rename_fasta: Rename Representative Sequences
In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description Usage Arguments Details Value Author(s) See Also Examples

This function renames representative sequences from their machine names to their OTU names.

1	rename_fasta(in_file = "names_trimmed.fasta", out_file = "renamed.fasta", rename_table)

`in_file`	The name of the fasta file containing representative sequences with their machine names.
`out_file`	The name of the fasta file containing representative sequences with their OTU names.
`rename_table`	A data frame associating the machine names of representative sequences with their corresponding OTU names.

The output of the function assoc_repseq_IDs_with_otus_by_fasta or assoc_repseq_IDs_with_otus_by_clstr can be used as the rename_table.

Before representative sequences can be renamed with this function, their IDs have to be shortened to include only their machine names with the function trim_fasta_names.

A fasta file with renamed representative sequences is written to disk. This function is not normally assigned to a variable. The function returns a message that it has completed.

John Quensen

assoc_repseq_IDs_with_otus_by_clstr

assoc_repseq_IDs_with_otus_by_fasta

trim_fasta_names

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in.file <- system.file("extdata", "names_trimmed.fasta", package="RDPutils")
data(assoc.table)
rename_fasta(in_file = in.file, out_file = "renamed.fasta", rename_table = assoc.table)