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)
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tax:
¶
QIIME-style taxonomy identifiers, e.g. [‘k__Bacteria’, u’p__Firmicutes’, u’c__Bacilli’, …]
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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.
usage: phylotoast.otu_calc.load_core_file(core_fp)
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core_fp:
¶
A file containing core OTU data. Output text file from QIIME’s compute_core_microbiome.py script.
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return:
¶
Returns genus-species identifier based on identified taxonomical level.