[Bioperl-l] Scanning GenPept entries does not work

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Mon, 30 Oct 2000 20:45:44 +0100

GenPept parsing using the genbank parser works in the development (main)
trunk, and this capability will be included in the 0.7 release. It does not
work in the 0.6.x versions because the genbank parser was specific for
nucleotide entries.


Henrik.Seidel@schering.de@bioperl.org on 30.10.2000 16:28:32

Sent by:  bioperl-l-admin@bioperl.org

To:   bioperl-l@bioperl.org
Subject:  [Bioperl-l] Scanning GenPept entries does not work

Dear all,

obviously, NCBI-GenPept entries in GenBank file format cannot be parsed,
the regular expression in line 185 of genbank.pm expects "bp" while protein
entries have "aa" in their LOCUS line. Furthermore, GenPept entries don't
have a
molecule in their LOCUS line.

Do you think it would suffice to alter the regular expression, or are there
other implications with using the GenBank parser for GenPept files?



Dr. Henrik Seidel, physicist/research scientist in bioinformatics
Schering AG, Enabling Technologies, Genomics/Bioinformatics, S109 7.OG,
D-13342 Berlin, Germany, Tel.: +49 30 468 16683, Fax.: +49 30 468 96683,
henrik.seidel@schering.de, http://www.schering.de

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