[Biopython-dev] Bio.IntelliGenetics

[Peter]

>> Do you want to make these changes, or should I?
>
> Either way is fine with me. If you want to include this in Bio.SeqIO, go ahead.

OK.  I've added a simple parser to CVS as Bio/SeqIO/IgIO.py for
IntelliGenetics/MASE files using the format name "ig" to match EMBOSS.
 The existing three sample files are now being used in test_SeqIO.py
and one of them also in test_AlignIO.py as well.

If anyone wants to scan over the code, I'd be delighted to have feedback.

Adding support for writing these files should be easy.  Do you think
this is worth implementing?

Before we deprecate Bio.IntelliGenetics I suggest we ask on the
mailing list if anyone is using it.

> In the example files in test/IntelliGenetics, lines with a ';;' clearly have a different interpretation
> from the sequence-specific comments starting with ';'. I am fine with skipping the ';;' lines, but
> if we'd include them with the sequence-specific comments we'd be misrepresenting the file.

I am ignoring the ";;" lines at the start of the file.

Peter