Read a mothur-formatted taxonomy file into R as a data frame
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://, orftps://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)
#> id taxonomy
#> 1 seqA A;B;C
#> 2 seqB A;B;C
#> 3 seqC A;B;C
#> 4 seqD A;B;C
#> 5 seqE A;B;C
#> 6 seqF A;B;C
#> 7 seq G A;B;C