neherlab / pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

Home Page:http://pangenome.de

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xb_xref err

Bruce-BC opened this issue · comments

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.