Bioperl: Checking DNA alphabeth

[James Gilbert]

Gert,

I don't think there is an actual function, but
this is very simply implemented:

	# $seq_obj is a Bio::Seq (or Bio::PrimarySeq)
	my $str = $seq_obj->seq();
	# $str is now the actual sequence string
	die "Sequence contains non [ACGT] characters"
	    if $str =~ /[^ACGT]/;

    James

On Thu, 18 May 2000, gert thijs wrote:

> I am writing a script to process some DNA
> sequences which are in fasta format.  Now I
> would like to check if these sequences contain
> other symbols then ACGT, like N or degenerate
> symbols.  Is there a function in bioperl that
> does this or has someone any idea which
> regular expression to use?
> 
> Thanks,
> Gert Thijs
> 
> 
> -- 
> ==========================================================
> + Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
> +                                                        +
> + Dept. Elektrotechniek ESAT-SISTA                       +
> + Kardinaal Mercierlaan, 94                              +
> + B-3001 HEVERLEE  Belgium                               +
> + Tel :  +32-16-32 18 84 ---- Fax : +32-16-32 19 70      +
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919


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