# 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)
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