Parse the `*.tax.summary` file that is returned by the `Classify.seqs` command in mothur.
parse_mothur_tax_summary(file = NULL, text = NULL, table = NULL)taxmap
(character of length 1) The file path to the input file.
Either "file", "text", or "table" must be used, but only one.
(character) An alternate input to "file". The contents of
the file as a character. Either "file", "text", or "table" must be used,
but only one.
(character of length 1) An already parsed data.frame or
tibble. Either "file", "text", or "table" must be used, but only one.
The input file has a format like:
taxlevel rankID taxon daughterlevels total A B C
0 0 Root 2 242 84 84 74
1 0.1 Bacteria 50 242 84 84 74
2 0.1.2 Actinobacteria 38 13 0 13 0
3 0.1.2.3 Actinomycetaceae-Bifidobacteriaceae 10 13 0 13 0
4 0.1.2.3.7 Bifidobacteriaceae 6 13 0 13 0
5 0.1.2.3.7.2 Bifidobacterium_choerinum_et_rel. 8 13 0 13 0
6 0.1.2.3.7.2.1 Bifidobacterium_angulatum_et_rel. 1 11 0 11 0
7 0.1.2.3.7.2.1.1 unclassified 1 11 0 11 0
8 0.1.2.3.7.2.1.1.1 unclassified 1 11 0 11 0
9 0.1.2.3.7.2.1.1.1.1 unclassified 1 11 0 11 0
10 0.1.2.3.7.2.1.1.1.1.1 unclassified 1 11 0 11 0
11 0.1.2.3.7.2.1.1.1.1.1.1 unclassified 1 11 0 11 0
12 0.1.2.3.7.2.1.1.1.1.1.1.1 unclassified 1 11 0 11 0
6 0.1.2.3.7.2.5 Bifidobacterium_longum_et_rel. 1 2 0 2 0
7 0.1.2.3.7.2.5.1 unclassified 1 2 0 2 0
8 0.1.2.3.7.2.5.1.1 unclassified 1 2 0 2 0
9 0.1.2.3.7.2.5.1.1.1 unclassified 1 2 0 2 0
or
taxon total A B C
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";... 1 0 1 0
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";... 1 0 1 0
"k__Bacteria";"p__Actinobacteria";"c__Actinobacteria";... 1 0 1 0
Other parsers:
extract_tax_data(),
lookup_tax_data(),
parse_dada2(),
parse_edge_list(),
parse_greengenes(),
parse_mothur_taxonomy(),
parse_newick(),
parse_phylo(),
parse_phyloseq(),
parse_qiime_biom(),
parse_rdp(),
parse_silva_fasta(),
parse_tax_data(),
parse_ubiome(),
parse_unite_general()