New Gene Diagnostic Analysis

models/ecoli/analysis/AnalysisPaths.py

@@ -204,6 +204,15 @@ def get_seeds(self, variant: Optional[int] = None) -> List[int]:
 		mask = self._path_data['variant'] == variant if variant is not None else slice(None)
 		return sorted(np.unique(self._path_data["seed"][mask]))
 
+	def get_generations(self, variant: Optional[int] = None,
+						seed: Optional[int] = None) -> List[int]:
+		"""Return all the generation values for the given variant and seed."""
+		mask = np.logical_or(np.array(self._path_data['variant'] ==
+							 variant if variant is not None else slice(None)),
+							 np.array(self._path_data['seed'] ==
+									seed if seed is not None else slice(None)))
+		return sorted(np.unique(self._path_data["generation"][mask]))
+
 	def get_cell_variant(self, path: str) -> int:
 		"""Return the variant index for the given get_cells() sim path."""
 		return self._path_data['variant'][self._path_index(path)]

models/ecoli/analysis/cohort/__init__.py

@@ -4,9 +4,11 @@
 	"aa_conc.py",
 	"centralCarbonMetabolismCorrelationTimeCourse.py",
 	"centralCarbonMetabolismScatter.py",
+	"complexed_monomer_counts.py",
 	"doubling_times_histogram_all.py",
 	"ecocyc_table.py",
 	"expression_dynamics.py",
+	"free_monomer_counts.py",
 	"growthDynamics.py",
 	"growth_time_series.py",
 	# "proteinFoldChangeVsTranscriptionFrequency.py",
@@ -21,6 +23,7 @@
 	"replisome_rnap_collision_per_gene.py",
 	"rnaCopyNumberDistribution.py",
 	"subgenerational_expression_table.py",
+	"total_monomer_counts.py",
 	# "transcriptFrequency.py",
 	# "transcriptionGenomeCoverage.py",
 	# "transcriptionGenomeCoverageSecondHalf.py",