-my ( $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $entry, $chunk, @lines, $line, $s_id, $type, $s_beg, $s_end, $strand, @fields, $def,
- @commands, $command );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'full', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- ]
-);
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-$tmp_dir = Maasha::Biopieces::get_tmpdir();
-$tmp_file = "$tmp_dir/tmp.seq";
-$fh_out = Maasha::Filesys::file_write_open( $tmp_file );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
- Maasha::Fasta::put_entry( $entry, $fh_out );
- }
-
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-close $fh_out;
-
-push @commands, "-c" if $options->{ 'full' };
-push @commands, "< $tmp_file > $tmp_file.out";
-push @commands, "2> /dev/null" unless $options->{ 'verbose' };
-
-$command = join " ", @commands;
-
-Maasha::Common::run( "prodigal", $command );
-
-$fh_in = Maasha::Filesys::file_read_open( "$tmp_file.out" );
-
-$/ = "//\n";