From 09968e1a85678d829b2267f1ad38775ed5cb465d Mon Sep 17 00:00:00 2001
From: Stefan Lang <Stefan.Lang@med.lu.se>
Date: Thu, 10 Mar 2016 07:57:00 +0100
Subject: [PATCH] An urgent fix to FACS data handling.

---
 SCExV/lib/HTpcrA/Controller/GEOfiles.pm | 47 +++++++++++++++++++++++++
 SCExV/lib/HTpcrA/EnableFiles.pm         |  3 +-
 SCExV/lib/HTpcrA/Model/GEO_files.pm     | 31 ++++++++++++++++
 SCExV/root/R_lib/Tool_Pipe.R            |  1 +
 SCExV/root/R_lib/Tool_grouping.R        | 16 +++++++++
 SCExV/t/model_GEO_files.t               |  8 +++++
 6 files changed, 105 insertions(+), 1 deletion(-)
 create mode 100644 SCExV/lib/HTpcrA/Controller/GEOfiles.pm
 create mode 100644 SCExV/lib/HTpcrA/Model/GEO_files.pm
 create mode 100644 SCExV/t/model_GEO_files.t

diff --git a/SCExV/lib/HTpcrA/Controller/GEOfiles.pm b/SCExV/lib/HTpcrA/Controller/GEOfiles.pm
new file mode 100644
index 0000000..278a222
--- /dev/null
+++ b/SCExV/lib/HTpcrA/Controller/GEOfiles.pm
@@ -0,0 +1,47 @@
+package HTpcrA::Controller::GEOfiles;
+use Moose;
+use namespace::autoclean;
+
+BEGIN { extends 'Catalyst::Controller'; }
+
+=head1 NAME
+
+HTpcrA::Controller::GEOfiles - Catalyst Controller
+
+=head1 DESCRIPTION
+
+Catalyst Controller.
+
+=head1 METHODS
+
+=cut
+
+
+=head2 index
+
+=cut
+
+sub index :Path :Args(0) {
+    my ( $self, $c ) = @_;
+
+    $c->response->body('Matched HTpcrA::Controller::GEOfiles in GEOfiles.');
+}
+
+
+
+=encoding utf8
+
+=head1 AUTHOR
+
+Stefan Lang
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
diff --git a/SCExV/lib/HTpcrA/EnableFiles.pm b/SCExV/lib/HTpcrA/EnableFiles.pm
index c8e9669..65eed37 100644
--- a/SCExV/lib/HTpcrA/EnableFiles.pm
+++ b/SCExV/lib/HTpcrA/EnableFiles.pm
@@ -229,11 +229,12 @@ sub __fix_file_problems {
 		## 1,000 == 1000 !!!!!!!
 		while (<IN>) {
 			foreach my $problem ( $_ =~ m/(["']-?\d+,\d+,?\d*["'])/g ) {
+				##Carp::confess( join(":::", $_ =~ m/(["']-?\d+,\d+,?\d*["'])/g) );
 				$rep = $problem;
 				$rep =~ s/["',]//g;
 				$_   =~ s/$problem/$rep/;
-				$_ =~ s/["']//g;
 			}
+			$_ =~ s/["']//g;
 			print OUT $_;
 		}
 	}
diff --git a/SCExV/lib/HTpcrA/Model/GEO_files.pm b/SCExV/lib/HTpcrA/Model/GEO_files.pm
new file mode 100644
index 0000000..7876365
--- /dev/null
+++ b/SCExV/lib/HTpcrA/Model/GEO_files.pm
@@ -0,0 +1,31 @@
+package HTpcrA::Model::GEO_files;
+use Moose;
+use namespace::autoclean;
+
+extends 'Catalyst::Model';
+
+=head1 NAME
+
+HTpcrA::Model::GEO_files - Catalyst Model
+
+=head1 DESCRIPTION
+
+Catalyst Model.
+
+
+=encoding utf8
+
+=head1 AUTHOR
+
+Stefan Lang
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
diff --git a/SCExV/root/R_lib/Tool_Pipe.R b/SCExV/root/R_lib/Tool_Pipe.R
index 621e92a..a3aacb9 100644
--- a/SCExV/root/R_lib/Tool_Pipe.R
+++ b/SCExV/root/R_lib/Tool_Pipe.R
@@ -186,6 +186,7 @@ read.PCR.heatmap <- function (fname,use_pass_fail=T){
 }
 
 read.FACS <- function(fname,use_pass_fail=T) {
+	browser()
 	ftab <- matrix(ncol=0, nrow=1)
 	try( ftab <- read.PCR  ( fname, use_pass_fail ), silent=T )
 	if ( ncol(ftab) == 0 ){
diff --git a/SCExV/root/R_lib/Tool_grouping.R b/SCExV/root/R_lib/Tool_grouping.R
index c17e47e..2b3071d 100644
--- a/SCExV/root/R_lib/Tool_grouping.R
+++ b/SCExV/root/R_lib/Tool_grouping.R
@@ -43,6 +43,14 @@ group_1D_worker <- function (ma, gene, ranges ) {
 	userGroups
 }
 
+#' @name checkGrouping
+#' @aliases checkGrouping,FluidigmSet-method
+#' @rdname checkGrouping-methods
+#' @docType methods
+#' @description 
+#' @param userGroups a data.frame with three column the first being the sample name and the third the group ID
+#' @param data the fluidigm data object to check against
+#' @export 
 checkGrouping <- function ( userGroups,  data=NULL ){
 	userGroups$groupID <- as.vector( as.numeric( userGroups$groupID ))
 	if ( !is.null(data) ){
@@ -78,6 +86,14 @@ checkGrouping <- function ( userGroups,  data=NULL ){
 	if ( min(userGroups$groupID) > 1 ){
 		userGroups$groupID <- userGroups$groupID - ( min(userGroups$groupID) -1 )
 	}
+	for ( i in 1:max(userGroups$groupID) ) {
+		if ( length( grep (i,userGroups$groupID) ) == 0 ){
+			m <- which( userGroups$groupID > i)
+			if ( length(m) >0 ) {
+				userGroups$groupID[m] <- userGroups$groupID[m] -1
+			}
+		}
+	}
 	userGroups
 }
 
diff --git a/SCExV/t/model_GEO_files.t b/SCExV/t/model_GEO_files.t
new file mode 100644
index 0000000..24dbb7d
--- /dev/null
+++ b/SCExV/t/model_GEO_files.t
@@ -0,0 +1,8 @@
+use strict;
+use warnings;
+use Test::More;
+
+
+BEGIN { use_ok 'HTpcrA::Model::GEO_files' }
+
+done_testing();