From ed44fdb59fe5c2489ff2b000227615fc0e857f7b Mon Sep 17 00:00:00 2001
From: Sebastian Mackowiak <Drmirdeep@users.noreply.github.com>
Date: Mon, 9 Sep 2019 13:30:18 +0200
Subject: [PATCH] Output 5p and 3p arms in bed files

---
 src/get_mirdeep2_precursors.pl | 85 ++++++++++++++++++++--------------
 1 file changed, 50 insertions(+), 35 deletions(-)

diff --git a/src/get_mirdeep2_precursors.pl b/src/get_mirdeep2_precursors.pl
index 472015e..9962a45 100755
--- a/src/get_mirdeep2_precursors.pl
+++ b/src/get_mirdeep2_precursors.pl
@@ -23,20 +23,15 @@
 # and writes a fasta file and a bed file for these
 # See 'Usage' for more information.
 #
-# Bed files are only created for the precursor sequences.
-#
-# S.M. Jan. 2012
+# S.M. Jan. 2019
 #
 ######################################
 
 
-
-
 use strict;
 use Getopt::Std;
 
 
-
 my %options=();
 getopts("r:s:dpht:mkT:o:",\%options);
 if(not -f $options{'r'} or $options{'h'}){
@@ -65,8 +60,6 @@
 $options{'T'} = 'notTrackname';
 }
 
-
-
 my @l1=split(/result/,$options{'r'});
 my ($timestamp,$dmp)=split(".csv",$l1[1]);
 
@@ -101,10 +94,6 @@
 
 my @names=qw(0 1 2 3 4 5 6 7 8 9 10 11 12 mature star pres);
 
-
-
-
-
 while(<IN>){
 	if(/novel miRNAs predicted by miRDeep2/){
 		$novel=1;
@@ -136,15 +125,21 @@
 		close OUT;
         close BED;
 		open OUT,">$od/not_$names[$seqcol]${timestamp}_score${score}_to_$max.fa";
-        open BED,">$od/not_$names[$seqcol]${timestamp}_score${score}_to_$max.bed";
 		next;
 	}else{}
 	next if(/^\s*$/);
+			
+
 	if($novel or $known){
 		chomp;
 		@line=split(/\t/);
 		my $coord='na';
 		$coord=$line[16] if($line[16]);
+		my $c5p = index($line[15],$line[13]);
+		my $c3p = index($line[15],$line[14]);
+		my $l5p = length($line[13]);
+		my $l3p = length($line[14]);
+
 		if($known){
 			if($line[1] >= $thres and $line[1] < $maxs){
 				if($options{'d'}){
@@ -163,7 +158,26 @@
 
                 $strandcol="0,0,255";
                 if($coord =~ /^(\S+):(\d+)\.\.(\d+):(\S)$/){
-                  $pcoord="$1:$2-$3";
+					my ($c,$b,$e,$s) = ($1,$2,$3,$4);
+					if($options{'m'}){
+						if($s eq '+'){
+							$b+=$c5p;
+							$e=$b+$l5p;
+						}else{
+							$b=$e-$c5p-$l5p;
+							$e=$e-$c5p;
+						}
+					}
+					if($options{'k'}){
+						if($s eq '+'){
+							$b+=$c3p;
+							$e=$b+$l3p;
+						}else{
+							$b=$e-$c3p-$l3p;
+							$e=$e-$c3p;
+						}
+					}
+                  $pcoord="$1:$b-$e";
                   $strandcol="255,0,0" if($4 eq "+");
                   if($first){
                      $first=0;
@@ -173,7 +187,7 @@
                      $bedh1 =~ s/BPOS/$pcoord/;
                      print BED "$bedh1";
                   }
-                  print BED "$1\t$2\t$3\t$line[0]\t$line[1]\t$4\t$2\t$3\t$strandcol\n";
+                  print BED "$c\t$b\t$e\t$line[0]\t$line[1]\t$s\t$b\t$e\t$strandcol\n";
                 }
 			}
 		}else{
@@ -193,6 +207,26 @@
                 chomp $coord;
                 $strandcol="0,0,255";
                 if($coord =~ /^(\S+):(\d+)\.\.(\d+):(\S)$/){
+					my ($c,$b,$e,$s) = ($1,$2,$3,$4);
+					if($options{'m'}){
+						if($s eq '+'){
+							$b+=$c5p;
+							$e=$b+$l5p;
+						}else{
+							$b=$e-$c5p-$l5p;
+							$e=$e-$c5p;
+						}
+					}
+					if($options{'k'}){
+						if($s eq '+'){
+							$b+=$c3p;
+							$e=$b+$l3p;
+						}else{
+							$b=$e-$c3p-$l3p;
+							$e=$e-$c3p;
+						}
+					}
+					#$pcoord="$1:$b-$e";
                   $strandcol="255,0,0" if($4 eq "+");
                   if($first){
                      $first=0;
@@ -202,7 +236,7 @@
                      $bedh1 =~ s/BPOS/$pcoord/;
                      print BED "$bedh1";
                   }
-                  print BED "$1\t$2\t$3\t$line[0]\t$line[1]\t$4\t$2\t$3\t$strandcol\n";
+                  print BED "$c\t$b\t$e\t$line[0]\t$line[1]\t$s\t$b\t$e\t$strandcol\n";
                 }
 
 			}
@@ -212,8 +246,6 @@
 	if($not){
 		chomp;
 		@line=split(/\t/);
-		my $coord='na';
-		$coord=$line[16] if($line[16]);
 		if($options{'d'}){
 			$line[$seqcol] =~ tr/uU/tT/;
 		}
@@ -222,23 +254,6 @@
 		}else{
 			print OUT ">${line[0]}_x${line[4]}\n",uc($line[$seqcol]),"\n";
 		}
-        chomp $coord;
-        $strandcol="0,0,255";
-        if($coord =~ /^(\S+):(\d+)\.\.(\d+):(\S)$/){
-          $strandcol="255,0,0" if($4 eq "+");
-          if($first){
-                     $first=0;
-                     $bedh1=$bedh;
-                     $bedh1 =~ s/TNAME/$options{'T'}.not_detected_miRNAs/;
-                     $bedh1 =~ s/TDESC/miRNAs not detected by miRDeep2 for $options{'T'}/;
-                     $bedh1 =~ s/BPOS/$pcoord/;
-                     print BED "$bedh1";
-                  }
-          print BED "$1\t$2\t$3\t$line[0]\t$line[1]\t$4\t$2\t$3\t$strandcol\n";
-        }
-
-
-
 		next;
 	}
 }