From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 28 Jul 2009 14:00:24 +0000 (+0000)
Subject: changed read_solexa
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=07ad2954f22907a77b58118273f6915c73e9dfa7;p=biopieces.git

changed read_solexa

git-svn-id: http://biopieces.googlecode.com/svn/trunk@605 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 8aeedf9..088f8d6 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -63,7 +63,10 @@ if ( $options->{ 'data_in' } )
     {
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
-            lowercase_low_scores( $record, $options->{ 'quality' } );
+            Maasha::Fastq::lowercase_low_scores( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'quality' } );
+
+            $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
+            $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
 
             Maasha::Biopieces::put_record( $record, $out );
         }
@@ -83,37 +86,6 @@ Maasha::Biopieces::close_stream( $out );
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-sub lowercase_low_scores
-{
-    # Martin A. Hansen, July 2009.
-
-    # Lowercase residues in sequence that are below a given score threshold.
-
-    # This one would be lovely to have written in C.
-
-    my ( $record,    # Biopiece record
-         $quality,   # quality threshold
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( @seqs, @scores, $i );
-
-    @seqs   = split //, $record->{ 'SEQ' };
-    @scores = split /;/, $record->{ 'SCORES' };
-
-    for ( $i = 0; $i < @scores; $i++ ) {
-        $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $quality;
-    }
-
-    $record->{ 'SEQ' }    = join "",  @seqs;
-    $record->{ 'SCORES' } = join ";", @scores;
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
 BEGIN
 {
     Maasha::Biopieces::status_set();
diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index dc5d237..9bb251a 100755
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -28,9 +28,11 @@
 
 use warnings;
 use strict;
+use Data::Dumper;
 use Maasha::Biopieces;
 use Maasha::Filesys;
 use Maasha::Solexa;
+use Maasha::Fastq;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -60,31 +62,23 @@ if ( $options->{ 'data_in' } )
 
     $num = 1;
 
-    if ( $options->{ "format" } eq "octal" )
+    while ( $entry = Maasha::Fastq::get_entry( $data_in ) )
     {
-        while ( $entry = Maasha::Solexa::solexa_get_entry_octal( $data_in ) )
+        if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
-            $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
+            $record->{ 'SCORES' } =~ s/(\d+) ?/Maasha::Fastq::score2phred( $1 )/ge if $options->{ 'format' } eq 'decimal';
+            Maasha::Fastq::solexa2phred( $record->{ 'SCORES' } );
+            Maasha::Fastq::lowercase_low_scores( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'quality' } );
 
-            Maasha::Biopieces::put_record( $record, $out );
-
-            last if $options->{ "num" } and $num == $options->{ "num" };
-
-            $num++;
-        }
-    }
-    else
-    {
-        while ( $entry = Maasha::Solexa::solexa_get_entry_decimal( $data_in ) )
-        {
-            $record = Maasha::Solexa::solexa2biopiece( $entry, $options->{ "quality" } );
+            $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
+            $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
 
             Maasha::Biopieces::put_record( $record, $out );
-
-            last if $options->{ "num" } and $num == $options->{ "num" };
-
-            $num++;
         }
+        
+        last if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
     }
 
     close $data_in;
diff --git a/code_perl/Maasha/Fastq.pm b/code_perl/Maasha/Fastq.pm
index be3c87c..4782486 100644
--- a/code_perl/Maasha/Fastq.pm
+++ b/code_perl/Maasha/Fastq.pm
@@ -36,14 +36,117 @@ use Data::Dumper;
 use Maasha::Calc;
 use vars qw( @ISA @EXPORT );
 
-@ISA = qw( Exporter );
-
 use constant {
     SEQ_NAME => 0,
     SEQ      => 1,
     SCORES   => 2,
 };
 
+@ISA = qw( Exporter );
+
+use Inline ( C => <<'END_C', DIRECTORY => $ENV{ "BP_TMP" } );
+
+int phred2score( char c )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Converts a FASTQ/phred score in octal (a char) to a decimal score, */
+    /* which is returned. */
+
+    /* http://maq.sourceforge.net/fastq.shtml */
+
+    int score = 0;
+
+    score = ( int ) c - 33;
+
+    return score;
+}
+
+
+int solexa2score( char c )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Converts a Solexa score in octal (a char) to a decimal score, */
+    /* which is returned. */
+
+    /* http://maq.sourceforge.net/fastq.shtml */
+    /* $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10); */
+
+    int score = 0;
+    int ascii = ( int ) c - 64;
+
+    score = 10 * log( 1 + pow( 10, ascii / 10 ) ) / log( 10 );
+
+    return score;
+}
+
+
+char score2phred( int score )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Converts a decimal score in decimal to an octal score (a char), */
+    /* which is returned. */
+
+    /* http://maq.sourceforge.net/fastq.shtml */
+
+    char c;
+
+    if ( score <= 93 ) {
+        c = ( char ) score + 33;
+    } else {
+        c = ( char ) 93 + 33;
+    }
+
+//    printf( "score: %d   char: %c\n", score, c );
+
+    return c;
+}
+
+
+void lowercase_low_scores( char *seq, char *scores, int threshold )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Given a sequence string and a score string (in FASTQ/Phread range) */
+    /* lowercases all residues where the decimal score is below a given threshold. */
+
+    int i = 0;
+
+    for ( i = 0; i < strlen( seq ); i++ )
+    {
+        if ( phred2score( scores[ i ] ) < threshold ) {
+            seq[ i ] = tolower( seq[ i ] );
+        }
+    }
+}
+
+
+void solexa2phred( char *scores )
+{
+    /* Martin A. Hansen, July 2009 */
+
+    /* Convert Solexa scores to Phred scores for use with FASTQ format.*/
+
+    int  i     = 0;
+    int  score = 0;
+    char c;
+
+    for ( i = 0; i < strlen( scores ); i++ )
+    {
+        score       = solexa2score( scores[ i ] );
+        c           = score2phred( score );
+
+//        printf( "scores[i]: %c  score: %d  char: %c\n", scores[ i ], score, c );
+
+        scores[ i ] = c;
+    }
+}
+
+
+END_C
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -118,9 +221,6 @@ sub fastq2biopiece
     $record->{ 'SEQ_NAME' }   = $entry->[ SEQ_NAME ];
     $record->{ 'SCORES' }     = $entry->[ SCORES ];
 
-    $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
-    $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
-
     return wantarray ? %{ $record } : $record;
 }
 
diff --git a/code_perl/Maasha/Solexa.pm b/code_perl/Maasha/Solexa.pm
index a26b0ce..fa2764e 100644
--- a/code_perl/Maasha/Solexa.pm
+++ b/code_perl/Maasha/Solexa.pm
@@ -121,7 +121,7 @@ sub solexa_get_entry_decimal
 
     # Returns a list.
 
-    my ( $seq_header, $seq, $score_head, $score, @scores );
+    my ( $seq_header, $seq, $score_head, $score );
 
     $seq_header   = <$fh>;
     $seq          = <$fh>;
@@ -135,11 +135,8 @@ sub solexa_get_entry_decimal
     chomp $score_header;
     chomp $score;
 
-    @scores = split / /, $score;
-
     $seq_header =~ s/^@//;
-
-    $score = join( ";", @scores );
+    $score      =~ s/ /;/g;
 
     return wantarray ? ( $seq_header, $seq, $score ) : [ $seq_header, $seq, $score ];
 }