in reply to Re: splitting fasta file into individual fasta files
in thread splitting fasta file into individual fasta files

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 :-)

Replies are listed 'Best First'.
Re^3: splitting fasta file into individual fasta files
by moritz (Cardinal) on May 06, 2009 at 22:07 UTC

    Actually I was interested in what kinds of trouble you ran into, but anyway...

    There's a trick in Perl that makes that quite easy: you can set the input record separator to '>', so that the <DATA> iterator gives you chunks splitted by '>': 

    use strict;
use warnings;

local $/ = '>';

my $c = 0;
while (<DATA>) {
    chomp;
    next unless length;
    my $fn = "file" . ++$c;
    open my $handle, '>', $fn or die "Can't open `$fn' for writing: $!
+";
    print $handle '>', $_;
    close $handle or warn $!;
}

__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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Re^3: splitting fasta file into individual fasta files
by citromatik (Curate) on May 07, 2009 at 09:13 UTC

    You can use Tie::File::AnyData::Bio::Fasta to facilitate this task. This script reads a multi-fasta file and splits it in multiple single-fasta files:

    use strict;
use warnings;

use Tie::File::AnyData::Bio::Fasta;

tie my @in,'Tie::File::AnyData::Bio::Fasta', shift @ARGV, or die $!;

my $n = 0;
for my $seq (@in){
  tie my @out, 'Tie::File::AnyData::Bio::Fasta', "$n.fa" or die $!;
  $n++;
  @out = ($seq);
  untie @out;
}

untie @in;

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    citromatik

[reply]
[d/l]
      citromatik,
      Thanks. I have installed the files into 'C:\Perl\site\lib' and
      'C:\Perl\lib' on my windows system, but the error keeps stating that
      it 'Can't locate Tie/File/AnyData/Bio/Fasta.pm in @INC (@INC contains: C:/Perl/site/lib C:/Perl/lib .)'
      What could I be doing wrong?
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