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

Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/file2GenomeName.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,24 @@
+#!/usr/bin/perl
+
+#-------------------------------------------------------------------------------
+#
+# Transform file name to genome short name
+#
+#-------------------------------------------------------------------------------
+
+$file = $ARGV[0];
+print "$file";
+
+$base = `basename $file`;
+chomp $base;
+print "\t$base";
+
+if( $base =~ /(.*?)\.(.*)\..?dna\.(.*)\.fa\.gz/ ) { ($gen, $short) = ($1, $2); }
+elsif( $base =~ /(.*?)\.(.*)\.gtf\.gz/ ) { ($gen, $short) = ($1, $2); }
+elsif( $base =~ /(.*?)\.(.*)\.pep\.all\.fa\.gz/ ) { ($gen, $short) = ($1, $2); }
+$full = "$gen.$short";
+print "\t$full\t$gen\t$short";
+
+
+print "\n";
+