diff bin/rmap2eland.pl @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/rmap2eland.pl	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,103 @@
+use strict;
+
+my $rmapfilename=$ARGV[0];
+my $readsfilename=$ARGV[1];
+my $elandfilename=$ARGV[2];
+
+my $detectformat=`head -c 1 $readsfilename`;
+
+#system("grep \"$detectformat\" $readsfilename |sort >$readsfilename.sort");
+system("awk 'NR%2==1' $readsfilename |sort >$readsfilename.sort");
+system("sort -k4,4 $rmapfilename >$rmapfilename.sort");
+
+
+open(readsfile, $readsfilename.".sort");
+
+
+
+#$looplinenumbers=2 if ($detectformat eq ">");
+open(rmapfile, $rmapfilename.".sort");
+open(elandfile, ">".$elandfilename);
+
+while(my $rmapline=<rmapfile>)
+{
+	chomp($rmapline);
+	my ($mapped_id, $start, $end, $rmapreadname, $mismatch, $strand)=split("\t",$rmapline);
+	while(my $readline=<readsfile>)
+	{
+		if($readline=~/^$detectformat/)
+		{
+			chomp($readline);
+			my $readname=substr($readline, 1, length($readline)-1);
+			
+			
+			if($readname ne $rmapreadname)
+			{
+				print elandfile $readname,"\tNA\tNM\n";
+				next;
+			}
+			else
+			{
+				my @mapped_ids=();
+				my @mapped_pos=();
+				my @mapped_strand=();
+				push(@mapped_ids, $mapped_id);
+				push(@mapped_pos,$start);
+				push(@mapped_strand,$strand);
+				while(1)
+				{
+					$rmapline=<rmapfile>;
+					chomp($rmapline);
+					($mapped_id, $start, $end, $rmapreadname, $mismatch, $strand)=split("\t",$rmapline);
+					if( $rmapreadname eq $readname )
+					{
+						push(@mapped_ids, $mapped_id);
+						push(@mapped_pos,$start);
+						push(@mapped_strand,$strand);
+					}
+					else
+					{
+						seek(rmapfile, -1*length($rmapline)-1,1);
+						print elandfile $readname,"\t";
+						print elandfile "NA\t";
+						print elandfile scalar(@mapped_ids),":0:0\t";
+						for(my $i=0;$i<@mapped_ids;$i++)
+						{
+							print elandfile "/",$mapped_ids[$i];
+							print elandfile ":",$mapped_pos[$i]+1;
+							if($mapped_strand[$i] eq "+")
+							{
+								print elandfile "F0,";
+							}
+							else
+							{
+								print elandfile "R0,";
+							}
+						
+						}
+						print elandfile "\n";
+						last;
+					}
+				}
+				last;
+					
+			}
+		}	
+	}
+}
+
+while(my $readline=<readsfile>)
+{
+        if($readline=~/^$detectformat/)
+        {
+             chomp($readline);
+             my $readname=substr($readline, 1, length($readline)-1);
+             print  elandfile $readname,"\tNA\tNM\n";
+        }
+}
+
+close(elandfile);
+close(rmapfile);
+
+
+close(readsfile);