Skip to content

Padmet 5.0.0

Choose a tag to compare

View all tags
@ArnaudBelcour ArnaudBelcour released this 26 Oct 14:22
· 94 commits to master since this release
5.0.0
e4385e4

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.
Assets 2
Loading