Generate bash command to resume a single phyloscanner run

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.

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)
#> Error in phsc.cmd.phyloscanner.one.resume(prefix.infiles, pty.args): length(file.patient) == 1 is not TRUE
#	print bash script to screen
cat(cmd)
#> Error in cat(cmd): object 'cmd' not found
#   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)