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

[Anand C. Patel]

Turns out that using the default namespace bioperl doesn't change  
anything.

Common name -- still "genbank common name" in name_class in the  
taxon_name table for "house mouse", which I think the module is  
looking for as "common name".

It's not behaving differently despite reloading the sequences.

I've created a horrible munge that fixes it for cosmetic purposes:
my $species = $seq->species;
my $justspecies = $species->scientific_name();
my $binspecies = $species->binomial();

my $gbstring2 = $gbstring;

$gbstring2 =~ s/$binspecies/$justspecies/g;
$gbstring2 =~ s/$justspecies/$binspecies/g;

But this does not strike me as a long term solution.

Thanks,
Anand

On Aug 22, 2009, at 6:21 PM, Hilmar Lapp wrote:

>
> 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 :
> ===========================================================
>
>
>