gmcvicker/genome — pull request #2 by funnell (2013-06-13 02:38:38+00:00)
Title: parse_ucsc_genes.py skip unknown chromosome

parse_ucsc_genes.py when encountering an unknown chromosome will skip that line, rather than raise an exception. A message is written to stderr so stdout can still be redirected to the output file.
There's a few minor PEP8 formatting changes in there as well.

I made this change because the chromInfo.txt file I'm using (from iGenomes) doesn't have all of the unlocalized contig names which I also don't care too much about. This change makes it a bit easier to process the gene table files that do include those contigs.

Let me know what you think.