read_taxonomy: Read in taxonomy files

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Read in taxonomy files

Description

Read a mothur-formatted taxonomy file into R as a data frame

Usage

read_taxonomy(file)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector) containing the sequence id and the taxonomy information for each sequence. Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded. Remote gz files can also be autom downloaded and decompressed.

Value

A data frame with two columns. The id column contains a name for each sequence and the taxonomy column, which contains the taxonomy for each sequence. The string in the taxonomy column is a series of taxonomic names separated by semi-colons. The string does not have a semi-colon at the end of the sequence

Note

There are no checks to insure that each sequence has a unique id value. It is also assumed that each sequence has the same number of taxonomic levels represented in the second column of the input file.

Examples

temp <- tempfile()
write("seqA\tA;B;C;", file = temp)
write("seqB\tA;B; C;", file = temp, append = TRUE)
write("seqC\tA; B;C;", file = temp, append = TRUE)
write("seqD\tA;B;C", file = temp, append = TRUE)
write("seqE\tA;B; C", file = temp, append = TRUE)
write("seqF\tA; B;C", file = temp, append = TRUE)
write("seq G\tA;B;C;", file = temp, append = TRUE)

read_taxonomy(temp)

phylotypr documentation built on April 3, 2025, 5:51 p.m.