[Bioperl-l] Empty FASTA files with Bio::SeqIO

[J.C. Diggans]

> It indeed came up some months ago, and it should be somewhere in the
> archives. The current design is intentional, but we decided to support
> empty sequences and reading and writing them in FASTA format (NOT in other
> formats). This will be part of the 0.7 release features. If you look at the
> task list, you'll find it.

I went ahead and patched my local version from 0.6.2 (patch below). It
was a quick fix, can anyone think of a case in which this would fail?

- jc

122,123c122,134
<   my ($top,$sequence) = $entry =~ /^(.+?)\n([^>]+)/s
<     or $self->throw("Can't parse entry");
---
>   # Check for empty sequences and handle gracefully
>   my ($top,$sequence);
>   if( $entry =~ /^(.+?)\n([^>]+)/s ) {
>       # There is valid sequence present
>       ($top,$sequence) = $entry =~ /^(.+?)\n([^>]+)/s
> 	     or $self->throw("Can't parse entry");
>   } else {
>       # There is no sequence present, 
>       $top = $entry =~ /^(.+?)\n/	
> 	     or $self->throw("Can't parse entry"); # save top
>       $sequence = "";	# set sequence to empty string
>   }
> 

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James Diggans              Phone:    301.987.1756
Gene Logic, Inc.           FAX:      301.987.1701
jdiggans@genelogic.com     Cell:     301.908.2477
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