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#!/usr/bin/perl
#------------------------------------------------------------------------------
# Split a fasta file (create one file per sequence)
#
# Pablo Cingolani
#------------------------------------------------------------------------------
use strict;
#------------------------------------------------------------------------------
# Write fasta file
#------------------------------------------------------------------------------
sub writeSeq($$) {
my($name, $seq) = @_;
if( $name !~ /^chr/ ) { $name = "chr$name"; }
$name = "$name.fa";
print "Writing to $name\n";
open OUT, "> $name";
print OUT $seq;
close OUT;
}
#------------------------------------------------------------------------------
# Main
#------------------------------------------------------------------------------
my($seq, $name) = ('', '');
my($lineNum, $l, $newName);
# Read fasta file
for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) {
if( $l =~/^>\s*(.*?)\s+.*/ ) {
$newName = $1;
if( $seq ne "" ) { writeSeq($name, $seq); }
# New sequence
$name = $newName;
$seq = $l;
} else { $seq .= $l; }
}
if( $seq ne "" ) { writeSeq($name, $seq); }
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