package the peptide order form assist scripts (create report and color peptide) into a tool

[mhoang22]

No description provided.

[malachig]

Specifically talking about these steps currently done in a more ad hoc fasion:

bsub -Is -q oncology-interactive -G $GROUP -a "docker(griffithlab/neoang_scripts)" /bin/bash

cd $WORKING_BASE
mkdir ../manual_review

python3 /opt/scripts/generate_reviews_files.py -a ../itb-review-files/*.xlsx -c ../generate_protein_fasta/candidates/annotated_filtered.vcf-pass-51mer.fa.manufacturability.tsv -variants final_results/variants.final.annotated.tsv -classI final_results/pVACseq/mhc_i/*.all_epitopes.aggregated.tsv -classII final_results/pVACseq/mhc_ii/*.all_epitopes.aggregated.tsv -samp $PATIENT_ID -o ../manual_review/

python3 /opt/scripts/color_peptides51mer.py -p ../manual_review/*Peptides_51-mer.xlsx -samp $PATIENT_ID -o ../manual_review/