Simplify v2 templates by naming outputs directly

[elenikiachaki]

The current v2 do.sh templates are hard to read because several outputs are produced with generic names and then renamed with mv.

Example path:

MAVISp_downstream_analysis/downstream_analysis_mavisp_templates/new_entry_templates/dotplot_clinvar_v2/do.sh

Current pattern:

python dot_plot_v2.py -i $csv -x 50 -pltD -pltR -pltC benign likely_benign pathogenic likely_pathogenic -vep none -cct germline -v dictionary.csv -o dot_plot_germline
mv mechanistic_indicators_out.csv mechanistic_indicators_out_germline.csv
mv log.txt log_germline.txt
python lolliplot.py -i mechanistic_indicators_out_germline.csv -x 50 -s
mv lolliplot.pdf lolliplot_germline.pdf

The same pattern is repeated for oncogenicity and clinical_impact.

Proposed changes

• In dot_plot_v2.py, name mechanistic_indicators_out.csv and log.txt internally based on -cct, e.g.:

  • mechanistic_indicators_out_germline.csv
  • log_germline.txt
  • mechanistic_indicators_out_oncogenicity.csv
  • log_oncogenicity.txt
  • mechanistic_indicators_out_clinical_impact.csv
  • log_clinical_impact.txt

• In lolliplot.py, add an output prefix flag, e.g. -o lolliplot_germline, so the PDF is written directly as lolliplot_germline.pdf.

Expected simplified template

module load python/3.10/modulefile
csv=$1

# Germline classification results:
python dot_plot_v2.py -i "$csv" -x 50 -pltD -pltR -pltC benign likely_benign pathogenic likely_pathogenic -vep none -cct germline -v dictionary.csv -o dot_plot_germline
python lolliplot.py -i mechanistic_indicators_out_germline.csv -x 50 -s -o lolliplot_germline
python filter_pLDDT.py -i "$csv" -m mechanistic_indicators_out_germline.csv -t 70 -o mech_plddt_germline