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Changeset 7:c3b93bce023e (2014-07-25)

Previous changeset 6:e08814f01490 (2014-07-25) Next changeset 8:3ed8026af2d5 (2014-07-25)

Commit message:
Uploaded

added:
convert_bowtie_to_blast.pl

diff -r e08814f01490 -r c3b93bce023e convert_bowtie_to_blast.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_bowtie_to_blast.pl Fri Jul 25 05:19:53 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;
+
+}
+
+
+