From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 9 Nov 2009 08:43:40 +0000 (+0000)
Subject: improved SAM parser
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6d0ad02102c50fbb115cbfe1b1c0dbebac1951d0;p=biopieces.git

improved SAM parser

git-svn-id: http://biopieces.googlecode.com/svn/trunk@752 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_perl/Maasha/Fastq.pm b/code_perl/Maasha/Fastq.pm
index 4027209..80fea57 100644
--- a/code_perl/Maasha/Fastq.pm
+++ b/code_perl/Maasha/Fastq.pm
@@ -195,7 +195,7 @@ void solexa_str2phred_str( char *scores )
 
     int i = 0;
     
-    for ( i + 0; i < strlen( scores ); i++ ) {
+    for ( i = 0; i < strlen( scores ); i++ ) {
         scores[ i ] = solexa2phred( scores[ i ] );
     }
 }
@@ -209,12 +209,35 @@ void phred_str2solexa_str( char *scores )
 
     int i = 0;
     
-    for ( i + 0; i < strlen( scores ); i++ ) {
+    for ( i = 0; i < strlen( scores ); i++ ) {
         scores[ i ] = phred2solexa( scores[ i ] );
     }
 }
 
 
+double phred_str_mean( char *scores )
+{
+    /* Martin A. Hansen, November 2009 */
+
+    /* Calculates the mean score as a float which is retuned. */
+
+    int    len  = 0;
+    int    i    = 0;
+    int    sum  = 0;
+    double mean = 0.0;
+
+    len = strlen( scores );
+
+    for ( i = 0; i < len; i++ ) {
+        sum += phred2dec( scores[ i ] );
+    }
+
+    mean = ( double ) sum / ( double ) len;
+
+    return mean;
+}
+
+
 void softmask_solexa_str( char *seq, char *scores, int threshold )
 {
     /* Martin A. Hansen, July 2009 */
diff --git a/code_perl/Maasha/SAM.pm b/code_perl/Maasha/SAM.pm
index 6683973..e794d75 100644
--- a/code_perl/Maasha/SAM.pm
+++ b/code_perl/Maasha/SAM.pm
@@ -32,9 +32,10 @@ package Maasha::SAM;
 use warnings;
 use strict;
 use Maasha::Common;
+use Maasha::Fastq;
 use Data::Dumper;
 
-use vars qw ( @ISA @EXPORT );
+use vars qw( @ISA @EXPORT );
 
 @ISA = qw( Exporter );
 
@@ -50,9 +51,6 @@ use constant {
     ISIZE => 8,
     SEQ   => 9,
     QUAL  => 10,
-    TAG   => 11,
-    VTYPE => 12,
-    VALUE => 13,
 };
 
 
@@ -104,7 +102,9 @@ sub sam2biopiece
     
     # Returns a hashref.
 
-    my ( $record );
+    my ( $record, $i, $tag, $vtype, $value );
+
+    return if $entry->[ RNAME ] eq '*';
 
     $record->{ 'REC_TYPE' } = 'SAM';
     $record->{ 'Q_ID' }     = $entry->[ QNAME ];
@@ -118,9 +118,7 @@ sub sam2biopiece
     $record->{ 'ISIZE' }    = $entry->[ ISIZE ];
     $record->{ 'SEQ' }      = $entry->[ SEQ ];
     $record->{ 'SCORES' }   = $entry->[ QUAL ];
-    $record->{ 'TAG' }      = $entry->[ TAG ];
-    $record->{ 'VTYPE' }    = $entry->[ VTYPE ];
-    $record->{ 'VALUE' }    = $entry->[ VALUE ];
+    $record->{ 'SCORE' }    = sprintf( "%.2f", Maasha::Fastq::phred_str_mean( $entry->[ QUAL ] ) );
 
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG' }  != 0;
     $record->{ 'S_BEG' } -= 1 if $record->{ 'S_BEG2' } != 0;
@@ -145,10 +143,114 @@ sub sam2biopiece
     $record->{ 'READ_FAIL' }      = $record->{ 'FLAG' } & 0x0200;
     $record->{ 'READ_BAD' }       = $record->{ 'FLAG' } & 0x0400;
 
+
+    # extra fields - (hate hate hate SAM!!!)
+    
+    for ( $i = QUAL + 1; $i < @{ $entry }; $i++ )
+    {
+        ( $tag, $vtype, $value ) = split /:/, $entry->[ $i ];
+
+        if ( $tag eq "MD" or $tag eq "NM" ) {
+            $record->{ $tag } = $value;       
+        }
+    }
+
+    if ( defined $record->{ "NM" } and $record->{ "NM" } > 0 ) {
+        $record->{ "ALIGN" } = sam2align( $record->{ 'SEQ' }, $record->{ 'CIGAR' }, $record->{ 'NM' }, $record->{ 'MD' } );
+    } else {
+        $record->{ "ALIGN" } = ".";
+    }
+
     return wantarray ? %{ $record } : $record;
 }
 
 
+sub sam2align
+{
+    my ( $seq,
+         $cigar,
+         $nm,
+         $md,
+       ) = @_;
+
+    # Returns a string.
+
+    my ( $offset, $len, $op, $i, $nt, $nt2, @align, $aln_str );
+
+    $offset = 0;
+
+    while ( length( $cigar ) > 0 )
+    {
+        if ( $cigar =~ s/^(\d+)(\w)// )
+        {
+            $len = $1;
+            $op  = $2;
+
+            if ( $op eq 'I' )
+            {
+                for ( $i = 0; $i < $len; $i++ )
+                {
+                    $nt = substr $seq, $offset + $i, 1;
+
+                    push @align, [ $offset + $i, "->$nt" ];
+
+                    $nm--;
+                }
+            }
+
+            $offset += $len;
+        }
+    }
+    
+    $offset = 0;
+
+    while ( $nm > 0 )
+    {
+        if ( $md =~ s/^(\d+)// )
+        {
+            $offset += $1;
+        }
+        elsif ( $md =~ s/^(\w)// )
+        {
+            $nt = $1;
+
+            $nt2 = substr $seq, $offset, 1;
+
+            push @align, [ $offset, "$nt>$nt2" ];
+
+            $offset++;
+
+            $nm--;
+        }
+        elsif( $md =~ s/^\^// )
+        {
+            $nt = substr $seq, $offset, 1;
+
+            push @align, [ $offset, "$nt>-" ];
+        
+            $offset++;
+
+            $nm--;
+        }
+        else
+        {
+            Maasha::Common::error( qq(Bad SAM field -> MD: "$md") );
+        }
+    }
+
+
+    $aln_str = "";
+
+    @align = sort { $a->[ 0 ] <=> $b->[ 0 ] } @align;
+
+    map { $aln_str .= "$_->[ 0 ]:$_->[ 1 ]," } @align;
+
+    $aln_str =~ s/,$//;
+
+    return $aln_str;
+}
+
+
 sub biopiece2sam
 {