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Published July 1, 2023 | Version v2.8.3
Software Open

SysBioChalmers/RAVEN: v2.8.3

Authors/Creators

  • 1. Chalmers University of Technology
  • 2. EV Biotech
  • 3. BioInnovation Institute
  • 4. Chr. Hansen
  • 5. @SysBioChalmers
  • 6. Aalto University
  • 7. Gitter
  • 8. KTH Royal Institute of Technology / Science For Life Laboratory

Description

  • fix:

    • checkFunctionUniqueness on Mac/Unix with non-RAVEN paths.
    • checkInstallation find printOrange on new RAVEN installations (closes #492).
    • readYAMLmodel allows for a model that has gene entries that are not present in any grRules: these are unused genes and should be allowed. This also prevents a bug where gene annotations are wrongly assigned.
    • writeYAMLmodel correct parsing of text to avoid escape characters (e.g. SMILES may contain \C).
    • importModel assigns -Inf and Inf if no LB and/or UB values are defined.
    • ravenCobraWrapper makes empty model.c if COBRA model had no c field (is not necessarily made by readCbModel)

  • feat:

    • keggPhylDist.mat includes species names.
    • getMetaCycModelForOrganism input and output of blastStructure (before cutoffs applied), so that function can repeatedly be run with different cutoffs without having to rerun blast/diamond.

Files

SysBioChalmers/RAVEN-v2.8.3.zip

Files (261.0 MB)

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md5:ab2d6c9bcde26d24633de48d1b3fbaed
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Additional details

Related works

Is supplement to
https://github.com/SysBioChalmers/RAVEN/tree/v2.8.3 (URL)