cmd.SeqGen.createInputFiles: Command line generator for...
In olli0601/PANGEA.HIV.sim: PANGEA.HIV.sim

Description Usage Value Examples

The prog.PANGEA.SeqGen.createInputFile reads files from the virus tree simulator in directory indir.vts and writes input files for SeqGen to directory outdir. The program reads simulated transmission chain phylogenies with branches in units of calendar time for sampled and unsampled individuals in a transmission chain. Within host evolutionary rates are drawn from a distribution, and within host branch lengths are converted into the expected number of substitutions along the branch. Transmission branches are multiplied with a multiplier to allow for slower evolution between hosts. The multiplier is drawn from a distribution. Starting sequences are drawn from a pool of precomputed sequences. GTR parameters are drawn from a distribution. This is all that s needed to specify the SeqGen input files for each transmission chain.

1 2	cmd.SeqGen.createInputFiles(indir.epi, infile.epi, indir.vts, infile.vts, infile.args, outdir, prog = PR.SEQGEN.FILECREATOR)

command line string

##--------------------------------------------------------------------------------------------------------
##	1)
##	simulate sequence sampling for epi simulation
##	sequences are sampled assuming an exponentially growing sequence sampling rate so that
##	1% is sampled in 1980
##	25% is sampled in 2020
##	In addition, 10% of transmissions are broken and treated as imported from outside the simulated population.
##	The infected of a broken transmission chain is considered a new index case of a transmission chain within the 
##	simulated population
##	2)
##	Call virus tree simulator with input args as below
##	3)
##	Call SeqGen input file creator
##--------------------------------------------------------------------------------------------------------
## Not run: 
indir			<- system.file(package="PANGEA.HIV.sim", "misc")
indir			<- ifelse(indir=='','/Users/Oliver/git/HPTN071sim/raw_trchain',indir)
#	re-name the following:
tmpdir			<- '/Users/Oliver/git/HPTN071sim/tmp140910'
dir.create(tmpdir, showWarnings=FALSE)
tmpdir.HPTN071	<- paste(tmpdir,'/HPTN071parser',sep='')
dir.create(tmpdir.HPTN071, showWarnings=FALSE)
#	simulation input files from the epi-simulator
infile.ind		<- '140716_RUN001_IND.csv'
infile.trm		<- '140716_RUN001_TRM.csv'
#	input arguments for the pipeline
pipeline.args	<- sim.regional.args()
infile.args		<- paste(tmpdir,'/',substr(infile.ind, 1, nchar(infile.ind)-7), 'PipeArgs.R',sep='')
save(pipeline.args, file=infile.args)
#	get input into 'argv'. this is needed because the input parser is usually called from the command line, and 'argv' mimics the way input is provided when the parser is called from the command line
cmd				<- cmd.HPTN071.input.parser.v2(indir, infile.trm, infile.ind, infile.args, tmpdir.HPTN071,  infile.trm, infile.ind)				 
argv			<<- unlist(strsplit(cmd,' '))
#
#	step: sequence sampler
#
prog.HPTN071.input.parser.v2()
#	
#	step: virus tree sampler
#
tmpdir.VTS		<- paste(tmpdir,'/VirusTreeSimulator',sep='')
dir.create(tmpdir.VTS, showWarnings=FALSE)
#	output file prefix for virus tree sampler
outfile			<- substr(infile.ind, 1, nchar(infile.ind)-7)
#	logistic growth within host coalescent model
prog.args		<- paste('-demoModel Logistic -N0 ',pipeline.args['v.N0tau',][,v] ,' -growthRate ', pipeline.args['v.r',][,v],' -t50 ',pipeline.args['v.T50',][,v], sep='')
cmd				<- cmd.VirusTreeSimulator(tmpdir.HPTN071, infile.trm, infile.ind, tmpdir.VTS, outfile, prog.args=prog.args)	
#	TODO run this command
cat(cmd)
#	
#	step: Seq-Gen input file creator
#
tmpdir.SG		<- paste(tmpdir,'/SeqGen',sep='')
dir.create(tmpdir.SG, showWarnings=FALSE)
infile.epi		<- paste( substr(infile.ind, 1, nchar(infile.ind)-7),'SAVE.R', sep='' )
infile.vts		<- substr(infile.ind, 1, nchar(infile.ind)-7)
cmd				<- cmd.SeqGen.createInputFiles(tmpdir.HPTN071, infile.epi, tmpdir.VTS, infile.vts, infile.args, tmpdir.SG)
argv			<<- unlist(strsplit(cmd,' '))
prog.PANGEA.SeqGen.createInputFile()

## End(Not run)