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" } );
+
+/*
+About Phred or FASTQ format:
+
+This format is an adaption of the fasta format that contains quality scores.
+However, the fastq format is not completely compatible with the fastq files
+currently in existence, which is read by various applications (for example,
+BioPerl). Because a larger dynamic range of quality scores is used, the
+quality scores are encoded in ASCII as 64+score, instead of the standard
+32+score. This method is used to avoid running into non-printable characters.
+
+
+About Solexa or SCARF format:
+
+SCARF (Solexa compact ASCII read format)—This easy-to-parse text based format,
+stores all the information for a single read in one line. Allowed values are
+--numeric and --symbolic. --numeric outputs the quality values as a
+space-separated string of numbers. --symbolic outputs the quality values as a
+compact string of ASCII characters. Subtract 64 from the ASCII code to get the
+corresponding quality values. Under the current numbering scheme, quality
+values can theoretically be as low as -5, which has an ASCII encoding of 59=';'.
+
+See also:
+
+http://maq.sourceforge.net/fastq.shtml */
+
+#define BASE_SOLEXA 64
+#define BASE_PHRED 33
+
+
+int phred2dec( char c )
+{
+ /* Martin A. Hansen, July 2009 */
+
+ /* Converts a Phred score in octal (a char) to a decimal score, */
+ /* which is returned. */
+
+ int score = 0;
+
+ score = ( int ) c - BASE_PHRED;
+
+ return score;
+}
+
+
+int solexa2dec( char c )
+{
+ /* Martin A. Hansen, July 2009 */
+
+ /* Converts a Solexa score in octal (a char) to a decimal score, */
+ /* which is returned. */
+
+ int score = 0;
+
+ score = ( int ) c - BASE_SOLEXA;
+
+ return score;
+}
+
+
+char dec2phred( int score )
+{
+ /* Martin A. Hansen, July 2009 */
+
+ /* Converts a decimal score to an octal score (a char) in the Phred range, */
+ /* which is returned. */
+
+ char c = 0;
+
+ c = ( char ) score + BASE_PHRED;
+
+ return c;
+}
+
+
+char dec2solexa( int score )
+{
+ /* Martin A. Hansen, September 2009 */
+
+ /* Converts a decimal score to an octal score (a char) in the Solexa range, */
+ /* which is returned. */
+
+ char c = 0;
+
+ c = ( char ) score + BASE_SOLEXA;
+
+ return c;
+}
+
+
+char solexa2phred( char score )
+{
+ /* Martin A. Hansen, September 2009 */
+
+ /* Converts an octal score in the Solexa range to an octal score */
+ /* in the Pred range, which is returned. */
+
+ int dec = 0;
+ char c = 0;
+
+ dec = solexa2dec( score );
+ c = dec2phred( c );
+
+ return c;
+}
+
+
+char phred2solexa( char score )
+{
+ /* Martin A. Hansen, September 2009 */
+
+ /* Converts an octal score in the Solexa range to an octal score */
+ /* in the Pred range, which is returned. */
+
+ int dec = 0;
+ char c = 0;
+
+ dec = phred2dec( score );
+ c = dec2solexa( c );
+
+ return c;
+}
+
+
+void solexa_str2phred_str( char *scores )
+{
+ /* Martin A. Hansen, September 2009 */
+
+ /* Converts a string of Solexa octal scores to Phred octal scores in-line. */
+
+ int i = 0;
+
+ for ( i = 0; i < strlen( scores ); i++ ) {
+ scores[ i ] = solexa2phred( scores[ i ] );
+ }
+}
+
+
+void phred_str2solexa_str( char *scores )
+{
+ /* Martin A. Hansen, September 2009 */
+
+ /* Converts a string of Phred octal scores to Solexa octal scores in-line. */
+
+ int i = 0;
+
+ 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;
+}
+
+
+double solexa_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 += solexa2dec( scores[ i ] );
+ }
+
+ mean = ( double ) sum / ( double ) len;
+
+ return mean;
+}
+
+
+void solexa_str_mean_window( char *scores, int window_size, double min )
+{
+ /* Martin A. Hansen, June 2010. */
+
+ /* Scans a score string by running a sliding window across */
+ /* the string and for each position calculate the mean score */
+ /* for the window. Terminates and returns mean score if this */
+ /* is lower than a given minimum otherwise the smallest mean */
+ /* score is returned. */
+
+ int found = 0;
+ int i = 0;
+ int pos = -1;
+ double sum = 0;
+ double mean = 0.0;
+
+ if ( window_size > strlen( scores ) )
+ {
+ fprintf( stderr, "ERROR: window_size > scores string: %d > %d\n\n", window_size, strlen(scores) );
+ exit( 1 );
+ }
+
+ /* ---- fill up window ---- */
+
+ for ( i = 0; i < window_size; i++ ) {
+ sum += solexa2dec( scores[ i ] );
+ }
+
+ mean = sum / window_size;
+
+ if ( mean <= min ) {
+ found = 1;
+ pos = 0;
+ }
+
+ /* --- scan the rest of the scores ---- */
+
+ while ( ! found && i < strlen( scores ) )
+ {
+ sum += solexa2dec( scores[ i ] );
+ sum -= solexa2dec( scores[ i - window_size ] );
+
+ mean = ( mean < sum / window_size ) ? mean : sum / window_size;
+
+ // printf( "char->%c score->%d sum->%f mean->%f\n", scores[i], solexa2dec(scores[i]),sum, mean);
+
+ i++;
+
+ if ( mean <= min ) {
+ found = 1;
+ pos = i - window_size;
+ }
+ }
+
+ Inline_Stack_Vars;
+ Inline_Stack_Reset;
+
+ Inline_Stack_Push( sv_2mortal( newSViv( mean ) ) );
+ Inline_Stack_Push( sv_2mortal( newSViv( pos ) ) );
+
+ Inline_Stack_Done;
+}
+
+
+void softmask_solexa_str( char *seq, char *scores, int threshold )
+{
+ /* Martin A. Hansen, July 2009 */
+
+ /* Given a sequence string and a score string (in Solexa range) */
+ /* lowercases all residues where the decimal score is below a given threshold. */
+
+ int i = 0;
+
+ for ( i = 0; i < strlen( seq ); i++ )
+ {
+ if ( solexa2dec( scores[ i ] ) < threshold ) {
+ seq[ i ] = tolower( seq[ i ] );
+ }
+ }
+}
+
+
+void softmask_phred_str( char *seq, char *scores, int threshold )
+{
+ /* Martin A. Hansen, July 2009 */
+
+ /* Given a sequence string and a score string (in Phred range) */
+ /* lowercases all residues where the decimal score is below a given threshold. */
+
+ int i = 0;
+
+ for ( i = 0; i < strlen( seq ); i++ )
+ {
+ if ( phred2dec( scores[ i ] ) < threshold ) {
+ seq[ i ] = tolower( seq[ i ] );
+ }
+ }
+}
+
+
+int trim_left( char *scores, int min )
+{
+ /* Martin A. Hansen, June 2010 */
+
+ /* Starting from the left in a score string, */
+ /* locate the position when the score is above */
+ /* a given min.*/
+
+ int pos = 0;
+
+ while ( pos < strlen( scores ) && solexa2dec( scores[ pos ] ) <= min ) {
+ pos++;
+ }
+
+ return pos;
+}
+
+
+int trim_right( char *scores, int min )
+{
+ /* Martin A. Hansen, June 2010 */
+
+ /* Starting from the right in a score string, */
+ /* locate the position when the score is above */
+ /* a given min.*/
+
+ int len = strlen( scores );
+ int pos = len;
+
+ while ( pos > 0 && solexa2dec( scores[ pos ] ) <= min ) {
+ pos--;
+ }
+
+ if ( pos == 0 ) {
+ pos = len;
+ }
+
+ return pos;
+}
+
+END_C
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+sub solexa_str2dec_str
+{
+ # Martin A. Hansen, September 2009
+
+ # Converts a string of Solexa octal scores to a ; separated
+ # string of decimal scores.
+
+ my ( $scores, # Solexa scores
+ ) = @_;
+
+ # Returns a string.
+
+ $scores =~ s/(.)/ solexa2dec( $1 ) . ";"/eg;
+
+ return $scores;
+}
+
+
+sub phred_str2dec_str
+{
+ # Martin A. Hansen, September 2009
+
+ # Converts a string of Phred octal scores to a ; separated
+ # string of decimal scores.
+
+ my ( $scores, # Phred scores
+ ) = @_;
+
+ # Returns a string.
+
+ $scores =~ s/(.)/ phred2dec( $1 ) . ";"/eg;
+
+ return $scores;
+}
+
+
+sub dec_str2solexa_str
+{
+ # Martin A. Hansen, May 2010.
+
+ # Converts a ; separated string of decimal scores to a
+ # string of Solexa octal scores.
+
+ my ( $scores, # Decimal score string
+ ) = @_;
+
+ # Returns a string.
+
+ $scores =~ s/(-\d{1,2})/0/g;
+ $scores =~ s/(\d{1,2});?/dec2solexa( $1 )/eg;
+
+ return $scores;
+}
+
+sub dec_str2phred_str
+{
+ # Martin A. Hansen, November 2013.
+
+ # Converts a ; separated string of decimal scores to a
+ # string of Phred scores.
+
+ my ( $scores, # Decimal score string
+ ) = @_;
+
+ # Returns a string.
+
+ $scores =~ s/(-\d{1,2})/0/g;
+ $scores =~ s/(\d{1,2});?/dec2phred( $1 )/eg;
+
+ return $scores;
+}
+
sub get_entry
{
# Martin A. Hansen, July 2009.
# Converts a FASTQ entry to a Biopiece record, where
# the FASTQ quality scores are converted to numerics.
- my ( $entry, # FASTQ entry,
+ my ( $entry, # FASTQ entry,
) = @_;
# Returns a hash.
$record->{ 'SEQ' } = $entry->[ SEQ ];
$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' } ] ) );
+ $record->{ 'SEQ_LEN' } = length $entry->[ SEQ ];
return wantarray ? %{ $record } : $record;
}
projects / biopieces.git / blobdiff