CovertLab/wcEcoli

9 analysis scripts confound multiple daughters with multiple generations

1fish2 opened this issue · 0 comments

Running:

DESC="2-gen" N_GENS=2 python runscripts/fw_queue.py

will queue up a 2-generation simulation including both daughter cells of the 2nd generation:

Queueing Variant 0
  Queueing Seed 0
    Queueing Gen 00.
      Queueing Cell 0
    Queueing Gen 01.
      Queueing Cell 0
      Queueing Cell 1

When running the fireworks, the following analysis scripts confound the multiple daughters with multiple generations, raising IndexError: index 2 is out of bounds for axis 0 with size 2:

multigen/proteinAvgCountVsBurstSize.py: line 134, in do_plot
    monomerExistMultigen[gen_idx,:] = monomerExist
multigen/proteinCountVsFoldChange.py: line 134, in do_plot
    monomerExistMultigen[gen_idx,:] = monomerExist
multigen/proteinExistVsBurstSize.py: line 131, in do_plot
    monomerExistMultigen[gen_idx,:] = monomerExist
multigen/proteinFoldChangeVsRnaDeg.py: line 131, in do_plot
    ratioFinalToInitialCountMultigen[gen_idx,:] = ratioFinalToInitialCount
multigen/proteinFoldChangeVsTranscriptionEvents.py: line 128, in do_plot
    ratioFinalToInitialCountMultigen[gen_idx,:] = ratioFinalToInitialCount
multigen/proteinFoldChangeVsTranslationEff.py: line 132, in do_plot
    monomerExistMultigen[gen_idx,:] = monomerExist
multigen/proteinMassFractionFoldChange.py: line 150, in do_plot
    monomerExistMultigen[gen_idx,:] = monomerExist

Queueing instead:

DESC="2-gen 2-sim" N_GENS=2 N_INIT_SIMS=2 python runscripts/fw_queue.py

will do likewise, and additionally the cohort analyses proteinCopyNumberDistribution and rnaCopyNumberDistribution will raise the IndexError exception. Those analyses only run for simulations with multiple seeds.