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neherlab / pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration
http://pangenome.de
GNU General Public License v3.0
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xb_xref err #36

Open Bruce-BC opened 4 years ago

Bruce-BC commented 4 years ago

Hi, What I am reporting is still ongoing issue since I noticed a few months ago. I attached system log below.

Traceback (most recent call last): File "/home/Program/pan-genome-analysis/panX.py", line 256, in myPangenome.extract_gbk_sequences() File "/home/Program/pan-genome-analysis/scripts/pangenome_computation.py", line 128, in extract_gbk_sequences extract_sequences(self.path, self.strain_list, self.folders_dict, self.gbk_present, self.enable_RNA_clustering) File "/home/Program/pan-genome-analysis/scripts/sf_extract_sequences.py", line 156, in extract_sequences gene_aa_dict, gene_na_dict, RNA_dict, enable_RNA_clustering) File "/home/Program/pan-genome-analysis/scripts/sf_extract_sequences.py", line 58, in gbk_translation locus_tag=feature.qualifiers['db_xref'][0].split(':')[1] KeyError: 'db_xref'

I analyzed the log and arguments, it has to be changed like

locus_tag = contig.features[0].qualifiers['db_xref'][0].split(":")[1]

Please check it out and update it. Thanks.