[Bioperl-l] removing duplicate fasta records

[Lincoln Stein]

Here's one way.  Note that it will remove duplicate records if the sequence is 
identical, but doesn't examine the description line.  You may want to modify 
this if you have a different definition of identical sequences.

Lincoln

#!/usr/bin/perl

use strict;

use Bio::SeqIO;
use Digest::MD5 'md5_hex';

my %digests;
my $in = Bio::SeqIO->new(-fh => \*ARGV);
my $out = Bio::SeqIO->new;

while (my $seq = $in->next_seq) {
	next if $digests{md5_hex($seq->seq)}++;
	$out->write_seq($seq);
}



On Tuesday 17 December 2002 02:41 pm, "Amit Indap wrote:
> I have a file with a list of fasta sequences. Is there a way to
> remove records with the identical sequence? I am a newbie to BioPerl,
> and my search through the documentation hasn't found anything.
>
> Thank you.
>
> Amit Indap
>
>
>
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> Bioperl-l@bioperl.org
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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