otu_calc module

otu_name

Determine a simple Genus-species identifier for an OTU, if possible. If OTU is not identified to the species level, name it as Unclassified (familly/genus/etc…).

usage: phylotoast.otu_calc.otu_name(tax)

tax:

QIIME-style taxonomy identifiers, e.g. [‘k__Bacteria’, u’p__Firmicutes’, u’c__Bacilli’, …]

return:

Returns genus-species identifier based on identified taxonomical level.

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load_core_file

For core OTU data file, returns Genus-species identifier for each data entry.

usage: phylotoast.otu_calc.load_core_file(core_fp)

core_fp:

A file containing core OTU data. Output text file from QIIME’s compute_core_microbiome.py script.

return:

Returns genus-species identifier based on identified taxonomical level.

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assign_otu_membership

Determines the OTUIDs present in each sample.

usage: phylotoast.otu_calc.assign_otu_membership(biomfile)

biomfile:

BIOM table object from the biom-format library.

return:

Returns a dictionary keyed on Sample ID with sets containing the IDs of OTUIDs found in each sample.