Mercurial > repos > big-tiandm > sirna_plant
changeset 16:7d12d9b130bc draft
Uploaded
| author | big-tiandm |
|---|---|
| date | Wed, 29 Oct 2014 05:03:28 -0400 |
| parents | 0e4b6b0c6e9d |
| children | b75750b21aa4 |
| files | get_genelist.pl |
| diffstat | 1 files changed, 62 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_genelist.pl Wed Oct 29 05:03:28 2014 -0400 @@ -0,0 +1,62 @@ +#!/usr/bin/perl -w +#Filename: +#Author: chentt +#Email: +#Date: 2012-4-6 +#Modified: +#Description: +my $version=1.00; + +use strict; +use Getopt::Long; + +my %opts; +GetOptions(\%opts,"i=s","o=s","h"); +if (!(defined $opts{i} and defined $opts{o}) || defined $opts{h}) { #necessary arguments +&usage; +} +open IN,"<$opts{i}"; +open OUT ,">$opts{o}"; +print OUT "#ID\tchr\tstart\tend\tstrand\n"; +my $n=1; +my %gene1; +while (my $aline=<IN>) { + chomp $aline; + next if($aline=~/^\#/); + my @tmp=split/\t/,$aline; + my $ID; + if ($tmp[2] eq "gene") { + $tmp[0]=~s/Chr\./Chr/; + #$tmp[0]=~s/Chr/chr/; + my @infor=split/;/,$tmp[8]; + for (my $i=0;$i<@infor ;$i++) { + if ($infor[$i]=~/Alias\=(\S+)$/) { + $ID=$1; + last; + } + else { + $ID="unknown$n"; + $n++; + } + } + #$gene{$tmp[0]}{$ID}=[$tmp[3],$tmp[4],$tmp[6]];#$gene{chr}{geneID}=[start,end,strand] + push @{$gene1{$ID}},[$tmp[3],$tmp[4],$tmp[0]]; + print OUT "$ID\t$tmp[0]\t$tmp[3]\t$tmp[4]\t$tmp[6]\n"; + } +} +close IN; +close OUT; + + +sub usage{ +print <<"USAGE"; +Version $version +Usage: +$0 -i -o -h +options: +-i input cluster file +-o output file +-h help +USAGE +exit(1); +} \ No newline at end of file