Mercurial > repos > greg > snpeff_v2_from_pablo
view snpEff_2_1a/scripts/fasta2tab.pl @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author | greg |
---|---|
date | Fri, 20 Apr 2012 14:47:09 -0400 |
parents | |
children |
line wrap: on
line source
#!/usr/bin/perl #------------------------------------------------------------------------------ # Split a fasta file (create one file per sequence) # # #------------------------------------------------------------------------------ use strict; #------------------------------------------------------------------------------ # Main #------------------------------------------------------------------------------ my($seq, $name) = ('', ''); my($lineNum, $l, $newName); #--- # Read fasta file #--- for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { chomp $l; if( $l =~/^>\s*(.*)\s*$/ ) { $newName = $1; if( $seq ne "" ) { print "$name\t$seq\n"; } # New sequence $name = $newName; $seq = ""; } else { $seq .= $l; } } if( $seq ne "" ) { print "$name\t$seq\n"; }