[Biopython-dev] GenBank parsing problem

[Chunlei Wu]

Hi, Brad,
    Thank you for your fix. But it seems I can not get
the latest version of genbank_format.py from CVS. The
current one is still the old one ver. 1.16. Maybe some
delay of the server?

Chunlei


--- Brad Chapman <chapmanb at arches.uga.edu> wrote:
> Hi Chunlei;
> Thanks for reporting the problem (and thanks to
> others who verified it).
> 
> > >>> from Bio import GenBank
> > >>> gi=GenBank.search_for("NM_007355")[0]
> > >>>
>
ncbi_dict=GenBank.NCBIDictionary(parser=GenBank.FeatureParser())
> > >>> record=ncbi_dict[gi]
> > Traceback (most recent call last):
> [...]
> > ParserPositionException: error parsing at or
> beyond character 55
> > >>> 
> > 
> > Did GenBank change the format?
> 
> Yup, it looks like they added a new "linear" word to
> the LOCUS line, to
> complement "circular" I guess:
> 
> LOCUS       AC091001              177066 bp    DNA  
>   linear   PRI 06-DEC-2001
> 
> Sorry, I'd tried to prepare for the new format
> changes, but hadn't
> realized this change was going to happen. The diff
> to
> Bio/GenBank/genbank_format.py is attached (fixes and
> tests for this case
> are also in CVS). I checked it out on a PRI download
> from NCBI, and it
> seems to be working for me.
> 
> Thanks again for the report! I hope this fixes your
> problem. Please let
> me know if you have any questions.
> Brad
> > Index: genbank_format.py
>
===================================================================
> RCS file:
>
/home/repository/biopython/biopython/Bio/GenBank/genbank_format.py,v
> retrieving revision 1.16
> retrieving revision 1.17
> diff -c -r1.16 -r1.17
> *** genbank_format.py	2002/01/05 22:09:58	1.16
> --- genbank_format.py	2002/01/30 13:54:05	1.17
> ***************
> *** 106,112 ****
>                              
> Martel.Opt(Martel.Alt(*residue_prefixes)) +
>                              
> Martel.Opt(Martel.Alt(*residue_types)) +
>                              
> Martel.Opt(Martel.Opt(blank_space) + 
> !                                       
> Martel.Str("circular")))
>   
>   date = Martel.Group("date",
>                       Martel.Re("[-\w]+"))
> --- 106,113 ----
>                              
> Martel.Opt(Martel.Alt(*residue_prefixes)) +
>                              
> Martel.Opt(Martel.Alt(*residue_types)) +
>                              
> Martel.Opt(Martel.Opt(blank_space) + 
> !                                       
> Martel.Alt(Martel.Str("circular"),
> !                                                  
> Martel.Str("linear"))))
>   
>   date = Martel.Group("date",
>                       Martel.Re("[-\w]+"))
> 


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