[BioPython] problems parsing alignment files

[Brad Chapman]

Hi Ashleigh;

> Hello biopythoneers!  I've been having problems parsing alignments, but
> I can parse fasta files with no problem so I don't think I'm totally off
> base.  I can't get either the NBRF parser or the Clustalw parser to
> work.  I have updated biopython on February 27th and just updated Martel
> - both via the command "CVS update", but I guess it looks like a Martel
> problem.  I think the NBRF (.pir) files and .aln files I'm using are
> fine as they open with no problem directly in ClustalX.  
> 
> Here's the traceback for NBRF:
[...]
> And here's the one from Clustalw (I'm not sure if I've got the syntax
> right on this as it doesn't seem to have the same RecordParser as NBRF
> or Fasta):
[...]

Yes, it looks like you are doing everything right -- the tracebacks
are indicating that the underlying Martel parser is having trouble
dealing with the files you are providing, for some reason. If you
could send me the NBRF and ALN files (off-list), I can
have a look and see if I can figure where they are failing and try
to get everything fixed.

Also, that is a good point about the Clustalw parser not having the
same syntax as the other parsers. Thanks for bringing that up.

Please do send the files and thanks for the bug report.
Brad