How can I split a file
__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

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based on the delimiter '>' and then print the lines
in between '>' and the next '>' then continue until I have
separate files like this
file1:
>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig1
TTTCTCCGGCCCCCTCCTCCCGCGGGGGAAAAAACCCGGGGAGCAGTCGG
GCAGGGGTTTTTTGGTTTTTTCAAAATAAAAAGGGGTGCCCGTTGGGGGGcd 
GGGGGGGTGCAGGTTTCAACCCCCCCCCCCAAAGAAAAAAAAATTTTGGG
GAATTTTTGGGGGGCTCCACCAGTTTTCGGGGTTTTTGGGCCTTTTCAGA
AGGTAGGTTGGACGCGGATTGGGCAATAAACCACCCCGCTTCATCGGATA
ATTTTCCCCGGCCGAAAAGGGCCGCGGGGCCGGTGGGCGGCCTTGGGTTT

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And file2:
>i:/13414 Ccl9 (88)/sequencing/13414_fasta.Contig2
TAAACCCAAGGCCCCCCAGGTAAAAAAAAAACCGGCCAGGGGGGGGGGGG
TAAAAAAAACCAAGTGTCACCCAGGGTGGAGATCCCCGGAAAAGGAAAAG
GGGGGTTTTTTATTCGAAACGGGGAAAACTTTCACAAAATTTTGGAAGAA
TCCCCTTTAATGTTTTCTTTTCAAAAGGGGGTAAAAAAACCACCTTTAAA
AAGAAGTCTACCTTGGGAAAAAATAATTTTTGGGAAAATTTAAAAATTGA

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I am running into some trouble with this code:
#!/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);

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Sorry for not being specific enough :-)

In reply to Re^2: splitting fasta file into individual fasta files by lomSpace
in thread splitting fasta file into individual fasta files by lomSpace

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