From 872cc26398670984c4e80fcad564a550290674a3 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 4 Nov 2009 08:06:24 +0000
Subject: [PATCH] fixed details in bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@743 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/bowtie_seq           | 19 ++++++--
 code_perl/Maasha/KISS/IO.pm | 94 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 108 insertions(+), 5 deletions(-)

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 6c1659b..44d09ae 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -28,6 +28,7 @@
 
 use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::Common;
 use Maasha::Fastq;
@@ -150,16 +151,28 @@ sub bowtie2biopiece
 
     # Returns a hash.
 
-    my ( $record, @scores );
+    my ( $record, $s_id, $s_len, $hits );
+
+    # S_ID: contig00005 length=75232   numreads=13115
+
+    if ( $entry->[ 2 ] =~ /^(.+) length=(\d+)\s+numreads=(\d+)$/ )
+    {
+        $record->{ 'S_ID' }  = $1;
+        # $record->{ 'S_LEN' } = $2;
+        $record->{ 'HITS' }  = $3;
+    }
+    else
+    {
+        Maasha::Common::error( qq(BAD S_ID: "$entry->[ 2 ]") );
+    }
 
     $record->{ 'Q_ID' }       = $entry->[ 0 ];
     $record->{ 'STRAND' }     = $entry->[ 1 ];
-    $record->{ 'S_ID' }       = $entry->[ 2 ];
     $record->{ 'S_BEG' }      = $entry->[ 3 ];
     $record->{ 'SEQ' }        = $entry->[ 4 ];
     $record->{ 'SCORES' }     = $entry->[ 5 ];
     $record->{ 'SCORE' }      = $entry->[ 6 ] + 1;
-    $record->{ 'DESCRIPTOR' } = $entry->[ 7 ];
+    $record->{ 'ALIGN' }      = $entry->[ 7 ] || '.';
     $record->{ 'S_LEN' }      = length $entry->[ 4 ];
     $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
     $record->{ 'S_END' }      = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;
diff --git a/code_perl/Maasha/KISS/IO.pm b/code_perl/Maasha/KISS/IO.pm
index 4c3ac14..a24f696 100644
--- a/code_perl/Maasha/KISS/IO.pm
+++ b/code_perl/Maasha/KISS/IO.pm
@@ -256,8 +256,6 @@ sub kiss_index_search
     {
         $try = int( ( $high + $low ) / 2 );
     
-        # print "low: $low   high: $high   try: $try\n";
-        
         if ( $num < $index->[ $try ]->[ 0 ] ) {
             $high = $try;
         } elsif ( $num > $index->[ $try ]->[ 1 ] ) {
@@ -301,6 +299,98 @@ sub kiss_index_get
 }
 
 
+sub kiss_align
+{
+    # S.aur_COL       41      75      5_vnlh2ywXsN1/1 1       -       .       17:A>T,31:A>N   .       .       .       .
+
+    my ( $s_seqref,   # subject sequence reference
+         $entry,      # KISS entry
+       ) = @_;
+
+    # Returns a string.
+
+    my ( $align, $pos, $s_symbol, $q_symbol, $s_seq, $q_seq );
+
+    $s_seq = substr ${ $s_seqref }, $entry->{ 'S_BEG' }, $entry->{ 'S_END' } - $entry->{ 'S_BEG' } + 1;
+    $q_seq = $s_seq;
+
+    foreach $align ( split /,/, $entry->{ 'ALIGN' } )
+    {
+        if ( $align =~ /(\d+):(.)>(.)/ )
+        {
+            $pos      = $1;
+            $s_symbol = $2;
+            $q_symbol = $3;
+
+            if ( $s_symbol eq '-' ) # insertion
+            {
+                substr $s_seq, $pos, 0, $s_symbol;
+                substr $q_seq, $pos, 0, $q_symbol;
+            }
+            elsif ( $q_symbol eq '-' ) # deletion
+            {
+                substr $q_seq, $pos, 1, $q_symbol;
+            }
+            else # mismatch
+            {
+                substr $q_seq, $pos, 1, $q_symbol;
+            }
+        }
+        else
+        {
+            Maasha::Common::error( qq(Bad alignment descriptor: "$align") );
+        }
+    }
+
+    print Dumper( "s_seq: $s_seq", "q_seq: $q_seq" ) and exit;
+}
+
+
+sub sam2kiss
+{
+    my ( $sam_entry,   # SAM entry
+       ) = @_;
+
+    # Returns a hashref
+
+    my ( $cigar, $offset, $op, $len, @descriptors, $kiss_entry );
+    
+    $cigar = $sam_entry->{ 'CIGAR' };
+
+    $cigar =~ tr/\*//d;
+
+    $offset = 0;
+
+    while ( length $cigar > 0 )
+    {
+        if ( $cigar =~ s/^([MINDSHP])(\d+)// )
+        {
+            $op  = $1;
+            $len = $2;
+
+            print "CIGAR: $cigar   OP: $op   LEN: $len\n";
+
+            if ( $op eq 'I' )
+            {
+            
+            }
+            elsif ( $op eq 'D' )
+            {
+            
+            }
+
+            $offset += $len;
+        }
+        else
+        {
+            Maasha::Common::error( qq(Bad CIGAR format: "$cigar") );
+        }
+    }
+
+    return wantarray ? %{ $kiss_entry } : $kiss_entry;
+}
+
+
 sub kiss2biopiece
 {
     my ( $entry,   # KISS entry
-- 
2.39.2