Add biome fomat as input formats

CAMI-challenge / OPAL

OPAL: Open-community Profiling Assessment tooL

https://cami-challenge.github.io/OPAL/

Apache License 2.0

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Add biome fomat as input formats #18

Closed alicemchardy closed 6 years ago

alicemchardy commented 6 years ago

there are phython libraries for reading and writing biome format. hackathon

AlphaSquad commented 6 years ago

For CAMISIM I already used the biom python library and think it is quite well documented on the BIOM homepage (http://biom-format.org/)

sjanssen2 commented 6 years ago

yes, biom-format is the one we should use! It can handle tab-separated, json and hdf5 compressed formats (the later is usually called the "biom" format)

fernandomeyer commented 6 years ago

I added support to biom and tool tsv2biom.py to convert from the CAMI tsv format to biom. It's currently in branch feature-new-file-formats, to be merged after more testing.

fernandomeyer commented 6 years ago

Merged and extended readme.