[Biopython-dev] Notification: incoming/108

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Message summary for PR#108
	From: andreas.kuntzagk at mdc-berlin.de
	Subject: Bug in parsing GenBank-Files with Header
	Date: Tue, 10 Dec 2002 12:31:46 -0500
	0 replies 	0 followups

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>From andreas.kuntzagk at mdc-berlin.de Tue Dec 10 12:31:46 2002
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Date: Tue, 10 Dec 2002 12:31:46 -0500
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From: andreas.kuntzagk at mdc-berlin.de
To: biopython-bugs at bioperl.org
Subject: Bug in parsing GenBank-Files with Header
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Full_Name: Andreas Kuntzagk
Module: Bio.GenBank.Iterator
Version: 
OS: 
Submission from: (NULL) (141.80.80.40)


While parsing the recent GenBank-Release, I got followin error:


>>> from Bio import GenBank
>>> f=file("gbest1.seq")
>>> help(GenBank.Iterator)

>>> GenBank.Iterator(f,has_header=1)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 171, in
__init__
    self._reader = RecordReader.StartsWith(handle, "LOCUS")
  File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 133, in
__init__
    self.tagtable)
  File "/usr/lib/python2.2/site-packages/Martel/RecordReader.py", line 92, in
_find_begin_positions
    raise ReaderError("invalid format starting with %s" % repr(text[:50]))
Martel.RecordReader.ReaderError: invalid format starting with 'DEFINITION 
zd84h07.s1 Soares_fetal_heart_NbHH19W '

Problems seems, that in this file there is only one empty line after the
"...reported sequences" instead of the expected two lines.