phsc.cmd.phyloscanner.one.resume: Generate bash command to resume a single phyloscanner run

In olli0601/Phyloscanner.R.utilities:

Generate bash command to resume a single phyloscanner run

Description

This function generates bash commands to resume a single phyloscanner run, from the point where all read alignments and read phylogenies were created. The bash script can be called via 'system' in R, or written to file to run on a UNIX system.

Usage

phsc.cmd.phyloscanner.one.resume(prefix.infiles, pty.args)

Arguments

prefix.infiles	File name that points phyloscanner output.
pty.args	List of phyloscanner input variables. See examples.

Value

Character string of phyloscanner commands.

Examples

#	setup output and working directories
work.dir			<- getwd()
out.dir				<- getwd()
#	link to phyloscanner.py
prog.pty			<- '/work/or105/libs/phylotypes/phyloscanner.py'
#   prefix that identifies phyloscanner output
prefix.infiles      <- '/work/or105/phyloscanner/ptyr1_'
#	define phyloscanner arguments
pty.args			<- list(	prog.pty=prog.pty, 
								prog.mafft=NA, 
								prog.raxml=NA, 
								data.dir=NA, 
								work.dir=work.dir, 
								out.dir=out.dir, 
								alignments.file=system.file(package="phyloscan", "HIV1_compendium_AD_B_CPX_v2.fasta"),
								alignments.root='REF_CPX_AF460972', 
								alignments.pairwise.to='REF_B_K03455',
								window.automatic= '', 
								merge.threshold=0, 
								min.read.count=1, 
								quality.trim.ends=23, 
								min.internal.quality=23, 
								merge.paired.reads=TRUE, 
								no.trees=FALSE, 
								dont.check.duplicates=FALSE,
								num.bootstraps=1,
								all.bootstrap.trees=TRUE,
								strip.max.len=350, 
								min.ureads.individual=NA, 
								win=c(800,9400,25,250), 
								keep.overhangs=FALSE, 
								duplicated.raw.threshold=3,
								duplicated.ratio.threshold=1/200,				
								select=NA)
#	generate bash script
cmd                 <- phsc.cmd.phyloscanner.one.resume(prefix.infiles, pty.args)
#	print bash script to screen
cat(cmd)
#   this can be started eg through system on a UNIX machine, or written to file and then started manually (recommended)
#system(cmd)
#file.out <- 'ZZZ'
#cat(cmd, file=file.out)

olli0601/Phyloscanner.R.utilities documentation built on April 13, 2025, 7:44 p.m.