error while executing panX script (KeyError: 'db_xref').
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14 months ago
Kumar ▴ 50

I have been working with panX. I ran the test dataset without any error. But, while running my genome of interest ( AF391541.1 AY585228.1 AY700211.1 ), I end up with the following error,

dinesh@dineshk:~/Documents/tools/panx/pan-genome-analysis$ sh run-TestSet.sh 
Traceback (most recent call last):
  File "./panX.py", line 256, in <module>
    myPangenome.extract_gbk_sequences()
  File "/home/dinesh/Documents/tools/panx/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/dinesh/Documents/tools/panx/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/dinesh/Documents/tools/panx/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'

To resolve this issue I googled the same and found that this error could be related to python version 2.7, upgradation of python version could solve this issue. Since the tool script itself written in python 2 panX.py script, so I do not know how to resolve this issue. Please help me to resolve this issue. Thanks in advance.

python biopython linux bioinformatics genome • 441 views
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The program specific issues are hard to resolve here because many of the tools are not that popular. Best option is to raise an issue of the respective github repository. I could see similar issue reported here with no solution

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I'm not sure, but I think your input file format is not genebank. Depending on the error, your file may be in fasta format, for example

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