mazimi/HYPNO — pull request #4 by nemami (2012-03-30 10:29:19+00:00)
Title: Fixed a couple of bugs in RTFetch.py

1) For genetic code translation table determination, commented out pretty much everything except for the Bacteria/Archaea case. These cases were breaking certain tests because they really only pertain to mitochondrial sequences, which are not readily identifiable in the UniProt lineage (for example, if you have something that's "Vertebrata," like bos taurus, you don't want to necessarily be using the mitochondrial genetic code for that).

2) Fixed a bug in DNA mapping which was messing up gappy sequences. This bug was apparent when you ran the previous version on an ID such as D3ZA56. Previously, the gappy-region-codons did not correspond directly to the gappy-region-amino-acids because of indexing errors. These are now fixed.