--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_bowtie_to_blast.pl	Thu Sep 18 21:40:25 2014 -0400
@@ -0,0 +1,126 @@
+#!/usr/bin/perl 
+
+
+use warnings;
+use strict;
+use Getopt::Std;
+
+######################################### USAGE ################################
+
+my $usage=
+"$0 file_bowtie_result file_solexa_seq file_chromosome
+
+This is a converter which changes Bowtie output into Blast format.
+The input includes three files: a Bowtie result file (default Bowtie
+output file), a fasta file consisting of small Reads and a chromosome
+fasta file. It outputs the alignments in blast_parsed format.
+
+file_bowtie_result likes:
+
+AtFlower100010_x2	+	MIR319c	508	AAGGAGATTCTTTCAGTCCAG	IIIIIIIIIIIIIIIIIIIII	0	
+AtFlower1000188_x1	+	MIR2933a	421	TCGGAGAGGAAATTCGTCGGCG	IIIIIIIIIIIIIIIIIIIIII	0	
+
+file_solexa_seq likes:
+
+>AtFlower100010_x2
+AAGGAGATTCTTTCAGTCCAG
+
+file_chromosome contains chromosome seq in fasta format
+
+";
+
+
+####################################### INPUT FILES ############################
+
+my $file_bowtie_result=shift or die $usage;
+my $file_short_seq=shift or die $usage;
+my $file_chromosome_seq=shift or die $usage;
+
+
+##################################### GLOBAL VARIBALES #########################
+
+my %short_seq_length=();
+my %chromosome_length=();
+
+
+######################################### MAIN ################################# 
+
+#get the short sequence id and its length
+sequence_length($file_short_seq,\%short_seq_length);
+
+#get the chromosome sequence id and its length
+sequence_length($file_chromosome_seq,\%chromosome_length);
+
+#convert bowtie result format to blast format;
+change_format($file_bowtie_result);
+
+exit;
+
+
+##################################### SUBROUTINES ##############################
+
+sub sequence_length{
+    my ($file,$hash) = @_;
+    my ($id, $desc, $sequence, $seq_length) = ();
+
+    open (FASTA, "<$file") or die "can not open $$file\n";
+    while (<FASTA>)
+    {
+        chomp;
+        if (/^>(\S+)(.*)/)
+	{
+	    $id       = $1;
+	    $desc     = $2;
+	    $sequence = "";
+	    while (<FASTA>){
+                chomp;
+                if (/^>(\S+)(.*)/){
+		    $$hash{$id}  = length $sequence;
+		    $id         = $1;
+		    $desc       = $2;
+		    $sequence   = "";
+		    next;
+                }
+		$sequence .= $_;
+            }
+        }
+    }
+    $seq_length=length($sequence);
+    $$hash{$id} = $seq_length;
+    close FASTA;
+}
+
+
+
+
+
+sub change_format{
+	#Change Bowtie format into blast format
+	my $file=shift @_;
+	open(FILE,"<$file")||die"can not open the bowtie result file:$!\n";
+  #open(BLASTOUT,">blastout")||die"can not create the blastout file:$!\n";
+	
+	while(<FILE>){
+		chomp;
+		my @tmp=split("\t",$_);
+	#Clean the reads ID
+		my @tmp1=split(" ",$tmp[0]);
+		print  "$tmp1[0]"."\t"."$short_seq_length{$tmp1[0]}"."\t"."1".'..'."$short_seq_length{$tmp1[0]}"."\t"."$tmp[2]"."\t"."$chromosome_length{$tmp[2]}"."\t";
+		if($tmp[1] eq "+"){
+			my $seq_end=$tmp[3] + $short_seq_length{$tmp1[0]};
+			my $seq_bg=$tmp[3] + 1;
+			print  "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Plus"."\n";
+			}
+		if($tmp[1] eq "-"){
+			my $seq_end=$chromosome_length{$tmp[2]} - $tmp[3];
+			my $seq_bg=$seq_end - $short_seq_length{$tmp1[0]} + 1;
+			print  "$seq_bg".'..'."$seq_end"."\t"."1e-04"."\t"."1.00"."\t"."42.1"."\t"."Plus / Minus"."\n";
+			}
+		}
+	
+#	close BLASTOUT;
+
+}
+
+
+