ddG parsing error
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While running pipeline stepwise, ran into an undefined variable error when calling the ddG parser (parser_ddg_v2):
called: python3 /groups/sbinlab/haagenb/repository/PRISM/software/rosetta_ddG_pipeline/parser_ddg_v2.py 1PGA_relaxed A MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE /lustre/hpc/sbinlab/lgood/benchmark_Rosetta/pipeline_test/run/ddG/run/legacy_unopt /lustre/hpc/sbinlab/lgood/benchmark_Rosetta/pipeline_test/run/ddG/output /lustre/hpc/sbinlab/lgood/benchmark_Rosetta/pipeline_test/run/prepare/cleaning/structure_input_A.json
output: ...{printed dict of all variants and three ddG scores} 'E56P': [-257.658, -257.658, -257.658], 'E56Q': [-273.089, -273.089, -273.089], 'E56R': [-266.044, -266.044, -266.044], 'E56S': [-267.88, -267.88, -267.88], 'E56T': [-266.493, -266.493, -266.493], 'E56V': [-267.251, -267.251, -267.251], 'E56W': [-262.073, -262.166, -262.073], 'E56Y': [-261.583, -261.583, -261.583]} Traceback (most recent call last): File "/groups/sbinlab/haagenb/repository/PRISM/software/rosetta_ddG_pipeline/parser_ddg_v2.py", line 89, in <module> parse_rosetta_ddgs(sys_name=sys.argv[1], chain_id=sys.argv[2], fasta_seq=sys.argv[3], ddG_run=sys.argv[4], ddG_output=sys.argv[5], structure_input=sys.argv[6]) File "/groups/sbinlab/haagenb/repository/PRISM/software/rosetta_ddG_pipeline/parser_ddg_v2.py", line 53, in parse_rosetta_ddgs join(path_to_run_folder, rosetta_summary_file), fasta_seq)) File "/lustre/hpc/sbinlab/haagenb/repository/PRISM/software/rosetta_ddG_pipeline/parse_cartesian_functions.py", line 53, in rosetta_cartesian_read return cartesian_scores,var NameError: name 'var' is not defined
If the parser run into an a position with an error (For example, if the job was cancelled due to walltime) it will give an error. I will look into making a more robust solution for this
should be resolved due to the rerun-checks added in the last version of the pipeline