[Patchwork-commits] r161 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/inst/perl pkg/patchwork/inst/python
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 13 14:14:27 CET 2013
Author: sebastian_d
Date: 2013-02-13 14:14:27 +0100 (Wed, 13 Feb 2013)
New Revision: 161
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/inst/perl/pile2alleles.pl
pkg/patchwork/inst/python/Pysamloader.py
Log:
Updated error handling for pile2alleles
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/COMMIT_EDITMSG 2013-02-13 13:14:27 UTC (rev 161)
@@ -1 +1 @@
-updates size of cex for karyotype plot to make the small pictures more interpretable
+Updated error handling in pile2alleles
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/logs/HEAD 2013-02-13 13:14:27 UTC (rev 161)
@@ -28,3 +28,5 @@
c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358776614 +0100 commit: minor update
8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358869240 +0100 commit: removed antique from bugfixing in patchworkCG
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable
+a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge
+acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761388 +0100 commit: Updated error handling in pile2alleles
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/logs/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161)
@@ -28,3 +28,5 @@
c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358776614 +0100 commit: minor update
8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358869240 +0100 commit: removed antique from bugfixing in patchworkCG
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037334 +0100 commit: updates size of cex for karyotype plot to make the small pictures more interpretable
+a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631509 +0100 commit: removed vercheck as it caused package to fail to build at R-forge
+acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761388 +0100 commit: Updated error handling in pile2alleles
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/logs/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161)
@@ -28,3 +28,5 @@
c39f1b06a56367684e8062040df7214da6a79455 8d49ce11a9941d73d7be44948f908a139958e029 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358776628 +0100 update by push
8d49ce11a9941d73d7be44948f908a139958e029 4577fee5ce0968b311fa252e9df8fba284522e5d Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1358869254 +0100 update by push
4577fee5ce0968b311fa252e9df8fba284522e5d a75b0350402a356de4d9991f66d7fd1bc785a46f Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359037348 +0100 update by push
+a75b0350402a356de4d9991f66d7fd1bc785a46f acd7e59391651e7076a021090d6020f57da24098 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1359631524 +0100 update by push
+acd7e59391651e7076a021090d6020f57da24098 f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1360761405 +0100 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/refs/heads/master 2013-02-13 13:14:27 UTC (rev 161)
@@ -1 +1 @@
-a75b0350402a356de4d9991f66d7fd1bc785a46f
+f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2013-01-31 11:22:11 UTC (rev 160)
+++ .git/refs/remotes/origin/master 2013-02-13 13:14:27 UTC (rev 161)
@@ -1 +1 @@
-a75b0350402a356de4d9991f66d7fd1bc785a46f
+f2ab85a08717e4eea8a9deaf3d0d7770b28b40a0
Modified: pkg/patchwork/inst/perl/pile2alleles.pl
===================================================================
--- pkg/patchwork/inst/perl/pile2alleles.pl 2013-01-31 11:22:11 UTC (rev 160)
+++ pkg/patchwork/inst/perl/pile2alleles.pl 2013-02-13 13:14:27 UTC (rev 161)
@@ -32,44 +32,51 @@
$iupac{'T'}{'S'} = 'G|C';
$iupac{'T'}{'M'} = 'A|C';
-
while (<STDIN>) {
chomp;
- my ($chr, $pos, $ref, $cons, $consQual, $depth, $baseString) = (split /\t/, $_)[0,1,2,3,4,7,8];
- $ref = uc $ref;
- if ($ref eq '*'){next;}
- if ($cons eq 'N'){next;}
- my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons};
- $snps{$chr}{$pos}{'ref'} = $ref;
- $snps{$chr}{$pos}{'snp'} = $snp;
- $snps{$chr}{$pos}{'qual'} = $consQual;
- my $snpCount;
- if ($snps{$chr}{$pos}{'snp'} eq 'A') {
- $snpCount = $baseString =~ tr/Aa/Aa/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'C') {
- $snpCount = $baseString =~ tr/Cc/Cc/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'G') {
- $snpCount = $baseString =~ tr/Gg/Gg/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'T') {
- $snpCount = $baseString =~ tr/Tt/Tt/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|C') {
- $snpCount = $baseString =~ tr/AaCc/AaCc/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|G') {
- $snpCount = $baseString =~ tr/AaGg/AaGg/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|T') {
- $snpCount = $baseString =~ tr/AaTt/AaTt/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|C') {
- $snpCount = $baseString =~ tr/GgCc/GgCc/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|T') {
- $snpCount = $baseString =~ tr/GgTt/GgTt/;
- } elsif ($snps{$chr}{$pos}{'snp'} eq 'C|T') {
- $snpCount = $baseString =~ tr/CcTt/CcTt/;
- } else {
- $snpCount = 0;
+ #if ($_ == ""){next;}
+ if ($_ =~ /(\S+)\t(\S+)\t(\S+)\t(\S+)\t(\S+)\t\S+\t\S+\t(\S+)\t(\S+)\t\S+/)
+ {
+ my ($chr, $pos, $ref, $cons, $consQual, $depth, $baseString) = ($1,$2,$3,$4,$5,$6,$7); #(split /\t/, $_)[0,1,2,3,4,7,8];
+ $ref = uc $ref;
+ if ($ref eq '*'){next;}
+ if ($cons eq 'N'){next;}
+ my $snp = ($cons =~ m/[AGCT]/) ? $cons : $iupac{$ref}{$cons};
+ $snps{$chr}{$pos}{'ref'} = $ref;
+ $snps{$chr}{$pos}{'snp'} = $snp;
+ $snps{$chr}{$pos}{'qual'} = $consQual;
+ my $snpCount;
+ if ($snps{$chr}{$pos}{'snp'} eq 'A') {
+ $snpCount = $baseString =~ tr/Aa/Aa/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'C') {
+ $snpCount = $baseString =~ tr/Cc/Cc/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'G') {
+ $snpCount = $baseString =~ tr/Gg/Gg/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'T') {
+ $snpCount = $baseString =~ tr/Tt/Tt/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|C') {
+ $snpCount = $baseString =~ tr/AaCc/AaCc/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|G') {
+ $snpCount = $baseString =~ tr/AaGg/AaGg/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'A|T') {
+ $snpCount = $baseString =~ tr/AaTt/AaTt/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|C') {
+ $snpCount = $baseString =~ tr/GgCc/GgCc/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'G|T') {
+ $snpCount = $baseString =~ tr/GgTt/GgTt/;
+ } elsif ($snps{$chr}{$pos}{'snp'} eq 'C|T') {
+ $snpCount = $baseString =~ tr/CcTt/CcTt/;
+ } else {
+ $snpCount = 0;
+ }
+ $snps{$chr}{$pos}{'depth'} = $depth;
+ $snps{$chr}{$pos}{'freq'} = $snpCount;
+ $snps{$chr}{$pos}{'pct'} = sprintf '%.2f', ($snpCount/$depth);
+ }
+ else
+ {
+ print STDERR "Line incompatible: $_ \n";
}
- $snps{$chr}{$pos}{'depth'} = $depth;
- $snps{$chr}{$pos}{'freq'} = $snpCount;
- $snps{$chr}{$pos}{'pct'} = sprintf '%.2f', ($snpCount/$depth);
}
Modified: pkg/patchwork/inst/python/Pysamloader.py
===================================================================
--- pkg/patchwork/inst/python/Pysamloader.py 2013-01-31 11:22:11 UTC (rev 160)
+++ pkg/patchwork/inst/python/Pysamloader.py 2013-02-13 13:14:27 UTC (rev 161)
@@ -4,10 +4,12 @@
import pysam
+filename = sys.argv[1]
+
try:
infile = pysam.Samfile(sys.argv[1],"rb")
except IOError,eStr:
- print "Error:Cannot open",infile," for reading: ", eStr
+ print "Error:Cannot open ",filename," for reading: ", eStr
sys.exit()
outfile = open(".Tmp_chr_pos","w")
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