gb2qiime

[Steve Haddock]

Great about the script for Shannon.

Just browsing through. In line 212, what about using

r.get('phylum_reg','p__')

instead of

r['phylum_reg'] if r['phylum_reg'] else 'p__',

I can't tell if you need to script in the retrieval of the taxonomic hierarchy, but I have some scripts using the Entrez API which can do that. Let me know.

[Mike McCann]

Yes, that is much more pythonic!

I don't think Shannon needs the full taxonomy for what she is doing in Qiiime.

[Mike McCann]

I just tried that change and it doesn't work for these dictionaries as the keys exist with empty strings as the values. It seems that my Perlish idiom works for this situation!

[Mike McCann]

Closed the issue based on the last comment.