Bioperl: Is this a bug?

Osborne, Brian
Fri, 30 Oct 1998 17:44:51 -0500

To the group,

First, congratulations on the impending release. This
group has been an example not just of fine coding but
but of fine collaboration as well. My question is
demonstrated here :

use Bio::Seq;

$myEnt = ">somesequence

$mySeq = Bio::Seq->new(-seq =>$myEnt,-ffmt => 'Fasta' );

print $mySeq->id;

The result is : 


If I do :

print $mySeq->layout

the result is :

>No_Id_Given No Description Given

If I invoke new() with the "-file" option, and the input file is a fasta
and I specify -ffmt => 'Fasta' the id is taken from the string
(skipping white space) after the ">" (and I can see why in the
method). But you can see that if I use the string above then no id is 
found. Is this the desired result? Shouldn't these behave the same?
That is, I'm specifying fasta so the header should at  least be removed.
I ftp'd my and from bio.perl.orgj this afternoon.

Thanks again,

Brian O.

Brian Osborne
Cadus Pharmaceutical Corporation
777 Old Saw Mill River Rd.
Tarrytown NY USA
TEL 914 467 6291
FAX 914 345 3565

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