Parse the `*.taxonomy` file that is returned by the `Classify.seqs` command in mothur. If confidence scores are present, they are included in the output.
parse_mothur_taxonomy(file = NULL, text = NULL)(character of length 1) The file path to the input file.
Either "file" or "text" must be used, but not both.
(character) An alternate input to "file". The contents of
the file as a character. Either "file" or "text" must be used, but not both.
The input file has a format like:
AY457915 Bacteria(100);Firmicutes(99);Clostridiales(99);Johnsone... AY457914 Bacteria(100);Firmicutes(100);Clostridiales(100);Johnso... AY457913 Bacteria(100);Firmicutes(100);Clostridiales(100);Johnso... AY457912 Bacteria(100);Firmicutes(99);Clostridiales(99);Johnsone... AY457911 Bacteria(100);Firmicutes(99);Clostridiales(98);Ruminoco...
or...
AY457915 Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J... AY457914 Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J... AY457913 Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J... AY457912 Bacteria;Firmicutes;Clostridiales;Johnsonella_et_rel.;J... AY457911 Bacteria;Firmicutes;Clostridiales;Ruminococcus_et_rel.;...
Other parsers: parse_dada2,
parse_edge_list,
parse_greengenes,
parse_mothur_tax_summary,
parse_newick, parse_phyloseq,
parse_phylo,
parse_qiime_biom, parse_rdp,
parse_silva_fasta,
parse_ubiome,
parse_unite_general