metacoder (version 0.3.7)

parse_mothur_taxonomy: Parse mothur Classify.seqs *.taxonomy output

Description

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.

Usage

parse_mothur_taxonomy(file = NULL, text = NULL)

Value

taxmap

Arguments

file

(character of length 1) The file path to the input file. Either "file" or "text" must be used, but not both.

text

(character) An alternate input to "file". The contents of the file as a character. Either "file" or "text" must be used, but not both.

Details

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.;...

See Also

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