Dev

[ArnaudBelcour]

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.
• 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.