[Bioperl-l] Fwd: [Bioperl-guts-l] [Bug 1734] New: a RefSeq entry not converted to SwissProt format

[Jason Stajich]

Do any Swissprot experts know what the feature table should look like 
for this type of feature table (genpept)?

      Site            join(243,538)
                      /note="involved in regulation of interaction with
                      glutamyl substrate"
                      /site_type="unclassified"
      Site            join(279,338,361)
                      /note="catalytic triad"
                      /site_type="active"
      Site            join(403,450,455)
                      /note="involved in Ca2+ complexation"
                      /site_type="unclassified"

-jason


Begin forwarded message:

> From: bugzilla-daemon at portal.open-bio.org
> Date: January 19, 2005 8:34:10 AM EST
> To: bioperl-guts-l at bioperl.org
> Cc: Subject: [Bioperl-guts-l] [Bug 1734] New: a RefSeq entry not 
> converted to SwissProt format
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=1734
>
>            Summary: a RefSeq entry not converted to SwissProt format
>            Product: Bioperl
>            Version: 1.4 branch
>           Platform: Sun
>         OS/Version: Solaris
>             Status: NEW
>           Severity: normal
>           Priority: P2
>          Component: Bio::SeqIO
>         AssignedTo: bioperl-guts-l at bioperl.org
>         ReportedBy: laurent.falquet at isb-sib.ch
>
>
> The RefSeq entry NP_443187 generates an error when I tried to convert 
> it to SwissProt format using
> Bio::SeqIO and genbank format as input. (all other RefSeq entries are 
> converted normally using the
> same method).
>
> Here is the error message:
> len 1 is 56 len 2 is 34
> Error sequence not parsable
> Programming error - cannot called write_line_swissprot_regex with 
> different length
> pre1 (FT   Site     join(279,338,361) join(279,338,361)       ) and
> pre2 (FT                                ) tags! at 
> /usr/local/lib/perl5/site_perl/5.8.3/Bio/SeqIO/swiss.pm line
> 1124, <GEN0> line 98.
>
>
>
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/
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