Mercurial > repos > yusuf > generate_genomeid

comparison generateID.pl @ 0:7e4eb6957b8a default tip

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initial commit for genomeid tool
author Yusuf Ali <ali@yusuf.email>
date Thu, 12 Mar 2015 09:49:46 -0600
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1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5 use Getopt::Long;
6
7 use Bio::Seq::GenomeID qw(generate_id);
8
9 my ($outFile, $inFile, $type, $index, $hg);
10 my ($noise, $baq, $sex, $ucn, $ref, $name);
11
12 GetOptions("o=s"=> \$outFile,
13 "n=f"=>\$noise,
14 "hg=s"=> \$hg,
15 "b=i"=> \$baq,
16 "s=s"=> \$sex,
17 "u=s"=> \$ucn,
18 "r=s"=> \$ref,
19 "type=s"=> \$type,
20 "file=s"=> \$inFile,
21 "sN=s"=> \$name,
22 );
23 $ucn = ($ucn eq "true")? 1:0; $sex = ($sex eq "true")?1:0; $ref = ($ref eq "true")?1:0;
24
25 my %obj;
26 $obj{'type'} = $type; $obj{'file'} = $inFile;
27 $obj{'ucn'} = $ucn; $obj{'sex'} = $sex; $obj{'ref'} = $ref;
28 $obj{'noise'} = $noise; $obj{'baq'} = $baq;
29
30 if($type eq "tbi"){
31 `tabix -p vcf $inFile`;
32 }
33
34
35 if($hg ne "none"){
36 $obj{'hg'} = $hg;
37 }
38
39 if( defined $name ){
40 $obj{'sampleName'} = $name;
41 }
42
43 my $genomeID = generate_id(%obj);
44 open(my $fh, '>', $outFile);
45 print $fh $genomeID;
46 close $fh;