[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

[Chris Fields]

Anand,

You should always post emails to the bioperl-l mailing list, never to  
individual developers (you'll get an answer much faster).  Keep  
responses on the list as well.

Though I use bioperl-db some, I'm probably not the best person to  
ask.  Does anyone know what's going on with this?  Does this have to  
do with the Species/Taxon refactoring?

chris

Begin forwarded message:

> From: "Anand C. Patel" <acpatel at gmail.com>
> Date: August 22, 2009 2:57:42 PM CDT
> To: cjfields at illinois.edu
> Subject: problem with bioperl (where's the Mus?)
>
> Dr. Fields,
>
> I'm struggling with what seems to be a strange quirk in Bioperl +/-  
> Bioperl-db/BioSQL.
>
> I've successfully loaded in genbank sequences into a biosql database.
>
> When I try to write a genbank sequence back out, a curious thing  
> happens -- the Genus is missing from the SOURCE and ORGANISM areas.
>
> Despite reporting:
> primary tag: source
>  tag: chromosome
>    value: 3
>
>  tag: db_xref
>    value: taxon:10090
>
>  tag: map
>    value: 3 74.5 cM
>
>  tag: mol_type
>    value: mRNA
>
>  tag: organism
>    value: Mus musculus
> The sequence when printed out via SeqIO looks like this:
> LOCUS       NM_017474               2935 bp    dna     linear   ROD  
> 13-AUG-2009
> DEFINITION  Mus musculus chloride channel calcium activated 3  
> (Clca3), mRNA.
> ACCESSION   NM_017474 XM_978159
> VERSION     NM_017474.2  GI:255918210
> KEYWORDS    .
> SOURCE      musculus
>  ORGANISM  musculus
>            Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa;  
> Bilateria;
>            Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata;
>            Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii;  
> Tetrapoda;
>            Amniota; Mammalia; Theria; Eutheria; Euarchontoglires;  
> Glires;
>            Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus.
> Confession -- I have a final project due Monday wherein I boldly  
> elected to interface Bioperl, MySQL, Perl, and CGI.
> (I'm an MD getting my MS in Bioinformatics.)
> After many misadventures, I'm getting to the point where I could  
> actually complete the objectives, but this is bug is rather  
> problematic.
> Thanks,
> Anand
> Anand C. Patel, MD
> Assistant Professor of Pediatrics
> Division of Allergy/Pulmonary Medicine
> Department of Pediatrics
> Washington University School of Medicine
> 660 South Euclid Ave, Campus Box 8052
> St. Louis, MO 63110
> acpatel at wustl.edu
> acpatel at gmail.com
> acpatel at jhu.edu
>