set.alignment.file: Defines alignment file but does not read it, then call...

Description Usage Arguments Value

View source: R/set.alignment.file.R

Description

Reading the alignment file is done by prep.aln for control of excise.refseq status.

Usage

1
set.alignment.file(S, f, pngs2o = NULL, alignment_format = "fasta")

Arguments

S

swarmtools object

f

alignment file

pngs2o

option to indicate whether or not to mark PNG Ns as O.

alignment_format

Format of alignment file/s; must be one of these: "fasta", "clustal", "phylip", "msf", or "mase".

Value

swarmtools object with defined aas_aln, refseq_lut, and tf_loss if possible


phraber/lassie documentation built on Jan. 15, 2018, 3:59 a.m.