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

my $file = "C:/Documents and Settings/mydir/fasta.contigs";
my $seqIO = Bio::SeqIO->new({-file=>'$file', -format=>'fasta'});
while (my $seq = $seqIO->next_seq()) {
   my $out = Bio::SeqIO->new(
                    -file    => ">$file"."_fasta",
                    -format    => 'Fasta');

	$out->write_seq($seq);
}
__DATA__
>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig1
TTTCTCCGGCCCCCTCCTCCCGCGGGGGAAAAAACCCGGGGAGCAGTCGG
GCAGGGGTTTTTTGGTTTTTTCAAAATAAAAAGGGGTGCCCGTTGGGGGGcd 
GGGGGGGTGCAGGTTTCAACCCCCCCCCCCAAAGAAAAAAAAATTTTGGG
GAATTTTTGGGGGGCTCCACCAGTTTTCGGGGTTTTTGGGCCTTTTCAGA
AGGTAGGTTGGACGCGGATTGGGCAATAAACCACCCCGCTTCATCGGATA
ATTTTCCCCGGCCGAAAAGGGCCGCGGGGCCGGTGGGCGGCCTTGGGTTT
>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig2
TAAACCCAAGGCCCCCCAGGTAAAAAAAAAACCGGCCAGGGGGGGGGGGG
TAAAAAAAACCAAGTGTCACCCAGGGTGGAGATCCCCGGAAAAGGAAAAG
GGGGGTTTTTTATTCGAAACGGGGAAAACTTTCACAAAATTTTGGAAGAA
TCCCCTTTAATGTTTTCTTTTCAAAAGGGGGTAAAAAAACCACCTTTAAA
AAGAAGTCTACCTTGGGAAAAAATAATTTTTGGGAAAATTTAAAAATTGA