parse_mothur_tax_summary: Parse mothur *.tax.summary Classify.seqs output

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Parse mothur *.tax.summary Classify.seqs output

Description

Parse the '*.tax.summary' file that is returned by the 'Classify.seqs' command in mothur.

Usage

parse_mothur_tax_summary(file = NULL, text = NULL, table = NULL)

Arguments

file	(character of length 1) The file path to the input file. Either "file", "text", or "table" must be used, but only one.
text	(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.
table	(character of length 1) An already parsed data.frame or tibble. Either "file", "text", or "table" must be used, but only one.

Details

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

Value

taxmap

See Also

Other parsers: extract_tax_data(), lookup_tax_data(), parse_dada2(), parse_edge_list(), parse_greengenes(), parse_mothur_taxonomy(), parse_newick(), parse_phyloseq(), parse_phylo(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome(), parse_unite_general()

metacoder documentation built on April 4, 2023, 9:08 a.m.