[BioPython] NCBI: from protein to CDS
Andrew Dalke
dalke at dalkescientific.com
Fri Apr 11 19:25:45 EDT 2003
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so you probably have an out-of-date copy of the Biopython code.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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