refine.fasta: Clean Up FASTA Files to User Specification

In andrew-hipp/morton: Tools for manipulation of phylogenetic, genetic, and other biodiversity data

Clean Up FASTA Files to User Specification

Description

Reverse-complement or delete sequences in a multiple sequence alignment based on a csv file input.

Usage

refine.fasta(basedir = choose.dir())

Arguments

basedir

The address of the directory which contains the FASTA files to be refined and corresponding log files.

Details

make.fasta.files automates the export of FASTA and log files. A separate FASTA file and corresponding log file is exported for each locus included in the analysis.

Any log files used in this function must match the format of those exported by make.fasta.files. Log files must be in csv format, and have the following columns: - orgs - seqLabels - whatToDo - comments orgs is the taxon name of the specimen. seqLabels is the label of the sequence in the corresponding alignment. whatToDo has three possible states depending on what needs to be done to a sequence in the alignment. - RC = reverse complement - D = delete - blank = do nothing Log files start blank when exported. The user should manually edit log files to add these values before running refine.fasta.

Value

Returns the string 'done!' when fasta files have been imported and processed. Function invoked for side-effect.

Author(s)

Andrew Hipp and Kasey Pham

See Also

make.gene.matrix, parse.INSDSeq

andrew-hipp/morton documentation built on April 7, 2024, 12:15 p.m.