[Patchwork-commits] r40 - in pkg/patchwork: R inst/python

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2011-12-07 11:49:08 +0100 (Wed, 07 Dec 2011)
New Revision: 40

Added:
   pkg/patchwork/inst/python/Check.py
Modified:
   pkg/patchwork/R/patchwork.CNA.r
   pkg/patchwork/R/patchwork.alleledata.r
   pkg/patchwork/R/patchwork.readChroms.r
   pkg/patchwork/inst/python/Pysamloader.py
Log:
Fixed installation of pysam to users system if needed. Also added a check for .python folder to be deleted if it already existed. Also changed data file handling in readChroms

Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r	2011-12-06 14:37:39 UTC (rev 39)
+++ pkg/patchwork/R/patchwork.CNA.r	2011-12-07 10:49:08 UTC (rev 40)
@@ -1,6 +1,7 @@
 patchwork.CNA <- function(BamFile,Pileup,reference,Alpha=0.0001,SD=1)
 	{
-	
+	#library(patchwork)
+	#patchwork.CNA("cancer.bam","pile.up",reference="illumina")
 	#Load DNAcopy
 	#library(DNAcopy)
 	#Load data included in package
@@ -16,7 +17,7 @@
 	#If it wasnt created, create it using the perl script pile2alleles.pl
 	#which is included in the package. Creates pile.alleles in whichever folder
 	#you are running R from. (getwd())
-	if(length(alf) == 1)
+	if(length(alf) == 0)
 		{
 		cat("Initiating Allele Data Generation \n")
 		alf = patchwork.alleledata(Pileup)

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2011-12-06 14:37:39 UTC (rev 39)
+++ pkg/patchwork/R/patchwork.alleledata.r	2011-12-07 10:49:08 UTC (rev 40)
@@ -6,8 +6,17 @@
 	#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
 	
 	data(commonSnps132,package="patchworkData")
-	#load(paste(packagepath,"/data/ideogram.RData",sep=""))
-	#load(paste(packagepath,"/data/normaldata.RData",sep=""))
+
+	#if .perl folder exists, delete it.
+	#test = getwd()
+	#try( setwd(".perl"),silent=TRUE)
+	#if(getwd() == paste(test,"/.perl",sep=""))
+	#	{
+	#	setwd("..")
+	#	system("rm -r .perl")
+	#	}
+	
+	
 	system(paste("cp -r ",packagepath,"/perl .perl",sep=""))
 	system(paste("cat ",Pileup," | perl .perl/pile2alleles.pl > ",getwd(),"/pile.alleles",sep=""))
 	system("rm -r .perl")

Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r	2011-12-06 14:37:39 UTC (rev 39)
+++ pkg/patchwork/R/patchwork.readChroms.r	2011-12-07 10:49:08 UTC (rev 40)
@@ -3,13 +3,42 @@
 	## Read chromosomes:
 	# Ideogram data downloaded from UCSC table browser.
 	
+	#library(patchwork)
+	#patchwork.CNA("cancer.bam","pile.up",reference="illumina")
+	
 	#Load data included in package
 	packagepath = system.file(package="patchwork")
-	#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
-	#load(paste(packagepath,"/data/ideogram.RData",sep=""))
-	#load(paste(packagepath,"/data/normaldata.RData",sep=""))
+	datapath = system.file(package="patchworkData")
+	
+	
+	
+	#if .python folder exists, delete it.
+	test = getwd()
+	try( setwd(".python"),silent=TRUE)
+	if(getwd() == paste(test,"/.python",sep=""))
+		{
+		setwd("..")
+		system("rm -r .python")
+		}
+	
+	
+	#copy python folder
 	system(paste("cp -r ",packagepath,"/python .python",sep=""))
+	
+	#if .python folder exists, delete it.
+	
+	#If import pysam doesnt work, ie pysam isnt installed yet, we install pysam.
+	if (system(paste("python ",getwd(),"/.python/Check.py",sep=""),intern=T) == "Pysam Not Available")
+			{
+			setwd(".python")
+			# build pysam
+			system("python setup.py build",invisible=F)
+			# install pysam to site.USER_BASE
+			system("python setup.py install --user",invisible=F)
+			setwd("..")
+			}
 
+
 	readlength=80 # this is currently hard coded and may be adjusted.
 	seglength=200 # (do not change)
 	data=NULL
@@ -24,8 +53,7 @@
 		# Load the newly created position file
 		unix = read.csv(".Tmp_chr_pos",sep='',header=F)$V1 + readlength/2
 		tmp = paste(c,".mark",sep="")
-		data(tmp,package="patchworkData")
-		#load(paste(packagepath,"/data/",c,'.mark.RData',sep=''))
+		load(paste(datapath,"/data/",c,".mark.RData",sep=""))
 		xpos=gc[,1]
 		xgc=gc[,2]
 		xgck=gc[,3]

Added: pkg/patchwork/inst/python/Check.py
===================================================================
--- pkg/patchwork/inst/python/Check.py	                        (rev 0)
+++ pkg/patchwork/inst/python/Check.py	2011-12-07 10:49:08 UTC (rev 40)
@@ -0,0 +1,11 @@
+import sys
+import os
+
+try:
+    import pysam
+    print "X"
+    sys.exit()
+except:
+	#It didnt work.
+    print "Pysam Not Available"
+    sys.exit()

Modified: pkg/patchwork/inst/python/Pysamloader.py
===================================================================
--- pkg/patchwork/inst/python/Pysamloader.py	2011-12-06 14:37:39 UTC (rev 39)
+++ pkg/patchwork/inst/python/Pysamloader.py	2011-12-07 10:49:08 UTC (rev 40)
@@ -6,13 +6,21 @@
 # soemthing like try(import pysam) 
 # if nono install it.
 
-try:
-	import pysam
-except:
-	p = "export PYTHONPATH=$PYTHONPATH:%s" % os.path.dirname(os.path.abspath(sys.argv[0]))
-	os.system(p)
-	import pysam
+	#library(patchwork)
+	#patchwork.CNA("cancer.bam","pile.up",reference="illumina")
 
+#try:
+#	import pysam
+#except:
+	#p = "export PYTHONPATH=$PYTHONPATH:%s" % os.path.dirname(os.path.abspath(sys.argv[0]))
+	#os.system(p)
+#	a = "python %s/.python/setup.py build" % os.path.dirname(os.path.abspath(sys.argv[0]))
+#	os.system(a)
+#	b = "python %s/python/setup.py install" % os.path.dirname(os.path.abspath(sys.argv[0]))
+#	print b
+#	os.system(b)
+import pysam
+
 try:
     infile = pysam.Samfile(sys.argv[1],"rb")
 except IOError,eStr: