--- /dev/null
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Calculate the mean or local mean of quality SCORES in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Fastq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'local', short => 'l', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'window_size', short => 'w', type => 'uint', mandatory => 'no', default => 5, allowed => undef, disallowed => 0 },
+ { long => 'min', short => 'm', type => 'float', mandatory => 'no', default => 15, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ 'SCORES' } )
+ {
+ if ( $options->{ "local" } )
+ {
+ $record->{ 'SCORES_LOCAL_MEAN' } = sprintf( "%.2f", Maasha::Fastq::solexa_str_mean_window(
+ $record->{ 'SCORES' },
+ $options->{ 'window_size' },
+ $options->{ 'min' }
+ ) );
+ }
+ else
+ {
+ $record->{ 'SCORES_MEAN' } = sprintf( "%.2f", Maasha::Fastq::solexa_str_mean( $record->{ 'SCORES' } ) );
+ }
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
http://maq.sourceforge.net/fastq.shtml */
+#define BASE_SOLEXA 64
+#define BASE_PHRED 33
+
int phred2dec( char c )
{
int score = 0;
- score = ( int ) c - 33;
+ score = ( int ) c - BASE_PHRED;
return score;
}
int score = 0;
- score = ( int ) c - 64;
+ score = ( int ) c - BASE_SOLEXA;
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. */
-//
-// /* 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 );
-//
-// // printf( "char: %c ascii: %d score: %d\n", c, ascii, score );
-//
-// return score;
-// }
-
-
char dec2phred( int score )
{
/* Martin A. Hansen, July 2009 */
char c = 0;
- c = ( char ) score + 33;
+ c = ( char ) score + BASE_PHRED;
return c;
}
char c = 0;
- c = ( char ) score + 64;
+ c = ( char ) score + BASE_SOLEXA;
return c;
}
}
+double 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 i = 0;
+ 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 ) {
+ return mean;
+ }
+
+ /* --- scan the rest of the scores ---- */
+
+ while ( 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);
+
+ if ( mean < min ) {
+ return mean;
+ }
+
+ i++;
+ }
+
+ return mean;
+}
+
+
void softmask_solexa_str( char *seq, char *scores, int threshold )
{
/* Martin A. Hansen, July 2009 */
projects / biopieces.git / commitdiff