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comparison snpEff_2_1a/scripts/file2GenomeName.pl @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/usr/bin/perl
2
3 #-------------------------------------------------------------------------------
4 #
5 # Transform file name to genome short name
6 #
7 #-------------------------------------------------------------------------------
8
9 $file = $ARGV[0];
10 print "$file";
11
12 $base = `basename $file`;
13 chomp $base;
14 print "\t$base";
15
16 if( $base =~ /(.*?)\.(.*)\..?dna\.(.*)\.fa\.gz/ ) { ($gen, $short) = ($1, $2); }
17 elsif( $base =~ /(.*?)\.(.*)\.gtf\.gz/ ) { ($gen, $short) = ($1, $2); }
18 elsif( $base =~ /(.*?)\.(.*)\.pep\.all\.fa\.gz/ ) { ($gen, $short) = ($1, $2); }
19 $full = "$gen.$short";
20 print "\t$full\t$gen\t$short";
21
22
23 print "\n";
24