get_repseq_IDs_from_fasta: Get Representative Sequence Names

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description

This function retrieves a vector of the representative sequence machine names from a fasta file of representative sequences.

Usage

get_repseq_IDs_from_fasta(repseq_file = "all_seq_complete.clust_rep_seqs.fasta")

Arguments

repseq_file

The file name of the combined fasta file containing the representative sequences.

Details

The function reads the fasta file of representative sequences from disk.

Value

A vector of the machine names of the representative sequences.

Author(s)

John Quensen

References

The web-based tool for retrieving representative sequences is here: http://pyro.cme.msu.edu/

A command line version of the tool is included in RDPTools, available on GitHub: https://github.com/rdpstaff

Examples

repseq.file <- system.file("extdata", "all_seq_complete.clust_rep_seqs.fasta", package="RDPutils")
rep.seqs <- get_repseq_IDs_from_fasta(repseq_file = repseq.file)
rep.seqs

jfq3/RDPutils documentation built on Nov. 8, 2019, 1:05 p.m.