added SHOGUN functional profiling

[qiyunzhu]

@tanaes @mortonjt

[qiyunzhu]

Note that the oecophylla self test won't pass, because the minimal function db is not present yet. I need to talk with Gabe and Ben to figure that out.

[qiyunzhu]

Also please note that in the beginning of function.rule, I imported parser.py from the taxonomy directory. This may not be the most clean way. Plus, I further thought that maybe we don't need Python in combining tables, but some simple Bash commands will do:

echo $'#OTU ID\tA\tB' > combined.tsv
join -j1 -e'0' -a1 -a2 -o 0,1.2,2.2 <(tail -n+2 A.txt | sort) <(tail -n+2 B.txt | sort) -t$'\t' >> combined.tsv
biom convert --to-hdf5 -i combined.tsv -o combined.biom

@sjanssen2 what do you think?

[tanaes]

I'd much prefer the python, personally---easier to understand / maintain / unit test.

[wasade]

Agree

On Oct 9, 2017 2:37 PM, "Jon Sanders" notifications@github.com wrote:

I'd much prefer the python, personally---easier to understand / maintain / unit test.

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[qiyunzhu]

@tanaes and @wasade thanks for your comments!