Check existence of InPreD_clinical_data_file when generating RNA_ori_name in PRONTO.py

InPreD / PRONTO

rePort geneRator fOr iNpred Tumor bOards

GNU General Public License v3.0

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Check existence of InPreD_clinical_data_file when generating RNA_ori_name in PRONTO.py #6

Closed tinavisnovska closed 8 months ago

tinavisnovska commented 9 months ago

The script crashes when both DNA and RNA samples are provided and InPreD_clinical_data_file does not exist.

A condition checking for InPreD_clinical_data_file existence could resolve the issue. It can be added somewhere nearby one of the following two locations:

line 349: definiton of get_RNA_ori_name line 1060: usage of get_RNA_ori_name

tinavisnovska commented 8 months ago

The issue here was that RNA sample was postprocessed but info about its existence was not filled in the InPreD_clinical_data_file and it got resolved when the RNA sample info was added into the metadata file