[BioPython] EMBL parsing in Biopython 1.43

[Michiel de Hoon]

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
> 
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