Open Juke34 opened 7 months ago
When reading such feature: chr10p ambMex60DD gene 313039 315424 1000 + . gene_id "AMEX60DD000001"; gene_name "ZFP37 [nr]|ZNF568 [hs]";
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
@Juke34 we can address this but can't commit to a timeline. If you know the specific fix we also (gladly!) accept pull requests.
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:
this part is problematic
and shouldn't appear as is ti absent from the GFF/GTF feature provided as input