v2.4.1

Main improvements in this release:

• Updating database files:
  • corrected capitalization of metBiGGID field for RAVEN <-> COBRA model conversion. This included modifications for functions ravenCobraWrapper, standardizeModelFieldOrder and file COBRA_structure_fields.csv. (PR #299)
  • updated function ravenCobraWrapper and COBRA_structure_fields.csv, cobraNamespaces.csv files according to the latest COBRA model structure (PR #313)
• Features:
  • getModelFromHomology: added a feature to retain homologous genes from template and target species (PR #301)
  • exportForGit: implemented more flexible folder selection with subDirs flag to write all files in one folder or model-specific subfolders (PR #303)
  • updateDocumentation: a newly added function for automatic HTML documents generation for RAVEN functions (PR #304)
  • getMetaCycModelForOrganism: added a check for the existence of query FASTA file under current path (PR #307)
  • randomSampling: added an option to set minFlux to 1 during each solveLP run. This allows removing loops in each sample. (PR #308)
  • addMets: implemented more flexible input when only one metabolite is added or metNames is not specified (PR #308)
  • writeYaml: added a preserveQuotes flag that defaults to true to ensure an export for a YAML compatible file. All mets/rxns are now stored within quotes and COBRApy's function load_yaml_model can properly load the model with no errors. (PR #309)
  • setColorToMapRxns; setOmicDataToRxns: newly added functions complementing for yeastGemMap manuscript (under review) (PR #314)
• Fixes:
  • ravenCobraWrapper: added a compatibility for COBRA models which come with non-unique metabolite ids after removing the compartment info, as it is common with BiGG models (PR #302)
  • importModel: COBRA's function writeCbModel adds M_ prefix to modelID. Unlikely that such prefix is meant to be included in model.id, M_ prefix is now removed when importing SBML file. (PR #303)
  • parseHPA; parseHPArna: added a compatibility with Human Protein Atlas (HPA), version 19 (PR #312)
• Code refactoring:
  • getIndexes: more informative error message (PR #308)
  • parseHPArna: reduced the amount of repeated code and separated the pieces that actually differ between Human Protein Atlas (HPA) versions (PR #312)
• Format changes:
  • removed authorship and timestamps from all RAVEN functions, as git blame and similar functionalities are better ways to keep track of code authorship. Also, exportToTabDelimited no longer writes a fake author in the output file if no author is provided in the model structure. (PR #300)