https://github.com/aureme/padmet - Padmet 5.0.3

Fix

• issue in GitHub CI.

- Python
Published by ArnaudBelcour over 1 year ago

https://github.com/aureme/padmet - 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 pgdbtopadmet.

Fix

• Bug in --enhance functionality from pgdbtopadmet, 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 enhancedmenecooutput.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).

- Python
Published by ArnaudBelcour over 1 year ago

https://github.com/aureme/padmet - Padmet 5.0.1

Fix

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

- Python
Published by ArnaudBelcour over 5 years ago

https://github.com/aureme/padmet - 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: visunetwork.py, visupath.py and visusimilaritygsmn.py.
• Script to create ontology from MetaCyc.
• Extraction of protein sequence find by exonerate in prot2genome.
• Option to pgdbtopadmet 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 pgdbtopadmet.
• Multiprocessing in compare_padmet.
• An option to create a file for frompgdbtopadmet in pgdbto_padmet.
• Input and output compounds to pathway in pgdbtopadmet.
• Getter for Relation.
• Output folder for padmet_stats.

Fix

• Dependencies for padmet are now flexible (>=) instead of being fixed (==).
• Consistency in padmettopadmet ';' to ','.
• Issue in padmettotsv when there is no padmetRef file.
• Error when trying to create node label in dendrogramreactionsdistance.py.
• Issue with pgdbtopadmet (complex with compounds/classes/RNAs).
• Issue in pgdbtopadmet not taking into account attributes with " - ".
• Issue in padmettopadmet when merging the same reaction but with different directions.
• Issue with biopython >= 1.78 in gbktofaa.
• 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 fluxbalanceanalysis.
• 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 dendrogramreactionsdistance.py.
• Rename .csv extension into .tsv because we only use tab delimiter.
• Regex for SBML ID.
• Replace `present' in comparepadmet and comapresbml 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.

- Python
Published by ArnaudBelcour over 5 years ago