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Alan-Collins / CRISPR_comparison_toolkit

Tools to analyze the differences and similarities between CRISPR arrays
GNU General Public License v3.0
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Update blast.py #2

Closed cganote closed 1 year ago

cganote commented 1 year ago

There's a \ on line 617 that adds a literal \ in front of the patterns for genome name. When I print all_assemblies_dict.items(), I see: Found \AML2_cluster_001_consensus, <cctkpkg.file_handling.AssemblyCRISPRs object at 0x2b9da84c61f0> Running cctk blast gives me: Traceback (most recent call last): File "/N/slate/cganote/apis/CRISPR_comparison_toolkit/CRISPR_comparison_toolkit/cctk_blast/../cctk", line 168, in main() File "/N/slate/cganote/apis/CRISPR_comparison_toolkit/CRISPR_comparison_toolkit/cctk_blast/../cctk", line 157, in main blast.main(args) File "/N/slate/cganote/apis/CRISPR_comparison_toolkit/CRISPR_comparison_toolkit/cctkpkg/blast.py", line 664, in main assembly = all_assemblies_dict[array.genome] KeyError: 'AML2_cluster_001_consensus'

I think you won't need the \ and it runs ok when I removed it.

Alan-Collins commented 1 year ago

Thanks for catching that! I swear I added that '/' for a reason. I remember that not escaping the % character caused an issue, but now I can't recreate it.