Issues

• bcbio-gff: pkg_resources deprecated

  chapmanb/bcbb#148 · Filter by author 0-wiz-0 opened on Feb 17, 2026

• GFF.parse modifies input order of base_dict

  chapmanb/bcbb#144 · Filter by author percyfal opened on Mar 28, 2024

• Warning in GFFParser: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.

  chapmanb/bcbb#143 · Filter by author victorlin opened on Jan 29, 2024

• Error in GFFParser: AttributeError: module 'Bio.SeqFeature' has no attribute 'SimpleLocation'

  chapmanb/bcbb#142 · Filter by author victorlin opened on Jan 29, 2024

• Error in GFFParser: UnknownSeq is deprecated in biopython 1.81

  chapmanb/bcbb#136 · Filter by author Kmassau opened on Feb 13, 2023
  7

• glimmergff_to_proteins.py / Alternative Codon Table

  chapmanb/bcbb#132 · Filter by author zeyak opened on Sep 18, 2020

• glimmergff_to_proteins.py / Reordering Fasta file

  chapmanb/bcbb#131 · Filter by author zeyak opened on Sep 18, 2020

• IndexError with NCBI gff

  chapmanb/bcbb#128 · Filter by author MrTomRod opened on Dec 5, 2019

• Did not find remapped ID location:

  chapmanb/bcbb#118 · Filter by author fbeghini opened on Jul 10, 2018
  2

• ValueError: need more than 0 values to unpack

  chapmanb/bcbb#115 · Filter by author zhengboying opened on Mar 15, 2018
  1

• Regarding gff2_to_gff3.py script

  chapmanb/bcbb#111 · Filter by author jeffinrockey opened on Sep 21, 2016

• GFF3 parent / id remapping issue.

  chapmanb/bcbb#109 · Filter by author hexylena opened on May 26, 2016
  2

• Missing features in GFF3 data

  chapmanb/bcbb#108 · Filter by author thobalose opened on Feb 9, 2016

• Declare dependency on biopython

  chapmanb/bcbb#105 · Filter by author detrout opened on Dec 9, 2015

• write Dbxref instead of db_xref when converting genbank to GFF3

  chapmanb/bcbb#102 · Filter by author timflutre opened on Oct 26, 2015
  4

• GFF module can write unreadable GFF3 sequences.

  chapmanb/bcbb#99 · Filter by author hexylena opened on May 29, 2015
  1

• CDS entries in GFF3 file are not merged to a CompoundLocation

  chapmanb/bcbb#95 · Filter by author mikdur opened on Jan 14, 2015
  5

• over url-encoding in attribute fields

  chapmanb/bcbb#86 · Filter by author bobbyo opened on Apr 18, 2014
  5