+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $new_record, $i, $subseq, %lookup );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7, allowed => undef, disallowed => 0 },
+ { long => 'uniq', short => 'u', type => 'flag', mandatory => 'no', default => undef, 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->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i++ )
+ {
+ $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
+
+ if ( $options->{ "uniq" } and not $lookup{ $subseq } )
+ {
+ $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+ $new_record->{ "SEQ" } = $subseq;
+
+ Maasha::Biopieces::put_record( $new_record, $out );
+
+ $lookup{ $subseq } = 1;
+ }
+ else
+ {
+ $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+ $new_record->{ "SEQ" } = $subseq;
+
+ Maasha::Biopieces::put_record( $new_record, $out );
+ }
+ }
+ }
+ else
+ {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+ Maasha::Biopieces::close_stream( $in );
+ Maasha::Biopieces::close_stream( $out );
+
+ $run_time_end = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__