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

[Hilmar Lapp]

That's a pretty strange bug. Anand, which version of BioPerl and  
Bioperl-db are you running?

Note that the genus *is* actually there in the lineage (and hence does  
get retrieved from the database). Apparently the Species object fails  
to pull it out correctly, though?

Anand - I suspect there have been some warnings printed to the  
terminal - can you post these, and otherwise confirm that there  
haven't been any?

	-hilmar

On Aug 22, 2009, at 4:17 PM, Chris Fields wrote:

> 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
>>
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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