Support for mOTUs2

[AlessioMilanese]

Hi @fbreitwieser,

I got a request from one of your users to use Pavian with profiles from mOTUs2. See mOTUs_issue_27.

Pavian seems a great tool and I would also like to visualize mOTUs2 profiles on it. Moreover, it would be easy to adapt it from the MetaPhlAn input parser.

When running mOTUs with -A, you will get as result:

#mOTUs2_clade	test1
k__Bacteria	1.0000000000
k__Bacteria|p__Proteobacteria	0.0732714431
k__Bacteria|p__Firmicutes	0.6479060231
k__Bacteria|p__Thermodesulfobacteria	0.0055578606
k__Bacteria|p__Actinobacteria	0.2200557062
k__Bacteria|p__Chlamydiae	0.0532089670
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	0.0557659685
k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria	0.0175054746
k__Bacteria|p__Firmicutes|c__Erysipelotrichia	0.0688211617
k__Bacteria|p__Firmicutes|c__Negativicutes	0.0234955832
k__Bacteria|p__Firmicutes|c__Bacilli	0.4538976397
k__Bacteria|p__Firmicutes|c__unknown Firmicutes	0.1016916385
...
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium sp. GD7 [ref_mOTU_v2_2683]	0.0390911725
k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Vibrionales|f__Vibrionaceae|g__Vibrio|s__Vibrio tubiashii [ref_mOTU_v2_3913]	0.0044390411
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Streptomycetales|f__Streptomycetaceae|g__Streptomyces|s__Streptomyces durhamensis [ref_mOTU_v2_4783]	0.0725347907

The only differences with MetaPhlAn2 are:

1. the header, your parser requires #SampleID\tMetaphlan2_Analysis. mOTUs profiles have a header like #mOTUs2_clade\tsample_name where sample_name change every time;
2. MetaPhlAn abundances sum up to 100, while mOTUs abundances sum up to 1.

Cheers, alessio