#!/usr/bin/perl 
use warnings;
use strict;
use Data::Dumper;


#
# split a fasta file into separate sequence files
#
open( my $seqs, "C:/Documents and Settings/mydir/13063_fasta.contigs");
open(my $seq_out,">C:/Documents and Settings/mydir/contig.fa" );
$/ = '\777'; # entire input to be read in one slurp

$seqs = <>;  # read input, assigning to single string

while (<$seqs>){
	if($seqs =~ m/^(>[^>]+)/mg) { # match indiv. sequences by '>'s
		push(my @seqs,$1);           # and store in array
	}

	for (my @seqs) {
	# only allow characters A-Z,a-z,0-9,'_','-', and '.' in names;
	# change if you're more liberal
	/^> *([\w\-\.]+)/ && (my $seq_name = $1);
		if ($seq_name) {
			open($seq_out,">$seq_name");
			print $seq_out "$_";
		}
		else {
		warn "couldn't recognise the sequence name in \n$_";
		}
	}
}
close($seqs);
close($seq_out);