[Bioperl-l] Validate Fasta

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Mar 3 05:16:04 EST 2004


I have searched the archives and only come up with one answer, and it didn't work - I want to validate a FASTA sequence (DNA).  What I mean is that if I am given a perfect FASTA sequence, then thats ok, but if there are ANY whitespace characters, or any other characters that really shouldn't be there, I want it to throw an error.  The script below was suggested by Jason in 2002:

use Bio::SeqIO;

my $in = Bio::SeqIO->new(-file => "rubbish.fasta");
my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta");

eval {
	LOOP: while( my $seq = $in->next_seq ) {

if( $@) {
	print "There's an Error!\n";
	goto LOOP;

I actually fired this at one of my scripts, a perl script that clearly wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA sequence characters.  Here is the result:

/mick/backups";my$date=`date`;my at date=split(/\s+/,$date);my$
date=join("_", at date[0..2],$date[$#date]);print"$date\n";#whi

This is undoubtedly a wonderfully FASTA formatted perl script, but...

Anyone?  Any ideas?

Thanks in advance for the help!


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