From 6fe24e422fc60700b124b67986bd8929b86bb070 Mon Sep 17 00:00:00 2001
From: Sebastian Mackowiak <sebastian.mackowiak@mdc-berlin.de>
Date: Tue, 6 Sep 2011 17:05:32 +0200
Subject: [PATCH] version 0.0.1

---
 miRDeep2.pl          |  8 ++++----
 prepare_signature.pl | 33 +++++++++++++++++++++++++++++++--
 repath_pdfs.pl       | 25 +++++++++++++++++++++++++
 3 files changed, 60 insertions(+), 6 deletions(-)
 create mode 100755 repath_pdfs.pl

diff --git a/miRDeep2.pl b/miRDeep2.pl
index 8c2a370..e18f97e 100755
--- a/miRDeep2.pl
+++ b/miRDeep2.pl
@@ -805,15 +805,15 @@ sub output_results{
     if($file_mature_ref_this_species !~ /none/i){
 		
         if($options{'q'}){
-            $line="make_html.pl -f $dir/output.mrd -k $dir_tmp/$file_mature_ref_this_species -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -q $options{'q'} -x $xopt -r ${scripts}Rfam_for_miRDeep.fa -g $sc -y $time $sort_by_sample";
+            $line="make_html.pl -f $dir/output.mrd -k $dir_tmp/$file_mature_ref_this_species -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -q $options{'q'} -x $xopt -r ${scripts}Rfam_for_miRDeep.fa -v $sc -y $time $sort_by_sample";
         }else{
-            $line="make_html.pl -f $dir/output.mrd -k $dir_tmp/$file_mature_ref_this_species -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -r ${scripts}Rfam_for_miRDeep.fa -g $sc -y $time  $sort_by_sample";
+            $line="make_html.pl -f $dir/output.mrd -k $dir_tmp/$file_mature_ref_this_species -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -r ${scripts}Rfam_for_miRDeep.fa -v $sc -y $time  $sort_by_sample";
         }
     }else{
         if($options{'q'}){
-            $line="make_html.pl -f $dir/output.mrd -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -q $options{'q'}  -x $xopt -r ${scripts}Rfam_for_miRDeep.fa -g $sc -y $time $sort_by_sample";
+            $line="make_html.pl -f $dir/output.mrd -p $dir_tmp/precursors.coords -s $dir/survey.csv -c -e -q $options{'q'}  -x $xopt -r ${scripts}Rfam_for_miRDeep.fa -v $sc -y $time $sort_by_sample";
         }else{
-            $line="make_html.pl -f $dir/output.mrd -p $dir_tmp/precursors.coords -g $sc -s $dir/survey.csv -c -e -r ${scripts}Rfam_for_miRDeep.fa -y $time $sort_by_sample";
+            $line="make_html.pl -f $dir/output.mrd -p $dir_tmp/precursors.coords -v $sc -s $dir/survey.csv -c -e -r ${scripts}Rfam_for_miRDeep.fa -y $time $sort_by_sample";
         }
     }
 
diff --git a/prepare_signature.pl b/prepare_signature.pl
index b774d9d..0f924fd 100755
--- a/prepare_signature.pl
+++ b/prepare_signature.pl
@@ -63,13 +63,20 @@
     
 #    system("cat $dir/reads_vs_precursors.arf $dir/mature_vs_precursors.arf > $dir/signature_unsorted.arf");
     #Sortarf("$dir/signature_unsorted.arf");
-	system("sort -k6 $dir/signature_unsorted.arf > $outfile");
+	presort("$dir/signature_unsorted.arf");
+	system("sort -nk1 $dir/signature_unsorted.arf.tmp > $dir/signature_unsorted.arf.tmp2");
+	system("cut -f2-14 $dir/signature_unsorted.arf.tmp2 > $outfile");
+#	system("sort -V -k6 $dir/signature_unsorted.arf > $outfile");
+	
 
 }else{
 
     if($options{b}){print STDERR "sorting rows\n";}
 	#Sortarf("$dir/reads_vs_precursors.arf");
-	system("sort -k6 $dir/reads_vs_precursors.arf > $outfile");
+	presort("$dir/reads_vs_precursors.arf");
+	system("sort -nk1 $dir/reads_vs_precursors.arf.tmp > $dir/reads_vs_precursors.arf.tmp2");
+	system("cut -f2-f14 $dir/reads_vs_precursors.arf.tmp2 > $outfile");
+#	system("sort -V -k6 $dir/reads_vs_precursors.arf > $outfile");
 }
 
 
@@ -88,6 +95,28 @@
 ############################################################
 ############################################################
 
+sub presort{
+	my $file=shift;
+	open IK,"$file" or die "no arf file given\n";
+	open IKT,">$file.tmp" or die "tmp file could not be opened\n";
+	
+	my %index=();
+	my $count=0;
+	my @l;
+
+	while(<IK>){
+		@l=split();
+		if(not $index{$l[5]}){
+			$count++;
+			$index{$l[5]}=$count;
+		}
+		print IKT "$index{$l[5]}\t$_";
+	}
+	close IK;
+	close IKT;
+}
+
+
 sub Sortarf {
 	my $file=shift;
 	open IN,"<$file" or die "FILE $file not found $!\n";
diff --git a/repath_pdfs.pl b/repath_pdfs.pl
new file mode 100755
index 0000000..01ae636
--- /dev/null
+++ b/repath_pdfs.pl
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+
+use strict;
+use File::Basename;
+use Cwd;
+
+my $cwd = cwd;
+$cwd .="/";
+
+my $pdfsdir = $ARGV[1] or die "Usage: $0 html_file pdfs_dir > outfile.html\n";
+
+open IN,"$ARGV[0]" or die "No html input file given\n";
+my ( $name0, $path0, $extension0 ) = fileparse ( $ARGV[0], '\..*' );
+
+
+open OUT,">${name0}_repath.html" or die "Could not create file ${name0}_repath.html\n";
+
+while(<IN>){
+	if(/a href="file:\/\/(\/\S+)$pdfsdir/){
+		$_ =~ s/$1/$cwd/;
+	}
+	print OUT;
+}
+close IN;
+close OUT;