[Biopython-dev] skipping a bad record read in SeqIO

[Iddo Friedberg]

hmm let me look into that... it it is a noted bug, I may wade into it if
nobody else had.

Thanks,

Iddo




On Sun, Jun 7, 2009 at 2:31 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On 6/7/09, Iddo Friedberg <idoerg at gmail.com> wrote:
> > Here is the stack dump, coming from the file:
> >
> > ftp://ftp.ncbi.nih.gov/genbank/gbcon11.seq.gz
> >
> > The offender:
> >
> > ACCESSION   CH991540 ABGB01000000
> >
> > Syntax error at or near `Tokens('close_paren')' token
> > Traceback (most recent call last):
> >   File "./filter_seqs.py", line 108, in <module>
> >     matching_seqs, non_matching_seqs = filter_sequences(open(inpath),
> > match_pairs, condition,seq_format)
> >    File "./filter_seqs.py", line 23, in filter_sequences
> >     for seq_record in SeqIO.parse(in_handle,format):
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/Scanner.py",
> > line 420, in parse_records
> >      record = self.parse(handle)
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/Scanner.py",
> > line 403, in parse
> >     if self.feed(handle, consumer) :
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/Scanner.py",
> > line 381, in feed
> >      self._feed_misc_lines(consumer, misc_lines)
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/Scanner.py",
> > line 1138, in _feed_misc_lines
> >     consumer.contig_location(contig_location)
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/__init__.py",
> > line 987, in contig_location
> >      self.location(content)
> >   File
> > "/home/idoerg/biopy_cvs/biopython/Bio/GenBank/__init__.py",
> > line 684, in location
> >     raise LocationParserError(location_line)
> > Bio.GenBank.LocationParserError:
> >
> join(complement(ABGB01000004.1:1..81568),gap(unk100),complement(ABGB01000012.1:1..1260),gap(unk100),ABGB01000013.1:1..1227,gap(unk100),ABGB01000011.1:1..1338,gap(unk100),complement(ABGB01000001.1:1..118303))
> >
>
> That look like Bug 2745 to me - does the patch on that bug work for
> you, and would you be happy storing the CONTIG line as string?
>
> Peter
>



-- 
Iddo Friedberg, Ph.D.
Atkinson Hall, mail code 0446
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0446, USA
T: +1 (858) 534-0570
http://iddo-friedberg.org