Generate bash command for a single phyloscanner run

This function generates bash commands for a single phyloscanner run, that can be called via 'system' in R, or written to file to run on a UNIX system.

phsc.cmd.phyloscanner.one(pty.args, file.input, file.patient)

Arguments

pty.args	List of phyloscanner input variables. See examples.
file.input	File name of the file that contains the list of bam files, reference files, and potentially aliases
file.patient	File name of the file that contains the list of unique individuals/units to which the bam files correspond. Multiple bam files are allowed per individual/unit.

Value

Character string of phyloscanner commands.

Examples

#	setup input, output and working directories
pty.data.dir            <- '/Users/Oliver/duke/2016_PANGEAphylotypes/data'
work.dir                        <- getwd()
out.dir                         <- getwd()
#	link to phyloscanner.py
prog.pty                        <- '/work/or105/libs/phylotypes/phyloscanner.py'
#   input file with reference to bams and refs
file.bam            <- 'XXX'
file.ref            <- 'YYY'
#	define phyloscanner arguments
pty.args                        <- list(        prog.pty=prog.pty,
                                prog.mafft='mafft',
                                prog.raxml='"raxmlHPC-AVX -m GTRCAT"',
                                data.dir=pty.data.dir,
                                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,
                                min.ureads.individual=NA,
                                win=c(800,2400,250,250),
                                keep.overhangs=FALSE,
                                duplicated.raw.threshold=3,
                                duplicated.ratio.threshold=1/200,
                                select=NA)
#	generate bash script
cmd                 <- phsc.cmd.phyloscanner.one(file.bam, file.ref, pty.args)
#> Error in phsc.cmd.phyloscanner.one(file.bam, file.ref, pty.args): is.character(file.patient) 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)