Skip to content

Bio::Tools::GFF add extra empty attribute problematic #388

Description

@Juke34

When reading such feature:
chr10p ambMex60DD gene 313039 315424 1000 + . gene_id "AMEX60DD000001"; gene_name "ZFP37 [nr]|ZNF568 [hs]";

with GFF parser set to 2 or 2.5 it creates this object:

$VAR1 = bless( {
                 '_primary_tag' => 'gene',
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_parse_h' => {},
                 '_gsf_seq_id' => 'chr10p',
                 '_gsf_tag_hash' => {
                                      'score' => [
                                                   '1000'
                                                 ],
                                      'gene_name' => [
                                                       'ZFP37 [nr]|ZNF568 [hs]'
                                                     ],
                                      'ID' => [
                                                ' '
                                              ],
                                      'gene_id' => [
                                                     'AMEX60DD000001'
                                                   ]
                                    },
                 '_location' => bless( {
                                         '_end' => '315424',
                                         '_start' => '313039',
                                         '_location_type' => 'EXACT',
                                         '_strand' => 1
                                       }, 'Bio::Location::Simple' ),
                 '_gsf_frame' => '.',
                 '_source_tag' => 'ambMex60DD'
               }, 'Bio::SeqFeature::Generic' );

this part is problematic

                                      'ID' => [
                                                ' '
                                              ],

and shouldn't appear as is ti absent from the GFF/GTF feature provided as input

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions