[Patchwork-commits] r166 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R pkg/patchwork/inst/perl
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Mar 19 11:43:37 CET 2013
Author: sebastian_d
Date: 2013-03-19 11:43:37 +0100 (Tue, 19 Mar 2013)
New Revision: 166
Modified:
.git/COMMIT_EDITMSG
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/patchwork/R/patchwork.alleledata.r
pkg/patchwork/R/patchwork.plot.r
pkg/patchwork/inst/perl/pile2alleles.pl
Log:
stable version, some changes to allele information and some changes to call correct snp list (hg18 or hg19).
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/COMMIT_EDITMSG 2013-03-19 10:43:37 UTC (rev 166)
@@ -1 +1 @@
-Add titles to patchwork plots among other things
+Added patchwork messaging to know which file is being used for allele data generation
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/logs/HEAD 2013-03-19 10:43:37 UTC (rev 166)
@@ -36,3 +36,5 @@
5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363095404 +0100 pull : Fast-forward
6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363252090 +0100 pull : Fast-forward
22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363350024 +0100 pull : Fast-forward
+028901af11a1b01a4147feab3f19214457984911 aa2927bca2c8a8dcd8482384ed8ed97995508514 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363604552 +0100 commit: fixed an issue where hg18 common snps list was not being used when it should have been
+aa2927bca2c8a8dcd8482384ed8ed97995508514 f25144d2475776c2cec713208516fe1072862311 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363613325 +0100 commit: Added patchwork messaging to know which file is being used for allele data generation
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/logs/refs/heads/master 2013-03-19 10:43:37 UTC (rev 166)
@@ -36,3 +36,5 @@
5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363095404 +0100 pull : Fast-forward
6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363252090 +0100 pull : Fast-forward
22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363350024 +0100 pull : Fast-forward
+028901af11a1b01a4147feab3f19214457984911 aa2927bca2c8a8dcd8482384ed8ed97995508514 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363604552 +0100 commit: fixed an issue where hg18 common snps list was not being used when it should have been
+aa2927bca2c8a8dcd8482384ed8ed97995508514 f25144d2475776c2cec713208516fe1072862311 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363613325 +0100 commit: Added patchwork messaging to know which file is being used for allele data generation
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/logs/refs/remotes/origin/master 2013-03-19 10:43:37 UTC (rev 166)
@@ -36,3 +36,5 @@
5a37be0dedd4d5f3720b63e057e7f2a5d363bbf5 6a55102231aa819f1e4616dde7c28ea32af8a06c Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363095404 +0100 pull : fast-forward
6a55102231aa819f1e4616dde7c28ea32af8a06c 22eb0c8de456d9ed783868a3db491b52008fb116 Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363252090 +0100 pull : fast-forward
22eb0c8de456d9ed783868a3db491b52008fb116 028901af11a1b01a4147feab3f19214457984911 Sebastian DiLorenzo <S_D at imv071.medsci.uu.se> 1363350024 +0100 pull : fast-forward
+028901af11a1b01a4147feab3f19214457984911 aa2927bca2c8a8dcd8482384ed8ed97995508514 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363604601 +0100 update by push
+aa2927bca2c8a8dcd8482384ed8ed97995508514 f25144d2475776c2cec713208516fe1072862311 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1363613338 +0100 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/refs/heads/master 2013-03-19 10:43:37 UTC (rev 166)
@@ -1 +1 @@
-028901af11a1b01a4147feab3f19214457984911
+f25144d2475776c2cec713208516fe1072862311
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-03-15 13:47:20 UTC (rev 165)
+++ .git/refs/remotes/origin/master 2013-03-19 10:43:37 UTC (rev 166)
@@ -1 +1 @@
-028901af11a1b01a4147feab3f19214457984911
+f25144d2475776c2cec713208516fe1072862311
Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r 2013-03-15 13:47:20 UTC (rev 165)
+++ pkg/patchwork/R/patchwork.alleledata.r 2013-03-19 10:43:37 UTC (rev 166)
@@ -66,12 +66,19 @@
#Check if HG18 or HG19 should be applied
con = file(Pileup,"rt")
- firstline = readLines(con,1)
+ line = readLines(con,1)
+ hgcheck = strsplit(line,"\t")
+
+ #Sometimes chr1 isnt first in the pileup file, traverse until you get to chr1 to see if hg18 or hg19 should be applied.
+ while(hgcheck[[1]][1] != "chr1")
+ {
+ line = readLines(con,1)
+ hgcheck = strsplit(line,"\t")
+ }
close(con)
- hgcheck = strsplit(firstline,"\t")
- if (hgcheck[[1]][2] <= 10000)
+ if (as.numeric(hgcheck[[1]][2]) <= 10000)
{
data(commonSnpsHG18,package="patchworkData")
}
Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r 2013-03-15 13:47:20 UTC (rev 165)
+++ pkg/patchwork/R/patchwork.plot.r 2013-03-19 10:43:37 UTC (rev 166)
@@ -31,14 +31,25 @@
#you are running R from. (getwd())
if(is.null(alf))
{
- cat("Initiating Allele Data Generation \n")
-
#If Normal.pileup exists, use with normal.vcf (if mpileup) or without (if pileup) to
#create normalalf in patchwork.alleledata()
#Create normalalf
- if (!is.null(Normal.pileup)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
+
+ if (!is.null(Normal.pileup))
+ {
+ normal.pileup.name = strsplit(Normal.pileup,"/")
+ normal.pileup.name = normal.pileup.name[[1]][length(normal.pileup.name[[1]])]
+ cat(paste("Initiating Normal Allele Data Generation (",normal.pileup.name,") \n",sep=""))
+ normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
+ }
+
+ tumor.pileup.name = strsplit(Tumor.pileup,"/")
+
+ tumor.pileup.name = tumor.pileup.name[[1]][length(tumor.pileup.name[[1]])]
+
+ cat(paste("Initiating Tumor Allele Data Generation (",tumor.pileup.name,") \n",sep=""))
alf = patchwork.alleledata(Tumor.pileup, vcf=Tumor.vcf)
# if(!is.null(Normal.pileup) & !is.null(Reference))
Modified: pkg/patchwork/inst/perl/pile2alleles.pl
===================================================================
--- pkg/patchwork/inst/perl/pile2alleles.pl 2013-03-15 13:47:20 UTC (rev 165)
+++ pkg/patchwork/inst/perl/pile2alleles.pl 2013-03-19 10:43:37 UTC (rev 166)
@@ -32,7 +32,11 @@
$iupac{'T'}{'S'} = 'G|C';
$iupac{'T'}{'M'} = 'A|C';
-while (<STDIN>) {
+#my $filename = <STDIN>;
+#$filename = chomp($filename);
+
+while (<STDIN>)
+{
chomp;
#if ($_ == ""){next;}
if ($_ =~ /(\S+)\t(\S+)\t(\S+)\t(\S+)\t(\S+)\t\S+\t\S+\t(\S+)\t(\S+)\t\S+/)
@@ -75,6 +79,7 @@
}
else
{
+ #print STDERR "In file $filename, line incompatible: $_ \n";
print STDERR "Line incompatible: $_ \n";
}
}
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