remove_model_seqs: Remove Model Sequences

Description Usage Arguments Details Value Author(s) Examples

View source: R/remove_model_seqs.R

Description

This function removes model sequences from a combined fasta file.

Usage

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remove_model_seqs(in_file, out_file = in_file)

Arguments

in_file

The name of a combined fasta file with model sequences.

out_file

The name of the corresponding fasta file written to disk without model sequences.

Details

This function operates on files. It is not normally assigned to a variable. By default, the input file is overwritten. If no model sequence is found in the input file, a message to that effect is returned.

RDP aligns 16S rRNA gene sequences using the Infernal aligner with model sequences for Bacteria or Archaea. A model sequence is introduced into each alignment. These model sequences are required by the cluster tool and the merge alignment tool. If a model sequence is present in the fasta file of representative sequences, it needs to be removed before the sequences can be treed with FastTree; this function provides the means to do so.

Value

The function returns a message that it has completed.

Author(s)

John Quensen

Examples

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in.file <- system.file("extdata", "all_seq_complete.clust_rep_seqs.fasta", package="RDPutils")
remove_model_seqs(in_file=in.file, out_file = file2tree.fasta)

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