mazimi/HYPNO — pull request #3 by nemami (2012-03-27 10:18:19+00:00)
Title: RTFetch updates

Features:
* Updated to do chromosomal parsing
* Now using EMBOSS package (specifically, the needle executable) for DNA to Needle Aligned Translated Protein to Query Protein mapping --> Result: Mapped DNA sequence now the 10th/final index of returned RTFetch tuple, with spaces in gap regions.** I can show you how this works when we meet next.

NOTES:
** Reverse translation for gap regions still needs to be implemented --> we can figure this out soon

* mRNA exon parsing still needs to be implemented, this is the plan for tomorrow / some time this week

* Needs to be adapted to BPG Unix environment --> certain things are hindering this such as ability to freely install python modules that don't conflict with things that already exist on the server but do not seem to be readily utilizable (i.e. old version of ElementTree preventing me from doing adaptation --> I bet this is an easy fix).

* Not urgent, but it would be nice to suppress the EMBOSS output (see my BioStar posting:
http://biostar.stackexchange.com/questions/19199/emboss-python-suppress-printing-messages-to-standard-output )

* This is not an immediate concern at all, but at some point we might want to look into adaptive genetic code usage based on taxonomic identifiers