[Biopython-dev] [Bug 1763] Bio.Fasta.RecordParser chokes on empty records

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1763





------- Additional Comments From ybastide at irisa.fr  2005-03-25 03:21 -------
A simple testcase:

/tmp$ cat a.fasta 
>seq
/tmp$ python
Python 2.3.5 (#2, Feb  9 2005, 00:38:15) 
[GCC 3.3.5 (Debian 1:3.3.5-8)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import Fasta
>>> f_iterator = Fasta.Iterator(file("a.fasta"))
>>> f_iterator.next()
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.3/site-packages/Bio/Fasta/__init__.py", line 79, in next
    rec = parser.convert_lax(result)
  File "/usr/lib/python2.3/site-packages/Bio/Fasta/__init__.py", line 116, in
convert_lax
    rec.sequence = "".join(result['bioformat:sequence'])
KeyError: 'bioformat:sequence'
>>> 

yves



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