$ python -m fun_proteomics setup --terminal --project ./study --run

fun_proteomics | Set up an analysis

1. Quantification matrix (DIA-NN, FragPipe or service table)
2. DIA-PASEF raw acquisitions
3. DDA-PASEF raw acquisitions
4. Continue an existing run folder
Analysis [1]: 1
Protein matrix (CSV, TSV or XLSX): inputs/proteins.csv
Sample table (sample_id, condition; raw_path for acquisitions): inputs/samples.csv
Matching FASTA for missing gene symbols (optional): 
Service matrix for a detection benchmark (optional): inputs/service.csv
Compare every condition against every other condition? (yes/no) [yes]: yes
Does each sample come from a different patient or biological replicate? (yes/no) [no]: yes
6 independent samples; 3 condition pairs at protein and available gene levels.
10 protein groups; 10 unambiguous genes.
Saved: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/config/run.json
6 independent samples; 3 condition pairs at protein and available gene levels.
10 protein groups; 10 unambiguous genes.
Configuration: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/config/run.json
/tmp/fun-proteomics-wheel-test/bin/python /tmp/fun-proteomics-walkthroughs-v070-final-terminal/workflow-cache/0.7.0-de0507f049fd7446/scripts/analyze_quantification.py --matrix /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/inputs/proteins.csv --samples /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/config/samples.csv --outdir /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/results/final_results --quantity auto --normalization none --fdr 0.05 --min-replicates 2 --differential --service-matrix /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/inputs/service.csv
Results: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/results/final_results/START_HERE.html
Open results: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/START_HERE.html
Open matrices (CSV + TSV): /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/MATRICES.html
$ python -m fun_proteomics --continue ./study
6 independent samples; 3 condition pairs at protein and available gene levels.
10 protein groups; 10 unambiguous genes.
Configuration: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/config/run.json
Completed outputs verified. No analysis needs repeating.
Results: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/results/final_results/START_HERE.html
Open results: /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/START_HERE.html
Open matrices (CSV + TSV): /tmp/fun-proteomics-walkthroughs-v070-final-terminal/terminal-analysis/study/MATRICES.html