# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Split sequences in the stream into overlapping subsequences.
+# Split sequences in the stream into subsequences.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, $record, $new_record, $i, $inc, $subseq, %lookup );
+my ( $options, $in, $out, $record, $new_record, $i, $step, $subseq, $subqual );
$options = Maasha::Biopieces::parse_options(
[
- { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7, allowed => undef, disallowed => 0 },
- { long => 'non_overlapping', short => 'n', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'uniq', short => 'u', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7, allowed => undef, disallowed => 0 },
+ { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
]
);
+if ( $options->{ "step_size" } > $options->{ "word_size" } ) {
+ Maasha::Common::error( qq(step_size > word_size: $options->{ "step_size" } > $options->{ "word_size" } ) );
+}
+
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-$inc = 1;
-$inc = $options->{ "word_size" } if $options->{ "non_overlapping" };
+$step = $options->{ "step_size" };
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 += $inc )
+ for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i += $step )
{
- $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;
- $new_record->{ "SEQ_LEN" } = $options->{ "word_size" };
-
- 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;
- $new_record->{ "SEQ_LEN" } = $options->{ "word_size" };
-
- Maasha::Biopieces::put_record( $new_record, $out );
- }
+ $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
+ $subqual = substr $record->{ "SCORES" }, $i, $options->{ "word_size" } if $record->{ "SCORES" };
+
+ $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+ $new_record->{ "SEQ" } = $subseq;
+ $new_record->{ "SCORES" } = $subqual if $record->{ "SCORES" };
+ $new_record->{ "SEQ_LEN" } = $options->{ "word_size" };
+
+ Maasha::Biopieces::put_record( $new_record, $out );
}
}
else