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biom.table.Table._extract_data_from_tsv

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biom.table.Table._extract_data_from_tsv

static Table._extract_data_from_tsv(lines, delim='t', dtype=<type 'float'>, md_parse=None)

Parse a classic table into (sample_ids, obs_ids, data, metadata, name)

Parameters:

lines: list or file-like object

delimted data to parse

delim: string

delimeter in file lines

dtype: type

md_parse: function or None

funtion used to parse metdata

Returns:

list

sample_ids

list

observation_ids

array

data

list

metadata

string

column name if last column is non-numeric

Notes

This is intended to be close to how QIIME classic OTU tables are parsed with the exception of the additional md_name field

This function is ported from QIIME (http://www.qiime.org), previously named parse_classic_otu_table. QIIME is a GPL project, but we obtained permission from the authors of this function to port it to the BIOM Format project (and keep it under BIOM’s BSD license).

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