+use Maasha::Filesys;
+use Maasha::Stockholm;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $num, $entry, $data_in, $record_anno, $key, $seq, $record_align );
+
+$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' },
+ ]
+);
+
+$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::Stockholm::get_stockholm_entry( $data_in ) )
+ {
+ $record = Maasha::Stockholm::parse_stockholm_entry( $entry );
+
+ undef $record_anno;
+
+ foreach $key ( keys %{ $record->{ "GF" } } ) {
+ $record_anno->{ $key } = $record->{ "GF" }->{ $key };
+ }
+
+ $record_anno->{ "ALIGN" } = $num;
+
+ Maasha::Biopieces::put_record( $record_anno, $out );
+
+ foreach $seq ( @{ $record->{ "ALIGN" } } )
+ {
+ undef $record_align;
+
+ $record_align = {
+ SEQ_NAME => $seq->[ 0 ],
+ SEQ => $seq->[ 1 ],
+ };
+
+ Maasha::Biopieces::put_record( $record_align, $out );
+ }
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__