Properties¶
- computeFluxConsistentReactionPresence(modelFolder, propertiesFolder, reconVersion)[source]¶
This function extracts the presence of flux consistent reactions for a resource of reconstructions that were refined through the semi-automatic refinement pipeline (1 = present in the flux consistent submodel, 0 = not present in the flux consistent submodel).
- USAGE
computeFluxConsistentReactionPresence(modelFolder,propertiesFolder,reconVersion)
INPUTS modelFolder Folder with COBRA models to be analyzed propertiesFolder Folder where the retrieved reaction presences will
be stored (default: current folder)
reconVersion Name assigned to the reconstruction resource
AUTHOR
Almut Heinken, 12/2020
- computeInternalMetaboliteProduction(modelFolder, propertiesFolder, reconVersion, metList, numWorkers)[source]¶
This function extracts all metabolites that could be produced internally by at least one refined reconstruction in the tested reconstruction resource. Disregards whether the metabolite can be transported.
- USAGE
computeInternalMetaboliteProduction(modelFolder,propertiesFolder,reconVersion,numWorkers)
INPUTS modelFolder Folder with reconstructions to be analyzed propertiesFolder Folder where the retrieved uptake and secretion
potential will be stored (default: current folder)
- reconVersion Name assigned to the reconstruction resource
(default: “Reconstructions”)
- metList List of VMH IDs of metabolites to analyze (default:
all metabolites in reconstruction resource)
numWorkers Number of workers in parallel pool (default: 0)
AUTHORS
Almut Heinken, 11/2020
- computeMetabolicDistance(propertiesFolder, reconVersion, numWorkers)[source]¶
This function computes the Jaccard distance for each pairwise combination of analysed strains in terms of reaction presence and metabolite uptake and secretion potential.
- USAGE
computeMetabolicDistance(propertiesFolder,reconVersion)
INPUTS propertiesFolder Folder where the reaction presences and uptake/secretion
potentials to be analysed are stored
reconVersion Name assigned to the reconstruction resource
AUTHOR
Almut Heinken, 07/2020
- computeModelProperties(refinedFolder, infoFilePath, reconVersion, varargin)[source]¶
Part of the DEMETER pipeline. This function analyzes and plots various properties of the refined and optionally the draft reconstructions. Note that this may be time-consuming.
- USAGE
propertiesFolder = computeModelProperties (refinedFolder, infoFilePath, reconVersion, varargin)
REQUIRED INPUTS refinedFolder Folder with refined COBRA models to analyze infoFilePath File with information on reconstructions to refine reconVersion Name of the refined reconstruction resource
(default: “Reconstructions”)
OPTIONAL INPUTS numWorkers Number of workers in parallel pool (default: 2) translatedDraftsFolder Folder with draft COBRA models with translated
nomenclature and stored as mat files
- customFeatures Features other than taxonomy to cluster microbes
by. Need to be a table header in the file with information on reconstructions.
- computeReconstructionFeatures(translDraftsFolder, refinedFolder, propertiesFolder, reconVersion, numWorkers)[source]¶
This function prints a comparison of basic reconstruction features of the draft and refined reconstructions for the refined reconstruction resource.
- USAGE
computeReconstructionFeatures(translDraftsFolder,refinedFolder,propertiesFolder,reconVersion,numWorkers)
INPUTS translDraftsFolder Folder with translated draft reconstructions refinedFolder Folder with refined reconstructions to be analyzed propertiesFolder Folder where the computed stochiometric and flux
consistencies will be stored
reconVersion Name assigned to the reconstruction resource numWorkers Number of workers in parallel pool
AUTHOR
Almut Heinken, 07/2020
- computeUptakeSecretion(modelFolder, propertiesFolder, reconVersion, metList, numWorkers)[source]¶
This function extracts all metabolites that could be consumed or secreted by at least one refined reconstruction in the tested reconstruction resource.
- USAGE
computeUptakeSecretion(modelFolder,propertiesFolder,reconVersion,metList,numWorkers)
INPUTS modelFolder Folder with reconstructions to be analyzed propertiesFolder Folder where the retrieved uptake and secretion
potential will be stored (default: current folder)
reconVersion Name assigned to the reconstruction resource metList List of VMH IDs of metabolites to analyze (default:
all metabolites in reconstruction resource)
numWorkers Number of workers in parallel pool (default: 0)
AUTHORS
Almut Heinken, 06/2020
- extractReconstructionResourceSubset(modelFolder, infoFilePath, subHeader, subFeature, subsetFolder)[source]¶
Extracts a subset of a reconstruction resource (e.g., AGORA) that shares a certain feature (e.g., belonging to a particular taxon. Requires providing a table containing the information based on which the subset should be extracted.
- USAGE
[extractedSubset,subsetFolder] = extractReconstructionResourceSubset (modelPath, infoFilePath, subHeader, subFeature, subsetFolder)
REQUIRED INPUTS modelFolder Path to folder with reconstruction resource from which
the subset should be retrieved
- infoFilePath Path to text or spreadsheet file with information on
each reconstruction in the resource (e.g., ‘AGORA_infoFile.xslx’)
- subHeader Name of column header in the information table which
contains the feature by which the subset should be extracted (e.g., ‘Phylum’)
- subFeature Name of the feature by which the subset should be
extracted (e.g., ‘Bacteroidetes’)
OPTIONAL INPUTS subsetFolder Path to folder in which the subset of reconstructions
should be saved (Default: ‘extractedModels’)
OUTPUTS extractedSubset List of IDs of reconstructions in the extracted subset subsetFolder Path to folder in which the subset of reconstructions
is located
- getReactionMetabolitePresence(modelFolder, propertiesFolder, reconVersion, numWorkers)[source]¶
This function extracts the presence of reactions and metabolites for a resource of reconstructions that were refined through the semi-automatic refinement pipeline (1 = present, 0 = not present).
- USAGE
getReactionMetabolitePresence(modelFolder,propertiesFolder,reconVersion)
INPUTS modelFolder Folder with COBRA models to be analyzed propertiesFolder Folder where the retrieved reaction presences will
be stored (default: current folder)
reconVersion Name assigned to the reconstruction resource
AUTHOR
Almut Heinken, 06/2020
- getSubsystemPresence(propertiesFolder, reconVersion)[source]¶
This function extracts the presence of subsystems for a resource of reconstructions that were refined through the semi-automatic refinement pipeline. Shown is the fraction of total reactions in each subsystem for each reconstruction in the resource. Requires the function getreactionPresenceOnTaxonLevels to be run first.
- USAGE
getSubsystemPresence(propertiesFolder,reconVersion)
INPUTS Folder with COBRA models to be analyzed propertiesFolder Folder where the retrieved subsystem presences will
be stored (default: current folder)
reconVersion Name assigned to the reconstruction resource
AUTHOR
Almut Heinken, 11/2020
- plotMetaboliteProducersConsumers(propertiesFolder, infoFilePath, reconVersion, varargin)[source]¶
This function creates plots of strains that can consume or secrete a given list of metabolites. Plots are created on the strain level (each reconstruction separately) and, if taxonomical information is provided, on the species, genus, family, order, class, and phylum level.
- USAGE
plotMetaboliteProducersConsumers(propertiesFolder,infoFilePath,reconVersion,varargin)
INPUTS propertiesFolder Folder where computed uptake and secretion profiles
are stored
- infoFilePath Path to spreadsheet with taxonomical information of
the refined strains
reconVersion Name assigned to the reconstruction resource OPTIONAL INPUTS metsToAnalyze Table with list of metabolites that should be
analyzed (default: all computed metabolites)
- metCategory Name for type of metabolites to analyze that should
be in the plots (Default: ‘Metabolites’)
AUTHOR
Almut Heinken, 07/2020
- predictGrowthRequirements(model)[source]¶
Predicts growth requirements for a genome-scale reconstruction. The list of predicted essential exchanges as well as a model constrained with these exchanges are returned.
INPUT model COBRA model structure biomassReaction String listing the biomass reaction
OUTPUT growthOnMinimalMedium Bool if growth on defined medium yes or no essentialExchanges Exchanges that need to be open to enable growth constrainedModel Model constrained with predicted essential
exchanges
Almut Heinken, November 2020
- printReconstructionContent(modelFolder, propertiesFolder, reconVersion, numWorkers)[source]¶
This function creates text files containing all reactions and metabolites in the reconstruction resource.
- USAGE
printReconstructionContent(modelFolder,propertiesFolder,reconVersion,numWorkers)
INPUTS modelFolder Folder with reconstructions to be printed propertiesFolder Folder where the computed stochiometric and flux
consistencies will be stored
reconVersion Name assigned to the reconstruction resource numWorkers Number of workers in parallel pool
AUTHOR
Almut Heinken, 07/2020
- producetSNEPlots(propertiesFolder, infoFilePath, reconVersion, customFeatures)[source]¶
This function plots reaction presence and uptake and secretion potential by taxon with t-SNE.
- USAGE
producetSNEPlots(propertiesFolder,infoFilePath,reconVersion)
INPUTS propertiesFolder Folder where the reaction presences and uptake and
secretion potential to be analyzed are stored (default: current folder)
- infoFilePath Path to spreadsheet with taxonomical information of
the refined strains
reconVersion Name assigned to the reconstruction resource OPTIONAL INPUT customFeatures Features other than taxonomy to cluster microbes
by. Need to be a table header in the file with information on reconstructions.
AUTHOR
Almut Heinken, 06/2020
- rankFeaturesByIncidence(propertiesFolder, reconVersion)[source]¶
This function counts the incidence of a number of features in the refined reconstruction resource and ranks them from most to least common.
- USAGE
rankFeaturesByIncidence(curatedFolder,propertiesFolder,reconVersion)
INPUTS propertiesFolder Folder where the analyzed features are stored and
the results will be stored (default: current folder)
reconVersion Name assigned to the reconstruction resource
AUTHOR
Almut Heinken, 07/2020
- summarizeFeaturesOnTaxonLevels(propertiesFolder, infoFilePath, reconVersion, customFeatures)[source]¶
This function summarizes calculated features of the reconstruction resource, if taxonomical information is provided, on the species, genus, family, order, class, and phylum level. A custom feature (.e.g, gram status, source of the strains) can also be used to summarize the data. In this case, the spreadsheet with strain information needs to contain a column with this information.
- USAGE
summarizeFeaturesOnTaxonLevels(propertiesFolder,infoFilePath,reconVersion,customFeatures)
INPUTS Folder with COBRA models to be analyzed propertiesFolder Folder where the retrieved reaction presences will
be stored (default: current folder)
- infoFilePath Path to spreadsheet with taxonomical information of
the refined strains
reconVersion Name assigned to the reconstruction resource OPTIONAL INPUT customFeatures Features other than taxonomy to cluster microbes
by. Need to be a table header in the file with information on reconstructions.
AUTHOR
Almut Heinken, 06/2020