[Rcolony-commits] r75 - pkg/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 16 12:18:42 CET 2012
Author: jonesor
Date: 2012-11-16 12:18:41 +0100 (Fri, 16 Nov 2012)
New Revision: 75
Modified:
pkg/R/build.colony.input.R
Log:
Changed build.colony.input so that you can specify what the delimiter is. Default is whitespace.
Modified: pkg/R/build.colony.input.R
===================================================================
--- pkg/R/build.colony.input.R 2012-11-16 10:55:57 UTC (rev 74)
+++ pkg/R/build.colony.input.R 2012-11-16 11:18:41 UTC (rev 75)
@@ -1,4 +1,4 @@
-build.colony.input<-function(wd=getwd(),name="Colony2.DAT"){
+build.colony.input<-function(wd=getwd(),name="Colony2.DAT",delim=""){
# wd = getwd()
# name = "Colony2.DAT"
@@ -159,8 +159,8 @@
Sys.sleep(.2)
flush.console()
colonyfile$AlleleFreqPATH<-file.choose()
- colonyfile$delim.for.allele.freq<-""
- colonyfile$allele.frequency<-read.table(colonyfile$AlleleFreqPATH,header=FALSE,colClasses=c("character"),sep=colonyfile$delim.for.allele.freq,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$AlleleFreqPATH)))
+
+ colonyfile$allele.frequency<-read.table(colonyfile$AlleleFreqPATH,header=FALSE,colClasses=c("character"),sep=delim,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$AlleleFreqPATH)))
flush.console()
}
@@ -261,9 +261,8 @@
flush.console()
colonyfile$MarkerPATH<-file.choose()
- colonyfile$delim.for.markers<-""
- colonyfile$Markers<-read.table(colonyfile$MarkerPATH,header=FALSE,colClasses=c("character"),sep=colonyfile$delim.for.markers)
+ colonyfile$Markers<-read.table(colonyfile$MarkerPATH,header=FALSE,colClasses=c("character"),sep=delim)
flush.console()
@@ -290,11 +289,8 @@
while(length(colonyfile$OSGenotypePATH)==0){
colonyfile$OSGenotypePATH<-file.choose()
-
- colonyfile$delim.for.OSGenotype<-""
-
-
- colonyfile$Offspring<-read.table(colonyfile$OSGenotypePATH,header=FALSE,colClasses=c("character"),sep=colonyfile$delim.for.OSGenotype)
+
+ colonyfile$Offspring<-read.table(colonyfile$OSGenotypePATH,header=FALSE,colClasses=c("character"),sep=delim)
if(colonyfile$n.offspring!=dim(colonyfile$Offspring)[1]){
colonyfile<-colonyfile[which(names(colonyfile)!="OSGenotypePATH")];
flush.console();
@@ -357,9 +353,8 @@
flush.console()
colonyfile$fathersPATH<-file.choose()
- colonyfile$delim.for.fathers<-""
- colonyfile$fathers<-read.table(colonyfile$fathersPATH,header=FALSE,sep=colonyfile$delim.for.fathers,colClasses=c("character"))
+ colonyfile$fathers<-read.table(colonyfile$fathersPATH,header=FALSE,sep=delim,colClasses=c("character"))
if(colonyfile$n.father!=dim(colonyfile$fathers)[1]){
colonyfile<-colonyfile[which(names(colonyfile)!="fathersPATH")];
flush.console();
@@ -367,7 +362,6 @@
}
}else{
colonyfile$fathersPATH<-NA
- colonyfile$delim.for.fathers<-""
colonyfile$fathers<-matrix(nrow=1,ncol=1)
}
@@ -409,16 +403,14 @@
colonyfile$mothersPATH<-file.choose()
flush.console()
- colonyfile$delim.for.mothers<-""
- colonyfile$mothers<-read.table(colonyfile$mothersPATH,header=FALSE,sep=colonyfile$delim.for.mothers,colClasses=c("character"))
+ colonyfile$mothers<-read.table(colonyfile$mothersPATH,header=FALSE,sep=delim,colClasses=c("character"))
if(colonyfile$n.mother!=dim(colonyfile$mothers)[1]){colonyfile<-colonyfile[which(names(colonyfile)!="mothersPATH")];
flush.console();
warning(paste("The number of defined MOTHERS ","(", colonyfile$n.mother,") does not equal the number of MOTHERS provided in the file selected (", dim(colonyfile$mothers)[1],").\n\n",sep=""),immediate.=TRUE)}
}
}else{
colonyfile$mothersPATH<-NA
- colonyfile$delim.for.mothers<-""
colonyfile$mothers<-matrix(nrow=1,ncol=1)
}
@@ -466,11 +458,9 @@
flush.console()
colonyfile$paternities.and.sibships.PATH<-file.choose()
- colonyfile$delim.for.paternities.and.sibships.PATH<-""
+ #Read in the data...
+ colonyfile$paternities.and.sibships<-read.table(colonyfile$paternities.and.sibships.PATH,header=FALSE,colClasses=c("character"),sep=delim,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$paternities.and.sibships.PATH)))
- #Read in the data...
- colonyfile$paternities.and.sibships<-read.table(colonyfile$paternities.and.sibships.PATH,header=FALSE,colClasses=c("character"),sep=colonyfile$delim.for.paternities.and.sibships.PATH,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$paternities.and.sibships.PATH)))
-
flush.console()
#split the file up
@@ -556,10 +546,10 @@
flush.console()
colonyfile$maternities.and.sibships.PATH<-file.choose()
- colonyfile$delim.for.maternities.and.sibships.PATH<-""
#Read in the data...
- colonyfile$maternities.and.sibships<-read.table(colonyfile$maternities.and.sibships.PATH,header=FALSE,colClasses=c("character"),sep=colonyfile$delim.for.maternities.and.sibships.PATH,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$maternities.and.sibships.PATH)))
+ colonyfile$maternities.and.sibships<-read.table(colonyfile$maternities.and.sibships.PATH,header=FALSE,colClasses=c("character"),
+ sep=delim,fill=TRUE,flush=TRUE,na.string="",col.names=1:max(count.fields(colonyfile$maternities.and.sibships.PATH)))
flush.console()
@@ -684,10 +674,10 @@
flush.console()
colonyfile$excluded.paternities.PATH<-file.choose()
- colonyfile$delim.for.excluded.paternities.PATH<-""
#Read in the data...
- colonyfile$excluded.paternities<-read.table(colonyfile$excluded.paternities.PATH,header=FALSE,sep=colonyfile$delim.for.excluded.paternities.PATH,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
+ colonyfile$excluded.paternities<-read.table(colonyfile$excluded.paternities.PATH,header=FALSE,
+ sep=delim,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
if(colonyfile$n.excluded.paternities>0){#Write ExcludedPaternity.txt file
@@ -767,11 +757,10 @@
cat("Provide the path to the excluded MATERNITY file.\n\n\n")
flush.console()
colonyfile$excluded.maternities.PATH<-file.choose()
-
- colonyfile$delim.for.excluded.maternities.PATH<-""
-
+
#Read in the data...
- colonyfile$excluded.maternities<-read.table(colonyfile$excluded.maternities.PATH,header=FALSE,sep=colonyfile$delim.for.excluded.maternities.PATH,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
+ colonyfile$excluded.maternities<-read.table(colonyfile$excluded.maternities.PATH,header=FALSE,
+ sep=delim,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
#Check the data
if(colonyfile$n.excluded.maternities!=dim(colonyfile$excluded.maternities)[1]){
@@ -849,11 +838,10 @@
cat("Provide the path to the excluded PATERNAL sibships file.\n\n\n")
flush.console()
colonyfile$excluded.paternal.sibships.PATH<-file.choose()
-
- colonyfile$delim.for.excluded.paternal.sibships.PATH<-""
-
+
#Read in the data...
- colonyfile$excluded.paternal.sibships<-read.table(colonyfile$excluded.paternal.sibships.PATH,header=FALSE,sep=colonyfile$delim.for.excluded.paternal.sibships.PATH,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
+ colonyfile$excluded.paternal.sibships<-read.table(colonyfile$excluded.paternal.sibships.PATH,header=FALSE,
+ sep=delim,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
#Check the data
if(colonyfile$n.excluded.paternal.sibships!=dim(colonyfile$excluded.paternal.sibships)[1]){
@@ -915,11 +903,10 @@
cat("Provide the path to the excluded MATERNAL sibships file.\n\n\n")
flush.console()
colonyfile$excluded.maternal.sibships.PATH<-file.choose()
-
- colonyfile$delim.for.excluded.maternal.sibships.PATH<-""
-
+
#Read in the data...
- colonyfile$excluded.maternal.sibships<-read.table(colonyfile$excluded.maternal.sibships.PATH,header=FALSE,sep=colonyfile$delim.for.excluded.maternal.sibships.PATH,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
+ colonyfile$excluded.maternal.sibships<-read.table(colonyfile$excluded.maternal.sibships.PATH,header=FALSE,
+ sep=delim,colClasses=c("character"),fill=TRUE,flush=TRUE,na.strings="")
#Check the data
if(colonyfile$n.excluded.maternal.sibships!=dim(colonyfile$excluded.maternal.sibships)[1]){
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