ae851c3ff2bbf7854275bc413f5b2c633bcc979d4c72abec3b5a19c97 | Perl | 2,107 | 76 | #!/usr/bin/perl
print "program for picking up seqs with \>4 in particular periodicity \n";
if( @ARGV ne 1){die "\nUSAGE\t\"ProgName MultSeqFile\"\t\n\n\n";}
$file = shift @ARGV;
#$n= shift @ARGV;
$n=3;
$f=1/$n;
use Math::Complex;
$pi=pi;
$i=sqrt(-1);
open (F, $file) || die "can't open \"$file\": $!";
$seq=""... |
33e8be786d1f9a2b73ab6702c2bb39df3883977de9472d4deafeb3453898102f | Perl | 2,125 | 64 | use strict;
use lib '/media/DATA/tariku/ensembl';
#use lib '/scratch/bac2fish/BioPerl-1.6.1';
use Bio::EnsEMBL::Registry;
my $file=shift @ARGV;
open(F,$file);
open(FO,">$file.seq.fna");
my $cover=100000;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
... |
60706d0e485818761d99d3ef333984b4ab79dd7fd698b85123cada393a20d3e4 | Perl | 2,129 | 60 | # This program is free software: you can redistribute it and/or modify
# # it under the terms of the GNU General Public License as published by
# # the Free Software Foundation, either version 3 of the License, or
# # (at your option) any later version.
# #
# # This program is distrib... |
d3d62e31999bddfecd2493898a30fe62358d63b654672ded21d3570f683c5a1d | Perl | 2,130 | 67 | use warnings;
use strict;
open(F1,$ARGV[0]);
open(F2,$ARGV[1]);
my $mc=$ARGV[2];
my $oc=$ARGV[3];
my $num=$ARGV[4];
if(!$ARGV[2]){$mc=0;}
if(!$ARGV[3]){$oc=$mc;}
if(!$ARGV[4]){$num=0;}
my @list=<F1>;
my @gop=<F2>;
@list = sort { uc($a) cmp uc($b) } @list;
@gop = sort { uc($a) cmp uc($b) } @gop;
my $cnt=0;... |
aeae44f5aef8d64c67f3ea2979d9903e37a7cce61ff4b4c1d364264c1f0992ca | Perl | 2,133 | 91 | # 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 ... |
afeb61cdc967d5d015b05445c8ca922a9701999f73c8d1c9c957e9f376cbafad | Perl | 2,136 | 78 | # 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 ... |
9f69e081f85743bde0c80deac84f3bacb3c040b4a5997917433ed69d98415a39 | Perl | 2,141 | 80 | #!/usr/bin/perl
use lib "/scratch/bioperl/";
use Bio::Perl;
use Bio::SeqIO;
my $window=200;
my $jump=180;
my $main_file=shift @ARGV;
#my $fas_file=$main_file."_in.fasta";
#open(FT,">$fas_file");
my ($wseqname,$wseq,$wseqlen)=get_other_source($main_file);
sub get_other_source{
my $foofile=shift;
my $... |
77e8b97b930af8e29b3ed882235afd5750a423a33da1329cb06f910934d288cb | Perl | 2,145 | 82 | #open(F1,"trimfile.txt");
open(F1,"tf");
$thresh=0;
#open_file("all.fna");
open_file("al");
while(<F1>){
chomp;
$c++;
$name=$_;
$name=~s/\s+/\_/g;
@tmp=split(/\s+/,);
$namesubstr=substr($name,9,5);
$dirstr=uc(substr($name,15,1));
$libstr=substr($name,0,9);
$n1=... |
b63ea37cdc183b8576f530466839326614a6e4a6e20453685ee6d2c816bc439c | Perl | 2,145 | 82 | open(F1,"trimfile.txt");
#open(F1,"tf");
$thresh=0;
open_file("all.all");
#open_file("al");
while(<F1>){
chomp;
$c++;
$name=$_;
$name=~s/\s+/\_/g;
@tmp=split(/\s+/,);
$namesubstr=substr($name,9,5);
$dirstr=uc(substr($name,15,1));
$libstr=substr($name,0,9);
$n1=... |
ee653a1c7071a57dc6ec1ef071823712022070165c57483351bdd9fd5b3918cf | Perl | 2,145 | 83 | #!/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... |
7c061537cb7202b443e6b3e18950febbc4b020a9ee3ef8f42db6f81460337175 | Perl | 2,166 | 64 | /**** A. CHESS QUEENS ****/
/* N er antall kollonner, Q er en loesning */
queen(N,Q) :- genlist(1,N,R),
perm(Q,R),
diagonal(Q).
/* Genererer en liste av alle tall mellom A og B */
genlist(A,A,[A]).
genlist(A,B,[A|L]) :- A < B, N is A+1,
genlist(N,B,L).
/... |
778ebd33c7747df84dbbfe6def0f001acd074ebb6150988e418bc7d75660d73b | Perl | 2,173 | 89 | #!/usr/bin/perl
use strict;
my $main_file=shift @ARGV;
my $coverage=50;
my $window=250;
my $per_win=20;
my $socl=$window*(1-$per_win/100);
my $eocl=$window*(1+$per_win/100);
my @gseq;
my @gseqname;
my $fot;
my $fas_file=$main_file.".C$coverage.L$window.read.fasta";
open(FT,">$fas_file");
get_other_so... |
2778ac8d72ef8e7d8520f2edb8570bb7765d20d9137544df2f771ad093a5d8a0 | Perl | 2,192 | 55 | for($c=0;$c<7;$c++){
$titanium="Titanium";
$seabass="seabass.fasta";
if($c==0){
$nt=($c+1)*30000;
}
else{
$nt=($c)*150000;
}
print "$c\t$nt\tNV\t800\n";
system("time ./flowsim-0.2.4 -G Titanium --model=nv.txt --degrad=\"Normal 0 0\" -n $nt $seabass -o $seabass.$c.$nt.$titanium.nv.800.sff");
print "... |
3d48e11258418d76ca17332ec41c41deb27466aa66ec98fc49e1b76254b1d9ec | Perl | 2,219 | 57 | for($c=0;$c<7;$c++){
$titanium="Titanium";
$gs20="GS20";
$ecoli="Ecoli-K12-MG1655.fasta";
$seabass="SeaBass_LG1_BOTTOM_final_scaffold.fasta";
if($c==0){
$ng=($c+1)*40000;
$nt=($c+1)*10000;
}
else{
$ng=($c)*200000;
$nt=($c)*50000;
}
print "$c\t$gs20\t$ecoli\t";
system("time /space/animesh/flowsim/flow... |
da5edf54cfe13783c6b1fa186ae1b2e9cd9b8bf4c261ef0b50bbeb1fcf663826 | Perl | 2,231 | 55 | for($c=0;$c<7;$c++){
$titanium="Titanium";
$seabass="seabass.fasta";
if($c==0){
$nt=($c+1)*30000;
}
else{
$nt=($c)*150000;
}
print "$c\t$nt\tNormalEmpSmooth\t800\n";
system("time ./flowsim-0.2.5 -G Titanium --model=empdist.ani.smooth.txt --degrad=\"Normal 0 0\" -n $nt $seabass -o $seabass.$c.$nt.$ti... |
bd38298e77cab776446119ade3ceca9d0f7419af1aeb7756968356f2d058f24a | Perl | 2,240 | 65 | # 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 ... |
612a4bc1d9b9e62263ccbbee8dccc65f586ff51ea12aa4a1e6b4609ac6c2e396 | Perl | 2,259 | 112 | #!/usr/bin/perl
use strict;
my $main_file_pattern=shift @ARGV;chomp $main_file_pattern;
open(F,$main_file_pattern)||die "can't open";
my ($line,$snames,@seqname,@seq,$fresall,$seq,$seqname);
while ($line = <F>) {
chomp ($line);
if ($line =~ /^>/){
$snames=$line;
chomp $snames;
$snames... |
1bbe66de88f825aafd4d99417d776d41ed93a80cf62c073c3a66b33d36d5d349 | Perl | 2,261 | 59 | for($c=0;$c<1;$c++){
$titanium="Titanium";
$gs20="GS20";
$ecoli="Ecoli-K12-MG1655.fasta";
$seabass="SeaBass_LG1_BOTTOM_final_scaffold.fasta";
if($c==0){
$ng=($c+1)*20000;
$nt=($c+1)*5000;
}
else{
$ng=($c)*200000;
$nt=($c)*25000;
}
print "$c\t$nt\t1600\n";
system("time ./flowsim-0.2.4 -G tiem --flowl... |
249984b25f516d35d98d567c19a0e5c402b994f775232f6d335b737bc4e85edc | Perl | 2,264 | 104 | #!/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;
while(<F>){
... |
7cab877d5b90c1efa476ac51b870d531c3e6cf69633744e4914e1bfe2930fb88 | Perl | 2,274 | 83 | use strict;
use warnings;
use Text::ParseWords;
my @files=<*mpileup.txt>;
my @filesb=<*mpileup.base.txt>;
my @filesq=<*mpileup.qual.txt>;
my %id;
my %idc;
my %ids;
my %cc;
my %ccb;
my %ccq;
my $cnt;
print "Seq-Pos-Nuc\t";
for($cnt=0;$cnt<=$#files;$cnt++){
my $f1=$files[$cnt];
my $fb=$filesb[$cnt];
my $fq=... |
7c71b60147f1339b0601740d30fe873501f7237ddfe851e5ca1acb87dd9f9932 | Perl | 2,284 | 95 | if( @ARGV ne 2){die "\nUSAGE\t\"ProgName MultSeqFile1 MultSeqFile2\t\n\n\n";}
$file1 = shift @ARGV;
open (F, $file1) || die "can't open \"$file1\": $!";
$seq="";
while ($line = <F>) {
if ($line =~ /^>/){
$c++;
chomp $line;
push(@seqname1,$line);
if ($seq ne ""){
push(@seq1,$seq);
... |
d79ef981d74dab0643ec7d0a8f6a1caac1b83eaa3d94e04d1bcc943222a86145 | Perl | 2,286 | 81 | #!/usr/local/bin/perl
# Permutation U-test (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) = ... |
acb397578760fe2ac5bd5c94a196c693f89c22ed4e8fedac32b2b810c2638072 | Perl | 2,297 | 84 | #!/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 ... |
66182b5195c2a651c88037ecc85bf03e935666a5cd60edc4ae484f0fc8d2371b | Perl | 2,305 | 91 | #!/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',
... |
cc5672db6787e5efec033471f4f5060b46885139464ba44efaf78ef45a86779d | Perl | 2,325 | 95 | #!/usr/bin/perl
use strict;
my $main_file=shift @ARGV;
my $coverage=shift @ARGV;
my $window=100;
my $per_win=100;
#my $socl=$window*(1-$per_win/100);
#my $eocl=$window*(1+$per_win/100);
my @randy=qw/3000 8000 20000 150000/;
my @gseq;
my @gseqname;
my $fot;
my $fas_file=$main_file.".pairedread.fasta";
open(FT,">$fas_fi... |
2c01f2304e7ad204cc54ba3d34edcdb3a9bb42752f60661ffb827d19675ed15e | Perl | 2,335 | 117 | #!/usr/bin/perl
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 =<FILE... |
0cc328494eb8219908fef02407ecc7549821b925f6aa7d020f75f204ebf98dcd | Perl | 2,365 | 80 | if($#ARGV<1){
die "Usage: perl list_clusters.pl file cutoff, where file contains output from Tree and cutoff is the value of the weakest connection to call a cluster in this listing\n";
}
$file=$ARGV[0];
open IN, $file;
$cutoff=$ARGV[1];
$num=0;
while($line=<IN>){
$num++;
}
$num++;
#the number of... |
03c8b27546c7eeac3f52a2f8ed3826e6806092b09b0c5e57e531d26eaca93c62 | Perl | 2,379 | 97 | #!/usr/bin/env perl
use File::Basename;
use Getopt::Long;
GetOptions(
'cmd=s' => \my $cmd,
);
sub help {
print("
HELP:
\t--cmd=input.txt file\n\n");
exit;
}
sub error {
my $msg = $_[0];
print ("$msg\n");
help();
}
sub findMax {
my $fileName = $_[0];
my $dirName = $_[1];
my $max = 0;
open(PCFIL... |
374057bbc4c2e99e2d74ed6ffe0ce3c6111e09f1c1383e74c154a487c5b4cf78 | Perl | 2,387 | 79 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
eac949da0bf27542b50fdd54e3ec0bc06e52536e41304ca3f60f2afef419dd39 | Perl | 2,387 | 83 | # This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it ... |
3b4cd290209323913587a3bd3946e749a968dd7310d7857551654d9c8a139a75 | Perl | 2,393 | 93 | #!/usr/bin/env perl
if ($#ARGV < 0) {
print "usage: assemble.pl readsFile [-vertexSize v] [-exeDir e]\n";
exit(0);
}
$vertexSize = 20;
$machtype = $ENV{"MACHTYPE"};
$srcDir = $ENV{"MCSRC"};
$exeDir = "$srcDir/assembly/$machtype";
$readsFile = shift @ARGV;
$curdir = "";
if (! -e $readsFile ){
print ... |
9762ecfd9a66c956a74f0c078cee62248f33f8c5bf9026964c59a008f26df227 | Perl | 2,419 | 66 | #! /usr/bin/perl -w
# Galaxy (universe) wrapper for Rico's extractAxt
# For this to work extractAxt should be intalled in bins/
# directory of universe's tools section
# Takes the following parameters:
# extractorAxt_wrapper.pl -i $inp_file1 -o $out_file1 --species $species -g $dbkey $chroCol $startCol $endCol $... |
3ace9006f21245bd8eeb01517a19efb5d4096b5a2eb0e5603ef9080f53e0bb95 | Perl | 2,491 | 82 | use strict;
use lib '/home/ash022/Desktop/bac2fish/ensembl/modules';
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
my @db_adaptors = @{ $registry->get_all_DBAdaptors() };
my $slice_a... |
fae0c2807c954297a32179dc2c5d3d1a9db1b24669e8ee0c2edc38865d51273f | Perl | 2,496 | 64 | # 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... |
efd235243bf5b6a1ddf95c6142fee42cc83fd4fdd82e08dea9ee21b416493f9d | Perl | 2,506 | 82 | use strict;
use warnings;
use XML::Simple;
my $f = shift @ARGV;
my $par1 = shift @ARGV;
my $par2 = shift @ARGV;
my $par3 = shift @ARGV;
my $par4 = shift @ARGV;
my $par5 = shift @ARGV;
my $d = XMLin($f);
#print $f,$d;
#use Data::Dumper;
#print Dumper($d);
my %maxrtr;
foreach my $p (keys %{$d->{$par1}}) {
if(ref($d->{$... |
41a87b7119254bafbe6b2d27930c23c7bbc6442cbcaf81b86500ca0028bc8e51 | Perl | 2,524 | 67 | use lib '/scratch/bac2fish/BioPerl-1.6.1';
use strict;
use Bio::SearchIO;
my $f=shift @ARGV;
open(FO,">$f.pb");
chomp $f;
my $lent=10;
my $pert=10;
my $eval=5*10e-2;
my $gapa=5*10e2;
my %alignlen;
my %alignspan;
my %alignmin;
my %alignmax;
my %alignevalc;
my $in = new Bio::SearchIO(-format => 'blast',
... |
b44d0d3012ce2c130b0f26c530ad2f16ce34be9135d185be5352d3df58805163 | Perl | 2,533 | 115 | # 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 ... |
b502222d04d9d079f573932326d09389e33b430dbacccd83e3145c307f22e3ef | Perl | 2,535 | 69 | #!/usr/local/bin/perl
if (! -d "TEST") {
mkdir("TEST") || die("Cannot create directory TEST: $!\n");
}
open(LOG, ">>runtest.log") || die ("Cannot open runtest.log: $!\n");
print LOG "test readlen spread small_lib large_lib fraction coverage\n";
close(LOG);
my $test = 1;
#foreach $readlen (600, 700, 800, 9... |
a98d1d745dc109fceab259d3a0eddc07f685468519b9e23b4c5a80e6ea3147b0 | Perl | 2,583 | 81 | # 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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