[Biopython-dev] GenBank parser problem

kawagash at affrc.go.jp kawagash at affrc.go.jp
Tue May 7 21:58:18 EDT 2002

Dear Sir,

I am using Biopython module 1.00a4. But there is a GenBank parser
problem. It might be the change of GenBank file header.

in Tests/GanBank/arab1.gb:

LOCUS       AC007323    86436 bp    DNA             PLN       19-JAN-2000
DEFINITION  Genomic sequence for Arabidopsis thaliana BAC T25K16 from
            chromosome I, complete sequence.
VERSION     AC007323.5  GI:6587720

But the latest GenBank file AP003349:

LOCUS       AP003349              147334 bp    DNA     linear   HTG 21-MAR-2002
DEFINITION  Oryza sativa (japonica cultivar-group) chromosome 1 clone P0674H09,
            *** SEQUENCING IN PROGRESS ***, in ordered pieces.
VERSION     AP003349.2  GI:17132539

So I replace genbank_format.py to rev. 1.19 and add new files as 
Std.py 1.6 and StdHandler.py 1.6.
But I got another warning message.

Traceback (most recent call last):
  File "./parse_genbank.py", line 8, in ?
    from Bio import GenBank
  File "/usr/local/lib/python2.1/site-packages/Bio/GenBank/__init__.py", line 68
, in ?
    import genbank_format
  File "/usr/local/lib/python2.1/site-packages/Bio/GenBank/genbank_format.py", l
ine 144, in ?
  File "/usr/local/lib/python2.1/site-packages/Bio/GenBank/genbank_format.py", l
ine 78, in define_block
    Martel.Str(identifier + " " * diff) +
AttributeError: 'Martel' module has no attribute 'UntilEol'

I am using Martel 0.5. What can I do next? Could you help me?
Thank you,

Nobuyuki Kawagashira

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