[Biopython-dev] [BioPython] Martel-based parsing of Unigene flat files

Chris Lasher chris.lasher at gmail.com
Wed Oct 25 02:22:06 UTC 2006

Hi Sean,

FWIW this should probably have been posted to BioPython-dev, but I
don't think that would improve your chances of getting a response. I
am cross-posting it there, anyways. Unfortunately for you, I do not
have an answer for you. :-(

I, myself, would be interested in a response to this question from the
Devs, as I would like to write a parser for PTT files. Last I saw
there was a lot of chatter about the Martel parsers being incredibly
slow compared to straightforward solutions. It seems that standard
format parsers would be one of the easiest ways for BioPython newbies
to contribute to developing the BioPython project, however, there
isn't very much in the way of documentation on the BioPython way to do
so, let alone developer documentation at all. I would like to know
what can be done to get some dev docs going on the wiki.


On 10/20/06, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> I am relatively new to python and biopython (coming from perl side of
> things).  I would like to make a parser for Unigene flat file format.
> However, after digging through the LocusLink parsing code (as probably
> the most similar format, etc.), I'm still at a loss for how Martel-based
> parsing works.  I understand the big picture (converting an re-based
> parsing of a file into events), but it is the detail that I am missing.
> I know about pydoc, but the pydoc for much of Martel is not very helpful
> to me, at least not in my current state of knowledge.  Any suggestions
> on how to get started?
> Thanks,
> Sean
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