Bioperl: bioperl swissprot (fwd)

[Elia Stupka]

---------- Forwarded message ----------
Date: Wed, 3 May 2000 17:40:28 +0200 (MEST)
From: Michael Wildpaner <mike@rainbow.studorg.tuwien.ac.at>
To: Elia Stupka <elia@ebi.ac.uk>
Subject: bioperl swissprot

Dear Elia,

I'm currently trying to read swissprot rel38 with bioperl. many FT lines
contain uncertain or missing information and are not recognized by the
parser.

examples:

FT   SIGNAL        1      ?       POTENTIAL.
FT   CHAIN         ?     75       10 KD PROTEIN.
FT   CHAIN        20   >154       17 KD SURFACE ANTIGEN.
FT   SIGNAL        1    ?24       POTENTIAL.

Currently I am implementing patches to swiss.pm and FTHelper.pm to convert
these values to '?' and subsequently to undef.

Are there any "official" plans how to treat unknown values?

many thanks, Michael Wildpaner

-- 
Don't feed.                                               DI Michael Wildpaner
Don't provoke.                                                Ph.D. Student at
Don't enter the cage.                          Vienna University of Technology



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