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Bio::Tools::GFF: empty group tag hash #82

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Jan Teichmann (Jan Teichmann) Original Redmine Issue: 3087, https://redmine.open-bio.org/issues/3087 Original Date: 2010-05-28 Original Assignee: Bioperl Guts

hi there, I’m using Bio::Tools::GFF to parse a GFF file version 2 from the mirbase homepage:

gff-version 2

date 2010-04-22

#

  1. Chromosomal coordinates of Homo sapiens microRNAs
  2. miRNA data: miRBase Sequence (version 15)
  3. Genome assembly: GRCh37 # 1 . miRNA 30366 30503 . + . ACC=“MI0006363”; ID=“hsa-mir-1302-2”; 1 . miRNA 1102484 1102578 . + . ACC=“MI0000342”; ID=“hsa-mir-200b”; 1 . miRNA 1103243 1103332 . + . ACC=“MI0000737”; ID=“hsa-mir-200a”;

and unfortunately, I can’t access the group field. The hash created by $feat->add_tag_value($key, $value); from the _from_gff2_string() function is empty and the functions like get_all_tags() don’t return anything.

Kind regards, Jan

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2010-05-28T09:28:38Z

Changing to core components (Bio::Tools::GFF is not part of Bio::FeatureIO)