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

Description Usage Arguments Details Value See Also

View source: R/parsers.R

Description

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

Usage

1

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:

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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

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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: parse_edge_list, parse_greengenes, parse_mothur_taxonomy, parse_newick, parse_phyloseq, parse_phylo, parse_qiime_biom, parse_rdp, parse_silva_fasta, parse_ubiome, parse_unite_general


grunwaldlab/metacoder documentation built on Nov. 30, 2018, 7:53 p.m.