trim_fasta_names: Trim Representative Sequence Names
In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description Usage Arguments Details Value Author(s) Examples

This function trims the fasta IDs of the representative sequences to include only the machine name.

1	trim_fasta_names(repseq_file, trimmed_names, strip = FALSE)

`repseq_file`	The name of the combined fasta file of representative sequences.
`trimmed_names`	The name of the modified fasta file written to disk.
`strip`	A logical. If TRUE, then the output fasta file is unaligned and any model sequences are removed. The default is FALSE.

This function is a necessary prerequisite to renaming representative sequences with their corresponding OTU names.

Unaligning the sequences results in a smaller file size and is acceptable if the sequences are to be classified only. It may be desirable if using the web-based classifier because the smaller file size makes for shorter upload time. Unaligning must not be done if the sequences are to be treed.

This function operates on files. It returns a message that it has completed. It is not normally assigned to a variable; if so, the variable contains only the message.

John Quensen

1 2	repseq.file <- system.file("extdata", "all_seq_complete.clust_rep_seqs.fasta", package="RDPutils") trim_fasta_names(repseq_file = repseq.file, trimmed_names = "names_trimmed.fasta", strip = FALSE)