[Bioperl-l] Question regarding BioPerl / BioSQL - InterPro Optional IDs
John LaCava
lacava at gmail.com
Fri Jul 3 18:07:50 UTC 2009
Hi all,
I am trying to use the BioPerl-db script:
load_seqdatabase.pl to parse a SwissProt.dat file (Yeast.dat, this is
the yeast proteome with annotations etc.).
The particular entry I am interested is the InterPro optional ID,
which is the domain name.
I have put a short stub up which displays the 4 pieces of info I want
to parse into my data base.
That can be found here:
http://github.com/johnraekwon/BioPerl---BioSQL---InterPro-Optional-IDs/tree/master
You can see that near the bottom, we get the optional ID:
$protein_ids->{interpro_domain} = $dblink->{optional_id};
I do not think the bioperl script load_seqdatabase.pl retrieves this
information. At least, I cannot find it in the db built from parsing
a test .dat file.
I would like some help figuring out:
1) WHY doesn't it retrieve this information, since it seems to be
parsing "all" annotations...
2) HOW might I edit the script to include this particular annotation
of interest in the info it passes to my db (biosql)
I am a bit out of my depth on this, and so, any help is appreciated.
Cheers,
John
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