-my ( $options, $in, $out, $record, $data_in, $num, $entry );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
- { long => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, 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 ) ) {
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-if ( $options->{ 'data_in' } )
-{
- $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
-
- $num = 1;
-
- while ( $entry = Maasha::Fastq::get_entry( $data_in ) )
- {
- if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
- {
- lowercase_low_scores( $record, $options->{ 'quality' } );
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- last if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
-}
-
-Maasha::Biopieces::close_stream( $in );
-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;
-}