sidier (version 4.1.1)

assign.whole.taxo: Get taxonomy described in sequence names

Description

Assign taxonomy to every line in a BLAST output using the information provided in the name of the subject sequences (stitle)

Usage

assign.whole.taxo(BLAST)

Value

a data.frame contining all the information provided in the input data.frame and seven additional columns containing the name of kingdom, phylum, class, order, family, genus, and species for this sequence

Arguments

BLAST

data.frame containing the output of a BLAST analysis. The first column must be the name of the sequences matching the queries and must contain information on the taxonomy of the subject sequences. See details.

Author

A. J. Muñoz-Pajares

Details

The expected input data.frame must contain information about taxonomy in the first column. Additional information is accepted if separated by "|", but taxonomy must be the last bit of information. Taxonomical information must be provided for kingdom, phylum, class, order, family, genus, and species, each separated by ";" and identified by a letter as follows:

optionalTEXT | optionalTEXT | k__kingdomName;p__phylumName;c__className; o__orderName;f__familyName;g__genusName;s__speciesName

This is the typical format of sequence names in several databases. Thus a BLAST output using any of these databases will automatically produce the desired format.

See Also

filter.whole.taxo, and get.majority.taxo

Examples

# data(ex_BLAST)
# TAXO <- assign.whole.taxo(ex_BLAST)