Reports

compareVersions(previousFolder, newFolder, reportFolder, microbeID, ncbiID)[source]

Compares the test functions in a previous and a new version of AGORA and writes a report of the differences in a .tex file. Writes a PDF using pdf2latex.

USAGE:

[outputFile, outputSummary, onlyInNewModel, onlyInPreviousModel] = compareVersions (previousFolder, newFolder, reportFolder, microbeID, ncbiID)

INPUTS:

  • previousFolder – Folder with COBRA models of the previous reconstruction version to compare, each saved as a file named after its microbeID

  • newFolder – Folder with COBRA models of the new reconstruction version to compare, each saved as a file named after its microbeID

  • reportFolder – Path to folder where report documents should be written (e.g., ‘C:Reports’)

  • microbeID – Microbe ID in carbon source data file

OPTIONAL INPUTS:

ncbiID – Organism NCBI ID

OUTPUTS:

  • outputFile – Name of the output file with report

  • outputSummary – Summary of results in matfile format

  • onlyInNewModel – Reactions/metabolites/genes only in new model

  • onlyInPreviousModel – Reactions/metabolites/genes only in previous model

printRefinementReport(testResultsFolder, reconVersion)[source]

This function prints a report of the results of the DEMETER test suite ran on the reconstructs refined in the present project.

USAGE:

curationReport = printRefinementReport (testResultsFolder, reconVersion)

INPUTS:

  • testResultsFolder – Folder where the test results are saved

  • reconVersion – Name of the refined reconstruction project

OUTPUTS:

curationReport – Summary of results of QC/QA tests

reportPDF(model, microbeID, biomassReaction, inputDataFolder, reportFolder, ncbiID)[source]

Runs all test functions and writes a report in a .tex file. Writes a PDF using pdf2latex. Requires a LaTex installation, e.g. MiKTex (https://miktex.org/download) and pdftex (https://ctan.org/pkg/pdftex).

USAGE:

outputFile = reportPDF (model, microbeID, biomassReaction, inputDataFolder, reportFolder, ncbiID)

INPUTS:

  • model – COBRA model structure with fields:

    • .rxns - Reaction identifiers

    • .mets - Metabolite identifiers

    • .genes - Gene identifiers

  • microbeID – Microbe ID in carbon source data file

  • biomassReaction – Model biomass reaction

  • inputDataFolder – Folder with experimental data and database files to load

  • reportFolder – Path to folder where report documents should be written (e.g., ‘C:Reports’)

OPTIONAL INPUTS:

ncbiID – Organism NCBI ID

OUTPUTS:

outputFile – Name of the output file with report