+use Maasha::Common;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'percent', short => 'p', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$count = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "SEQ" } )
+ {
+ for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
+ {
+ $res = substr $record->{ "SEQ" }, $i, 1;
+
+ $freq_hash{ $i }{ $res }++;
+ $res_hash{ $res } = 1;
+ }
+
+ $count++;
+ }
+ else
+ {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+foreach $res ( sort keys %res_hash )
+{
+ undef $record;
+
+ $record->{ "V0" } = $res;
+
+ for ( $i = 0; $i < keys %freq_hash; $i++ )
+ {
+ $freq = $freq_hash{ $i }{ $res } || 0;
+
+ if ( $options->{ "percent" } ) {
+ $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0;
+ }
+
+ $record->{ "V" . ( $i + 1 ) } = $freq;
+ }
+
+ 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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+