Reports

compareVersions(previousFolder, newFolder, reportFolder, microbeID, ncbiID)

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.

INPUT modelPrevious COBRA model structure of older model to compare modelNew COBRA model structure of newer model to compare microbeID Microbe ID in carbon source data file reportFolder Path to folder where report documents should be written

(e.g., ‘C:Reports’)

OPTIONAL INPUT ncbiID Organism NCBI ID

OUTPUT 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

Almut Heinken, Dec 2017, adapted from script reportPDF

printRefinementReport(testResultsFolder, reconVersion)

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

OUTPUT curationReport Summary of results of QC/QA tests

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

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).

INPUT model COBRA model structure 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 INPUT ncbiID Organism NCBI ID

OUTPUT outputFile Name of the output file with report

Stefania Magnusdottir, Nov 2017 Almut Heinken, Sep 2018-adapted nomenclature