Add modelSummary, walkFluxes, traceFluxPath#660
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modelSummary (queries/): COBRApy-style model overview — prints model dimensions, objective, and when a flux vector is supplied, the objective value and exchange fluxes partitioned into uptake and secretion. walkFluxes (analysis/): interactive CLI flux navigator. Starting from a chosen reaction, shows all flux-carrying neighbours grouped by shared metabolite. The user steps to any neighbour by number; a history stack supports going back with 'b'. Useful for manually tracing how flux flows through the network without knowing the full topology. traceFluxPath (analysis/): finds the highest-flux-fraction path between two reactions. At each metabolite junction flux is split proportionally among consuming reactions; the path maximising the cumulative fraction is returned via best-first search. Returns pathRxns, pathMets, cumFrac and prints an annotated one-line path with per-junction percentages.
Function test results211 tests 190 ✅ 37s ⏱️ Results for commit d07e8ca. ♻️ This comment has been updated with latest results. |
col = model.S(:,j) is sparse, so col(m) is a sparse scalar; cellfun cannot collect sparse values into a double array. full() converts it before multiplication so the cell stores a plain double.
model.S is sparse, so col(m) and row(n) yield sparse scalars. fprintf/sprintf reject sparse inputs; arithmetic propagates the sparsity. Convert column/row extractions from model.S to full arrays at the point of extraction so all downstream math is dense.
- Add gene-protein-reaction rules (grRules) to the reaction header - Always show a reaction number, even when the same reaction appears under multiple metabolites; drop the "(same as #N)" cross-reference line - Label each neighbour as 'produces' or 'consumes' relative to the shared metabolite, making flux direction immediately readable - Simplify metabolite header: drop "here" and the redundant sign; show absolute net flux magnitude alongside consumed/produced - Rewrite prompt to explicit action labels (1-N: step, b: back, q: quit) - Skip metabolites with net flux below cutoff to avoid zero-flux noise - Apply full() to S column/row extractions to avoid sparse-scalar errors
By default (traceMaterial=true) the path search now skips common currency
and cofactor metabolites (ATP/ADP, NAD/NADH, CoA, H2O, Pi, CO2, redox
carriers, …) so the returned path represents carbon-skeleton flow rather
than energy-carrier shortcuts.
Three new name-value parameters:
traceMaterial (default true) — enable the built-in currency exclusion
carbonOnly (default false) — additionally require C≥1 from metFormulas
excludeMets (default {}) — user-supplied additions to the list
The exclusion is applied at metabolite-selection time in the best-first
search, so ATP→ADP shortcuts are simply never explored. When no material
path exists the verbose output suggests trying traceMaterial=false.
Bare comment-only lines inside a {} literal act as row separators in MATLAB,
creating a ragged cell array that fails vertcat when rows have different
element counts. Replaced section-header comments inside the cell with
inline comments after ... on data lines.
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Summary
Three new analysis functions for exploring and summarising flux distributions:
modelSummary(model)— COBRApy-inspired model overview: prints dimensions, objective definition, and — when a flux vector is supplied — the objective value plus uptake/secretion tables for all active exchange reactionswalkFluxes(model, fluxes, startRxn)— interactive command-line flux navigator: shows flux-carrying reactions connected through shared metabolites, grouped by metabolite with role labels; type a number to step,bto go back,qto quittraceFluxPath(model, fluxes, fromRxn, toRxn)— best-first search for the highest-flux-fraction path between two reactions; returnspathRxns,pathMets, andcumFracAll three use
parseRAVENargsfor name-value argument handling. Tests added intQueries(modelSummaryNoFluxRuns,modelSummaryWithFluxRuns) andtAnalysis(traceFluxPathReturnsCells,traceFluxPathSameReactionIsIdentity).