Padmet 5.0.3

Fix

• issue in GitHub CI.

Padmet 5.0.2

Add

• Add getter for pathway with reactions.
• Add metexploreviz_export script.
• Add script to create input for GNN from padmet or sbml.
• Add pathway_production in padmet exploration.
• Implement adding uniprot ids refs from protein-seq-ids-reduced-70.dat file in pgdb_to_padmet.

Fix

• Bug in --enhance functionality from pgdb_to_padmet, reaction IDs were put in dicOfNode instead of reactant IDs (issue #12). Add a test to check this.
• Check if output file is writable for sbmlGenerator.
• Fix issue with pvclust dendrogram using old reactions.tsv.
• Fix an issue with multiprocessing in prot2genomes.
• Fix numerous issues in visualisation scripts.
• Fix doc building.

Modification

• Replace setup.py and setup.cfg by pyproject.toml.
• Extract inchi from PGDB.
• Update enhanced_meneco_output.py: add json + reactions options argument to consider json meneco output format and be able to extract other set of reactions than union (intersection, minimal, essential).

Padmet 5.0.1

Fix

• An issue in setup.py with PyPI and GitHub Actions.

Padmet 5.0.0

Padmet has now an entrypoint padmet to use all the padmet.utils scripts with the corresponding subcommand. More information in the readme.

Add

• Continuous Integration by using GitHub Actions.
• New visualization scripts: visu_network.py, visu_path.py and visu_similarity_gsmn.py.
• Script to create ontology from MetaCyc.
• Extraction of protein sequence find by exonerate in prot2genome.
• Option to pgdb_to_padmet to keep self-producing reactions.
• The possibility to create newick file from pvclust dendrogram.
• An option to keep temporary files in prot2genomes.
• Misc in padmet Node about spontaneous reactions to keep them in pgdb_to_padmet.
• Multiprocessing in compare_padmet.
• An option to create a file for from_pgdb_to_padmet in pgdb_to_padmet.
• Input and output compounds to pathway in pgdb_to_padmet.
• Getter for Relation.
• Output folder for padmet_stats.

Fix

• Dependencies for padmet are now flexible (>=) instead of being fixed (==).
• Consistency in padmet_to_padmet ';' to ','.
• Issue in padmet_to_tsv when there is no padmetRef file.
• Error when trying to create node label in dendrogram_reactions_distance.py.
• Issue with pgdb_to_padmet (complex with compounds/classes/RNAs).
• Issue in pgdb_to_padmet not taking into account attributes with " - ".
• Issue in padmet_to_padmet when merging the same reaction but with different directions.
• Issue with biopython >= 1.78 in gbk_to_faa.
• Numerous typos.

Modification

• Refactor padmet creation by implementing the instantiate_padmet function and the padmet/classes/instantiation.py script.
• Completely rewrite compare_sbml to be able to compare multiple sbml files.
• Better error message for menetools in flux_balance_analysis.
• Update readme and docs.
• Update cobra dependency to 0.17.1 and fix issue with old function of cobra.
• Replace intervene and upset graph by supervenn in dendrogram_reactions_distance.py.
• Rename .csv extension into .tsv because we only use tab delimiter.
• Regex for SBML ID.
• Replace `present' in compare_padmet and comapre_sbml by 1 (or 0).

Optimization

• Use a region - 10000 and + 10000 around the match query of tBlastn to use exonerate on it instead of using the all contig.
• Try to reduce the number of Orthologues files analysed in extract_orthofinder.py.