[Patchwork-commits] r61 - in pkg/patchwork: R inst/python man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 21 09:43:05 CET 2011
Author: sebastian_d
Date: 2011-12-21 09:43:04 +0100 (Wed, 21 Dec 2011)
New Revision: 61
Modified:
pkg/patchwork/R/patchwork.CNA.r
pkg/patchwork/R/patchwork.applyref.r
pkg/patchwork/R/patchwork.readChroms.r
pkg/patchwork/inst/python/Pysamloader.py
pkg/patchwork/man/patchwork.CNA.Rd
pkg/patchwork/man/patchwork.applyref.Rd
Log:
good morning commit
Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/R/patchwork.CNA.r 2011-12-21 08:43:04 UTC (rev 61)
@@ -10,15 +10,10 @@
#load(paste(packagepath,"/data/ideogram.RData",sep=""))
#load(paste(packagepath,"/data/normaldata.RData",sep=""))
- #Inhibit error message from try.
- options(show.error.messages=FALSE)
-
#Attempt to read file pile.alleles, incase its already been created.
alf = NULL
try( load("pile.alleles.Rdata"), silent=TRUE )
- options(show.error.messages=TRUE)
-
#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())
@@ -35,16 +30,11 @@
data(ideogram,package="patchworkData")
chroms = as.character(unique(ideogram$chr))
-
- #Inhibit error message from try.
- options(show.error.messages=FALSE)
## Read coverage data. If already done, will load "data.Rdata" instead.
data=NULL
try ( load('data.Rdata'), silent=TRUE )
- options(show.error.messages=TRUE)
-
#If data object does not exist, IE it was not loaded in the previous line
#perform the function on the chromosomes to create the object.
if(is.null(data))
@@ -77,14 +67,9 @@
save(data,file='data.Rdata')
}
- #Inhibit error message from try.
- options(show.error.messages=FALSE)
-
kbsegs = NULL
try( load("smoothed.Rdata"), silent=TRUE )
- options(show.error.messages=TRUE)
-
if(length(kbsegs) == 0)
{
#Apply smoothing to the data.
@@ -94,14 +79,9 @@
cat("Smoothing Complete \n")
}
- #Inhibit error message from try.
- options(show.error.messages=FALSE)
-
segs = NULL
try( load("Segments.Rdata"), silent=TRUE )
- options(show.error.messages=TRUE)
-
if(length(segs) == 0)
{
#Segment the data.
@@ -137,9 +117,6 @@
ylim=c(0.3,1))
cat("Plotting Complete \n")
cat("Shutting down..... \n")
-
- options(show.error.messages=FALSE)
-
}
\ No newline at end of file
Modified: pkg/patchwork/R/patchwork.applyref.r
===================================================================
--- pkg/patchwork/R/patchwork.applyref.r 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/R/patchwork.applyref.r 2011-12-21 08:43:04 UTC (rev 61)
@@ -1,29 +1,8 @@
patchwork.applyref <- function(data,reference)
{
- #Load data included in package
- #packagepath = system.file(package="patchwork")
- #load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
- #load(paste(packagepath,"/data/ideogram.RData",sep=""))
-
- if(tolower(reference) == "solid")
- {
- #load(paste(packagepath,"/data/datasolid.RData",sep=""))
- data(datasolid,package="patchworkData")
- normaldata = datasolid
- }
- else if(tolower(reference) %in% c("solexa","illumina"))
- {
- #load(paste(packagepath,"/data/datasolexa.RData",sep=""))
- data(datasolexa,package="patchworkData")
- normaldata = datasolexa
- }
- else
- {
- load(reference)
- }
- ## read and apply normal/reference
- #load('/proj/b2010074/GC/normaldata.Rdata')
+ load(reference)
+
data <- merge(data[,1:7],normaldata,all=F,by=1:2)
#data$ratio <- data$norm / data$norm_mean
data$reference <- data$norm_mean ## thats temporary
Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/R/patchwork.readChroms.r 2011-12-21 08:43:04 UTC (rev 61)
@@ -25,9 +25,6 @@
#copy python folder
system(paste("cp -r ",packagepath,"/python .python",sep=""))
- #Inhibit error message from try.
- options(show.error.messages=FALSE)
-
#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")
{
@@ -45,10 +42,7 @@
cat("Install complete. Output of install can be viewed in file pysam_install_output.txt. \n")
setwd("..")
}
-
- options(show.error.messages=TRUE)
-
readlength=80 # this is currently hard coded and may be adjusted.
seglength=200 # (do not change)
data=NULL
Modified: pkg/patchwork/inst/python/Pysamloader.py
===================================================================
--- pkg/patchwork/inst/python/Pysamloader.py 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/inst/python/Pysamloader.py 2011-12-21 08:43:04 UTC (rev 61)
@@ -2,23 +2,6 @@
import re
import os
-#If pysam already installed....
-# soemthing like try(import pysam)
-# if nono install it.
-
- #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:
Modified: pkg/patchwork/man/patchwork.CNA.Rd
===================================================================
--- pkg/patchwork/man/patchwork.CNA.Rd 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/man/patchwork.CNA.Rd 2011-12-21 08:43:04 UTC (rev 61)
@@ -28,9 +28,8 @@
samtools -vcf reference.fasta bamfile > outfile.
}
\item{reference}{
- Choose "solid" or "illumina".
- If a normal reference has been created using patchwork.createreference()
- you can point to the file here.
+ Path to a reference file that you have either downloaded from us or created yourself with
+ patchwork.createreference().
}
\item{Alpha}{
Default 0.0001, change if you want to try to get a better segmentation from patchwork.segment().
Modified: pkg/patchwork/man/patchwork.applyref.Rd
===================================================================
--- pkg/patchwork/man/patchwork.applyref.Rd 2011-12-20 09:59:11 UTC (rev 60)
+++ pkg/patchwork/man/patchwork.applyref.Rd 2011-12-21 08:43:04 UTC (rev 61)
@@ -20,7 +20,7 @@
The data object generated from patchwork.GCNorm().
}
\item{reference}{
- Either "illumina","solid" or the path to a file that you have created using
+ Path to a reference file that you have either downloaded from us or created yourself with
patchwork.createreference().
}
}
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