select_seqs: Select Fasta Sequences
In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description Usage Arguments Details Value Author(s) Examples

This function subsets a combined fasta file.

1	select_seqs(in_file, select_list, out_file)

`in_file`	The name of a combined fasta file to be read from disk.
`select_list`	A vector of the names of the individual fasta files to be kept.
`out_file`	The name of the modified combined fasta file to be written to disk.

This function can be used to select a subset of the renamed representative sequences corresponding to OTUs containing at least n sequences. See the example section below.

Reducing the number of representative sequences in this manner makes several subsequent steps go faster: classifying the representative sequences, making a phyloseq tax_table, and treeing the representative sequences.

This function operates on disk files. It is not normally assigned to a variable. It returns a message that it has completed.

John Quensen

renamed.fasta <- system.file("extdata", "renamed.fasta", package="RDPutils")
data(otu)
otu <- otu[ , colSums(otu)>=5]
select.list <- colnames(otu)
select_seqs(in_file=renamed.fasta, select_list=select.list, out_file="subset.renamed.repseqs.fasta")