Bioperl: Genbank location qualifiers.

[James Gilbert]

Ian,

You're right, these are not handled in the current
release, but will be handled better in the 0.6.1
release due out this Friday.

The '<' and '>' (end not found) indicators will be
correctly parsed.  They are stored in the
SeqFeature objects under the tag '_part_feature',
with the value '3_prime_missing' or
'5_prime_missing' (or both).

Positions between bases (eg: '21^22') are
parsed.  In this example it will generate a
SeqFeature with start=21, end=22 and the tag
'_zero_width_feature' set to 1.

Fuzzy locations (eg: '24.45') will still not be
parsed, because we haven't come up with a
meaningful representation of them in the
objects.  You will, however, get a warning that
the feature containing them is being ignored.

(There is a bug in this parsing in the 0.6.1-pre
release, so don't pick that up.)

	James

On Tue, 16 May 2000, Ian Davies wrote:

> Hi there,
> I have been playing around  with Bioperl,
> and have read a Genbank annotated sequence record,
> and written it out again as follows:
> 
> $in  = Bio::AnnSeqIO->new(-file => "$home/data/chopped_gb_file" , -format => 
> 'GenBank');
> $out = Bio::AnnSeqIO->new(-fh=>*STDOUT,-format => 'GenBank');
> 
> while ($seq = $in->next_annseq() ) {
>         $out->write_annseq($seq);
> }
> 
> I then diffed the input and output, and noticed
> that the location qualifiers < . >
> for fuzzy locations had been lost.
> 
> Are these not handled?
> 
> regards,
> Carl Dobson.
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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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