[Bioperl-l] Validate Fasta

[michael watson (IAH-C)]

Hi

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 ) {
		$out->write_seq($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:

>#!/usr/bin/perl
my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac
he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb
l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location="
/mick/backups";my$date=`date`;my at date=split(/\s+/,$date);my$
date=join("_", at date[0..2],$date[$#date]);print"$date\n";#whi
le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys
qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp
ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar")
;system("/bin/gzip$location/$name.$date.tar");}

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

Anyone?  Any ideas?

Thanks in advance for the help!

Mick