List index out of range interpreting serotype 39 result

[CarmenSheppard]

Analysing mash screen tsv for 709775 serotype 39 type strain:

Analysing mash screen output. Traceback (most recent call last): File "/home/carmen.sheppard/gitrepository/PneumoCaT2/pneumocat2.py", line 80, in <module> main(args, version) File "/home/carmen.sheppard/gitrepository/PneumoCaT2/pneumocat2.py", line 38, in main run_parse(analysis, tsvfile) File "/phengs/hpc_storage/home/carmen.sheppard/gitrepository/PneumoCaT2/run_scripts/run_stage1.py", line 160, in run_parse group_check(filtered_df, analysis.database) File "/phengs/hpc_storage/home/carmen.sheppard/gitrepository/PneumoCaT2/run_scripts/run_stage1.py", line 92, in group_check stage1_result = list(get_pheno_list(results, session)) File "/phengs/hpc_storage/home/carmen.sheppard/gitrepository/PneumoCaT2/run_scripts/run_stage1.py", line 34, in get_pheno_list out_res.append(pheno[0][0]) IndexError: list index out of range

[CarmenSheppard]

Error in database - no serotype hit for 39 - match to phenotype was 38 hence no hits. . Added catch and CtvdbError:

Traceback (most recent call last):
File "", line 1, in
File "/home/phe.gov.uk/carmen.sheppard/.pycharm_helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
pydev_imports.execfile(filename, global_vars, local_vars) # execute the script
File "/home/phe.gov.uk/carmen.sheppard/.pycharm_helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/pneumocat2.py", line 80, in
main(args, version)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/pneumocat2.py", line 38, in main
run_parse(analysis, tsvfile)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 164, in run_parse
group_check(filtered_df, analysis.database)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 96, in group_check
stage1_result = list(get_pheno_list(results, session))
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 40, in get_pheno_list
raise CtvdbError(f"No phenotype found for hit {hit} check CTVdb integrity")
exceptions.CtvdbError: CtvdbError: No phenotype found for hit 39 check CTVdb integrity

Update to CTVdb to be done shortly to fix issue.

[CarmenSheppard]

Database fixed in development - merge to master.