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TESTS

Tests 1: iSanXoT report from mouse heteroplasmia (heart)

1. NMpyCompare

python 1_NMpyCompare/NMpyCompare.py \
  -i tests/heteroplasmic_heart/inputs/isanxot_report_q2all_pdm.tsv \
  -c tests/heteroplasmic_heart/inputs/params.yml \
  -o tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM.tsv

2. ReportLimma

Rscript --vanilla 2_ReportLimma_wo_GUI/app_wo_GUI.R \
  -i tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM.tsv \
  -c tests/heteroplasmic_heart/inputs/params.yml \
  -s tests/heteroplasmic_heart/inputs/limma_comparisons.tsv \
  -o tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM_LIMMA.tsv

3. FDRoptimizer

python 3_FDRoptimizer/FDRoptimizer.py \
  -i tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM_LIMMA.tsv \
  -c tests/heteroplasmic_heart/inputs/params.yml \
  -o tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM_LIMMA_FDR.tsv

4. PTMMap

python 4_PTMMap/PTMMap.py \
  -i tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM_LIMMA_FDR.tsv \
  -c tests/heteroplasmic_heart/inputs/params.yml \
  -o tests/heteroplasmic_heart/results/PTMMaps/H-C

5. qTableReport

python 5_qTableReport/qReportMaker.py \
  -i tests/heteroplasmic_heart/results/isanxot_report_q2all_pdm_NM_LIMMA_FDR.tsv \
  -q tests/heteroplasmic_heart/inputs/myMitocarta.tsv \
  -p tests/heteroplasmic_heart/results/PTMMaps \
  -c tests/heteroplasmic_heart/inputs/params.yml \
  -o tests/heteroplasmic_heart/results/qReports