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

[Hilmar Lapp]

On Aug 22, 2009, at 6:44 PM, Anand C. Patel wrote:

> [...]
> I think I know what's broken.  Using load_seqdatabases.pl, I'd put a  
> set of sequences from genbank into a biosql db in mysql.
>
> I'd also loaded the ncbi taxonomy using the load_ncbi_taxonomy.pl  
> script from biosql.

Did you load the NCBI taxonomy first, or afterwards?

>
> When I searched for house (as in house mouse), I found that the name  
> of the type of taxon class was "genbank common name".
>
> When I searched for musculus, it does appear as a type of  
> "scientific name".

It is the 'scientific name' class names that Bioperl-db will onto the  
lineage array.

> [...]
> I'm not just getting warnings.  I'm getting errors.  Tons of them.   
> It's a wonder it's working at all.

I'm not sure what you're referring to, but what you pasted into your  
email were neither errors nor warnings but a debugging log (and what  
it prints looks like it's working fine). You triggered that by setting  
-verbose to a value greater than 0. If you don't want debugging  
output, then you can just leave off that argument (no debugging output  
is the default).

>
> I started with the getentry.cgi script in the cgi-bin folder, and  
> stripped most of it away.

I see - which reminds me that I need to look at that script; I'm  
afraid it hasn't been updated for a long time (that doesn't mean  
though that it can't work - the core API has been stable for years).

>
> Code:
> #!/usr/bin/perl
>
> [...]
> if( $@ || !defined $seq) {
>     print "Got fetch exception of...\n<pre>$@\n</pre>";
>     exit(0);
> }

Wouldn't you want to put that right after the eval() clause?

	-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
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>

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