=============== 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...). .. code-block:: bash usage: phylotoast.otu_calc.otu_name(tax) .. cmdoption:: tax: QIIME-style taxonomy identifiers, e.g. ['k__Bacteria', u'p__Firmicutes', u'c__Bacilli', ...] .. cmdoption:: return: Returns genus-species identifier based on identified taxonomical level. ----------------------------- load_core_file -------------- For core OTU data file, returns Genus-species identifier for each data entry. .. code-block:: bash usage: phylotoast.otu_calc.load_core_file(core_fp) .. cmdoption:: core_fp: A file containing core OTU data. Output text file from QIIME's compute_core_microbiome.py script. .. cmdoption:: return: Returns genus-species identifier based on identified taxonomical level. ----------------------------- assign_otu_membership --------------------- Determines the OTUIDs present in each sample. .. code-block:: bash usage: phylotoast.otu_calc.assign_otu_membership(biomfile) .. cmdoption:: biomfile: BIOM table object from the biom-format library. .. cmdoption:: return: Returns a dictionary keyed on Sample ID with sets containing the IDs of OTUIDs found in each sample.