# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
+my ( $options, $in, $out, $data_in, $num, $entry, $record );
$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' },
- { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'feats', short => 'f', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'quals', short => 'q', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { 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' },
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'features', short => 'f', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'qualifiers', short => 'q', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } };
-map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
-map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
-
while ( $record = Maasha::Biopieces::get_record( $in ) ) {
Maasha::Biopieces::put_record( $record, $out );
}
while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) )
{
- $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
-
- my ( $feat, $feat2, $qual, $qual_val, $record_copy );
-
- $record_copy = dclone $record;
-
- delete $record_copy->{ "FT" };
-
- Maasha::Biopieces::put_record( $record_copy, $out );
-
- delete $record_copy->{ "SEQ" };
-
- foreach $feat ( keys %{ $record->{ "FT" } } )
- {
- $record_copy->{ "FEAT_TYPE" } = $feat;
-
- foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
- {
- foreach $qual ( keys %{ $feat2 } )
- {
- $qual_val = join "; ", @{ $feat2->{ $qual } };
-
- $qual =~ s/^_//;
- $qual = uc $qual;
-
- $record_copy->{ $qual } = $qual_val;
- }
-
- Maasha::Biopieces::put_record( $record_copy, $out );
- }
- }
+ map { Maasha::Biopieces::put_record( $_, $out ) } Maasha::EMBL::embl2biopieces( $entry, $options );
last if $options->{ "num" } and $num == $options->{ "num" };