IndexError with NCBI gff #128
Description
Hi!
I annotated a bacterium (Acidipropionibacterium acidipropionici - strain FAM19036) with NCBI PGAP.
I wanted to create SeqIO-objects from the gff file, but it failed:
import pprint
from BCBio import GFF
from BCBio.GFF import GFFExaminer
examiner = GFFExaminer()
with open('data/FAM19036/annot.gff') as in_handle:
pprint.pprint(examiner.available_limits(in_handle))
print("------------------------------------------------------------")
with open('FAM19036/annot.gff') as in_handle:
for rec in GFF.parse(in_handle):
print(rec){'gff_id': {('CP040634.1',): 6772},
'gff_source': {('.',): 3361,
('GeneMarkS-2+',): 360,
('Local',): 1,
('Protein Homology',): 2916,
('cmsearch',): 24,
('tRNAscan-SE',): 110},
'gff_source_type': {('.', 'exon'): 8,
('.', 'gene'): 3208,
('.', 'pseudogene'): 137,
('.', 'rRNA'): 8,
('GeneMarkS-2+', 'CDS'): 360,
('Local', 'region'): 1,
('Protein Homology', 'CDS'): 2916,
('cmsearch', 'RNase_P_RNA'): 1,
('cmsearch', 'SRP_RNA'): 1,
('cmsearch', 'exon'): 7,
('cmsearch', 'rRNA'): 4,
('cmsearch', 'riboswitch'): 10,
('cmsearch', 'tmRNA'): 1,
('tRNAscan-SE', 'exon'): 55,
('tRNAscan-SE', 'tRNA'): 55},
'gff_type': {('CDS',): 3276,
('RNase_P_RNA',): 1,
('SRP_RNA',): 1,
('exon',): 70,
('gene',): 3208,
('pseudogene',): 137,
('rRNA',): 12,
('region',): 1,
('riboswitch',): 10,
('tRNA',): 55,
('tmRNA',): 1}}
------------------------------------------------------------
Error
Traceback (most recent call last):
File "/usr/lib64/python3.7/unittest/case.py", line 59, in testPartExecutor
yield
File "/usr/lib64/python3.7/unittest/case.py", line 628, in run
testMethod()
File "/project/gene_loci_comparison/test_gene_loci_comparison.py", line 129, in test_recreate_gff_bug
for rec in GFF.parse(in_handle):
File "/project/venvs/gene_loci_comparison/lib64/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 746, in parse
target_lines):
File "/project/venvs/gene_loci_comparison/lib64/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 327, in parse_in_parts
cur_dict = self._results_to_features(cur_dict, results)
File "/project/venvs/gene_loci_comparison/lib64/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 369, in _results_to_features
base = self._add_directives(base, results.get('directive', []))
File "/project/venvs/gene_loci_comparison/lib64/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 388, in _add_directives
val = (val[0], int(val[1]) - 1, int(val[2]))
IndexError: tuple index out of range
To recreate the bug, here is the relevant gff file.
Thanks in advance.
Edit: bcbio-gff version 0.6.6