[BioPython] NCBI: from protein to CDS

[Andrew Dalke]

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so you probably have an out-of-date copy of the Biopython code.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