Mercurial > repos > mnhn65mo > regionalgam
diff flight_curve.R @ 0:5b126f770671 draft
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author | mnhn65mo |
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date | Fri, 03 Aug 2018 08:28:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flight_curve.R Fri Aug 03 08:28:22 2018 -0400 @@ -0,0 +1,12 @@ +#!/usr/bin/env Rscript +#library('getopt') +#library(devtools) + +args = commandArgs(trailingOnly=TRUE) +source(args[1]) #TODO replace by library(regionalGAM) if available as official package from bioconda + +tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) +dataset1 <- input[,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")] +pheno <- flight_curve(dataset1) + +write.table(pheno, file="pheno", row.names=FALSE, sep=" ")