Merge branch 'release/5.0.0'

README.md

@@ -2,4 +2,5 @@
 Contains two scripts
 processGTF.pl - process gtf file to get following files 
 getPeak.pl - process bam file to get max coverage peak per gene using user provide gene boundaries
-
+runPeakRescue.pl - run the peakrescue pipeline
+peakRescue_readToGeneAssignment.py - runs read to gene assignement using max peak vales per gene

perl/bin/mergeFiles.pl

@@ -0,0 +1,145 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use File::Basename;
+use File::Spec;
+use Getopt::Long;
+use Pod::Usage qw(pod2usage);
+use Data::Dumper;
+
+# Author: sb43@sanger.ac.uk
+
+my ($options) = option_builder();
+
+open(my $fh1, $options->{'f1'}) || warn "print $!";
+open(my $fh2, $options->{'f2'}) || warn "print $!";
+
+my ($f1,$d1,$s1) = fileparse($options->{'f1'},qr/\.[^.]*/);
+my ($f2,$d2,$s2) = fileparse($options->{'f2'},qr/\.[^.]*/);
+
+my $col_f1=$options->{'c1'};
+my $col_f2=$options->{'c2'};
+chomp $col_f1;
+chomp $col_f2;
+
+my $fh_common;
+# create file handle for filed to write [ common columns and different columns
+if ($options->{'o'}) { 
+	open($fh_common, '>', $options->{'o'});
+}else{	
+	open($fh_common, '>', $f1.'_'.$f2.'common'.$s1);
+}
+
+# create hash of both the files....
+
+my ($file1_hash)=get_file_hash($fh1,$col_f1,$options->{'h'},$f1);
+my ($file2_hash)=get_file_hash($fh2,$col_f2,$options->{'h'},$f2);
+
+#combine files
+combine_hash($file1_hash,$file2_hash,$fh_common,$options->{'h'});
+
+# sub to combine file data...
+sub combine_hash {
+	my($hash_f1,$hash_f2,$fh_combined,$header)=@_;
+	my $count=0;
+	# Write common rows file...
+	if($header){
+		print $fh_common $hash_f1->{'header'}."\t".$hash_f2->{'header'}."\n";
+	}
+	#print Dumper $hash_f1;
+	foreach my $key(keys %$hash_f1) {
+		next if $key eq 'header';
+		if ($hash_f2->{$key}) {
+		  print $fh_combined $hash_f1->{$key}."\t".$hash_f2->{$key}."\n";
+		  $count++;
+		}
+	}	
+	print "Found $count matching lines\n"; 
+}
+
+# create hash from file
+sub get_file_hash {
+	my ($fh,$columns,$header,$f)=@_;
+	my $file_hash;
+	my $count=0;	
+	while (my $line=<$fh>) {	
+		$count++;
+		$line=~s/\n//g;
+		my ($col_key) = get_col_key($line,$columns);
+		if($header && $count == 1) {
+			$file_hash->{'header'}="$line";
+			print "Columns to compare from file: $f: $col_key\n"; 
+			next;
+		} 
+		$file_hash->{$col_key}="$line";
+	}
+
+return $file_hash
+
+
+}
+
+
+# get common key from both files
+sub get_col_key {
+	my ($line,$columns)=@_;
+	my $col_key;
+                my @col=split(',',$columns);
+                foreach my $col_num(@col) {
+                        my($field)=(split "\t", $line)[$col_num - 1];
+                        $col_key.='_'.$field;
+                }	
+return $col_key;	
+}
+
+
+
+1;
+
+
+#########################################
+
+sub option_builder {
+	my ($factory) = @_;
+
+	my %opts;
+
+	&GetOptions (
+					'h|help'    => \$opts{'h'},
+					'f1|file1=s' => \$opts{'f1'},
+					'f2|file2=s'  => \$opts{'f2'},
+					'c1|col1=s'  => \$opts{'c1'},
+					'c2|col2=s'  => \$opts{'c2'},
+					'o|outFile=s'  => \$opts{'o'},
+					'hd|header=s'  => \$opts{'hd'},
+					'v|version'  => \$opts{'v'},
+	);
+
+	pod2usage(q{'-f1' file1 must be specified.}) unless(defined $opts{'f1'}) ;
+	pod2usage(q{'-f2' file2 must be specified.}) unless(defined $opts{'f2'}) ;
+	return \%opts;
+}
+
+__END__
+=head1 NAME
+
+mergeFiles.pl - creates file with matching columns from both files    
+
+=head1 SYNOPSIS
+
+mergeFiles.pl [-h] -f1 -f2 -c1 -c2 -o  [-h -v ]
+
+  Required Options (project must be defined):
+    --help          (-h)  This message and format of input file
+     One or more of the following:
+     
+    --file1  (-f1) file1 
+    --file2  (-f2) file2 
+    --col1  (-c1) comma separated column numbers fom file1  
+    --col2  (-c2) comma separated columns numbers fom file2 
+    --outFile  (-o) outfile name
+    --header  (-hd) [1|0] print header line in output 
+
+=cut
+
+