parse_mothur_taxonomy

0th

Percentile

Parse mothur Classify.seqs *.taxonomy output

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)
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.;...

Value

taxmap

See Also

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

Aliases
  • parse_mothur_taxonomy
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

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