[Biopython-dev] [Bug 2968] Modifications to Emboss eprimer3 parser and associated files

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http://bugzilla.open-bio.org/show_bug.cgi?id=2968





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2010-03-03 10:06 EST -------
(In reply to comment #0)
> The existing Emboss primer3/eprimer3 code has a couple of issues, and some
> scope for improvement:
> 
> - The existing Primer3.py parser code can only parse output when eprimer3 is
> applied to a single sequence.  When eprimer3 is applied to multiple sequence
> input, it groups all primers for all sequences into a single record, which may
> incorrectly associate primers with the wrong sequences in downstream analysis.
> - The current parser lacks an iterator for iterating over multiple sequence
> output

I've made changes on github to support multiple targets (with a read and
a parse function) this based on Leighton's code which addresses the above
issues.

> - The current parser creates 'ghost' primers for all primer pairs, with length
> zero and sequence as an empty string; it does not do this for internal oligos. 
> A more intuitive solution might be to return None for absent primers/oligos
> - The current data model stores all primer data as individual attributes.  It
> might be more useful to group the attributes of individual primers into their
> natural associations

Regarding the object changes, I'll be doing some work with eprimer3 this month,
so will feel I can make a more informed choice later.

See also:
http://lists.open-bio.org/pipermail/biopython-dev/2010-January/007255.html
http://lists.open-bio.org/pipermail/biopython-dev/2010-March/007398.html


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