Bioperl: Two newbie questions

Kris Boulez
Mon, 17 Apr 2000 08:53:02 +0200

Quoting (
> 		Hi!
> Disclaimer: I am not at all experienced with perl in general and just start
> with bioperl...
> And I am trying to find my way around in the examples and documentation,
> because I want to write a litte script to do something usefull for me :-)
> I have two questions that I could not figure out with the documentation:
> 1) I read from a file: 
> 	$in = Bio::SeqIO->new( '-format' => $informat , -file => $file);
> 	while ($seq = $in->next_seq();){
				     ^     leave out the ';'
> 		...
> 	}
> This works fine for the fasta files included in the bioperl distribution.
> But my Sequence happens to come in gcg format - so i just set $informat to
> "gcg". Ok - my files include only one single sequence, but anyway... I
> expected it to work nevertheless. But this turns out to be an endless loop
> delivering the same sequence over and over again. Why is that?

How are these GCG files created ? Are they the result of a 'fetch' or
are they saved in SeqLab.
I'll need the ability to read in mulitple GCG files (and parse them)
real soon now. I already had a quick look and found a bug which
prevented me from reading more then the first sequence from a GCG file I
created using 'Fetch'. Patch is trivial however.

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