[BioPython] EMBL parsing in Biopython 1.43
Michiel de Hoon
mdehoon at c2b2.columbia.edu
Sun Apr 29 10:16:31 UTC 2007
Thanks Peter!
I tried this EMBL-formatted file (using the latest version of Biopython
in CVS):
ftp://ftp.pasteur.fr/pub/GenomeDB/SubtiList/FlatFiles/SLR16.1_embl.txt
but I got this error message:
>>> from Bio import SeqIO
>>> input = open("SLR16.1_embl.txt")
>>> records = SeqIO.parse(input, format="embl")
>>> records.next()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/GenBank/Scanner.py",
line 410, in parse_records
record = self.parse(handle)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/GenBank/Scanner.py",
line 393, in parse
if self.feed(handle, consumer) :
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/GenBank/Scanner.py",
line 360, in feed
self._feed_first_line(consumer, self.line)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/GenBank/Scanner.py",
line 540, in _feed_first_line
assert len(fields) == 7
AssertionError
>>>
Do you have an idea as to what may be going wrong here?
--Michiel.
Peter wrote:
> As part of the new SeqIO system introduced in Biopython 1.43, I added
> the ability to read in EMBL format sequences.
>
> http://biopython.org/wiki/SeqIO
>
> I would be interested to hear feedback (positive or negative) from
> anyone who has tried to use this.
>
> Peter
>
> _______________________________________________
> BioPython mailing list - BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
More information about the Biopython
mailing list