[BioPython] NCBI: from protein to CDS

[Iddo Friedberg]

Yup, that worked. CVS update, that is.

Cheers ./I

Andrew Dalke wrote:
> Iddo:
>  > What am I doing wrong? I am trying to efetch a sequence as gb, using 
> a gb ID. Works
>  > good for a FASTA fromat, but I think I am not persing it correctly 
> for GenBank.
> 
> Works for me.
> 
> I'm using latest CVS and Python 2.3a2+ from CVS as of two days ago.
> 
> Here's the output
> 
> % python iddo.py
>  >gi|12083602|ref|NM_022670.1| Rattus norvegicus Secretin (Sct), mRNA
> AAGGTGCAGCATTTATCACACCCAGAACCCGACCATGGAGCCTCTACTGCCCACGCCGCC
> GCTACTGCTGCTGCTGCTGCTGCTGCTCTCAAGTTCTTTCGTGCTTCCTGCACCTCCCAG
> GACCCCAAGACACTCGGACGGGACGTTCACCAGCGAGCTCAGCCGCTTGCAGGACAGTGC
> CAGGCTGCAGCGCCTGCTGCAGGGTCTGGTGGGGAAGCGCAGCGAGGAGGACACAGAAAA
> TATTCCAGAGAACAGCGTGGCCCGTCCCAAGCCATTAGAGGACCAACTCTGCTTGCTGTG
> GTCGAACACTCAGGCCCTACAGGATTGGCTTCTGCCCAGGCTGTCCCTGGATGGGTCCCT
> GTCTCTCTGGCTGCCTCCTGGACCAAGGCCTGCTGTCGACCATTCAGAGTGGACTGAAAC
> AACCAGGCAGCCCAGATGAGGGAGGAAGGGGAGTCTCCAGGAGCCTGACTGGAGTAGGGA
> TTGGTTGTCCTTGGCATCAATAAAGAAGGAATTTAGACCCTGGT
> <Bio.SeqRecord.SeqRecord instance at 0x9fb760>
> %
> 
>>   File "//usr/lib/python2.2/xml/sax/handler.py", line 38, in fatalError
>>     raise exception
>> Martel.Parser.ParserPositionException: error parsing at or beyond 
>> character 2424
>>
> 
> This is failing on
>                      /mol_type="mRNA"
> 
> which was added
> 1.25         (jchang   01-Jan-03):     "mol_type",       # In vivo 
> molecule type
> 
> so you probably have an out-of-date copy of the Biopython code.
> 
> 
>                     Andrew
> 
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> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://bioinformatics.ljcrf.edu/~iddo