[Bioperl-l] Review request: Merged hmmer2/3 parser

Kai Blin kai.blin at biotech.uni-tuebingen.de
Fri Nov 5 07:33:44 EDT 2010


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi folks,

https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser
contains my attempt to get a hmmer parser that is able to detect which
hmmer version output it's given and which parser to call in turn.

I chose to sneak in a Bio::SearchIO::hmmer class into the object
hierarchy that the hmmer2 parser (renamed to Bio::SearchIO::hmmer2) and
the hmmer3 parser subclass from.

I'm not sure if this is the best way to go, though, and I'd like to get
some feedback on the implementation.
The last six patches on
https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser are
the full changeset, the core of the change is in
https://github.com/kblin/bioperl-live/commit/2d4816f1d67880c69948b2ce529fdeb52e0d843f

Thanks in advance for your time,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iQEcBAEBAgAGBQJM0+uBAAoJEKM5lwBiwTTP7+8IAN6ivTfTa2NNCCvL7ImXiXEU
LF5BbYIEgtyu+7NZIvX0/eLrs9PBZ4BqOl+LqyiYP0GSOsgX1I7ndc2n67o06n+h
z+HGcNUScDGxx1jGheC4nWWs3sfWrS4KvxMlM6XlXGF/ioai9Im9JLKidsqRXPr0
Sf1r3GHYeNQPZ3eGdXhb7mEv2Ps7OOWyGGfZqyokoaTLItiLPrhpNCVg6liz0lh1
Mb0s3vpCRgsQpWqBJuwkkWFmS5ReokFu9Bnf0xXjGbGFHDGkI9YLXRtcbwu5kaBq
V52CS9SOuPJvDLPoCBzvDkEI6+tXeEjutoG52wQ8F0tgpbdrMlahlrze3gvCHJw=
=IGwD
-----END PGP SIGNATURE-----


More information about the Bioperl-l mailing list