parse_mothur_taxonomy {metacoder} | R Documentation |
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)
Arguments
file |
( |
text |
( |
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
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()
[Package metacoder version 0.3.7 Index]