Python rebuild of dMLPA-reporting #3
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EKPayne
commented
Oct 18, 2024
EKPayne
commented
- Initial rebuild of the dMLPA-reporting script originally written in R (https://github.com/moka-guys/dMLPA-reporting)
- PDF report generated from HTML and populated using Jinja2
- Includes alternative copy number calling for PMS2
- Error handling added
Adds more detailed information on the input files required.
connection port is changed from string to int.
Split upload directory for probe file and patient files. Created and output directory
This includes: - creation of html report template - parsing test data from results/excel file - converting copy number analysis script to python from original R script in https://github.com/moka-guys/dMLPA-reporting - Generating minimal pdf reports (from html template) per results/excel file - Updating backend.py to create zip of output files rather than of input files
Also corrects mistake of using "mean dosage quotient" as apposed to "dosage quotient" throughout.
Including: - One matplotlib generated graph per gene with identified CNV's - One summary table of probes associated with CNV's per gene.
1) Moving hardcoded elements to config.py 2) Removes generation of probe_df outside of the for loop 3) Updates report with version of app, genome build, warning message if not in production env 4) Adds reporting comment when no copy number variants are detected
- Alternative DQ ranges specified for PMS2 in config.py - Generates a different graph when reporting on PMS2
- Adds PMS2 reporting disclaimer - Adds exon 12 boundary demarcation - Renames categories used for PMS2 CN variants [Issue:]
Resolves conflicts from merging in PMS2_merged_categories
Error handling added: - Files submitted that don't match expected file naming for probe file and results file - Probe file submitted that doesn't meet expected file formatting CN Categories updated to 3dp to account for fact that dq in results file is rounded to 3dp by digital_mlpa script (see https://github.com/moka-guys/digital_mlpa)
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