biom.table.Table._extract_data_from_tsv¶
- static Table._extract_data_from_tsv(lines, delim='\t', dtype=<class '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
The expected 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).