PADMet is a python library to manage metabolic networks.

• PADMet
  • Table of contents
  • Description
  • License
  • Requirements
  • Installation
    • Installation with pip
  • Use
    • Entrypoint
    • Python import
    • Corresponding functions

The PADMet package allows conciliating genomics and metabolic network information used to produce a genome-scale constraint-based metabolic model within a database that traces all the reconstruction process steps. It allows representing the metabolic model in the form of a Wiki containing all the used/traced information. Other standard outputs are made available with the package.

The main concept underlying PADMet-Package is to provide solutions that ensure the consistency, the internal standardization and the reconciliation of the information used within any workflow that combines several tools involving metabolic networks reconstruction or analysis. The PADMet package is at the core of the AuReMe workflow, dedicated to the primary reconstruction of genome-scale metabolic networks from raw data. It allows the study of organisms for which few experimental data are available. Its main feature is to undergo the reconstruction of the metabolic network by combining several heterogeneous knowledge and data sources, including the information reported by several scaffold metabolic networks for cousin species.

If you use PADMet, please cite the following article:

Aite, M., Chevallier, M., Frioux, C., Trottier, C., Got, J., Cortés, M. P., Mendoza, S. N., Carrier, G., Dameron, O., Guillaudeux, N., Latorre, M., Loira, N., Markov, G. V., Maass, A., and Siegel, A. (2018). Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models. PLOS Computational Biology, 14(5), e1006146. https://doi.org/10.1371/journal.pcbi.1006146

This project is licensed under the GNU GPL-3.0-or-later, see the LICENSE.md file for details.

Padmet requires Python. It is tested on Python 3.6, 3.7 and 3.8 (with GitHub Actions). Due to dependencies (like biopython or docopt) it is recommended to use these versions and not version below 3.6.

If you use pip to install padmet, you should check that you have a version of setuptools >= 46.4.0. Version before the 46.4.0 will cause issue with how the padmet/init.py file is written. In this file, we have the version number with variable __version__ and 2 imports of padmet subfolder. In version before the 46.4.0, setuptools will search for __version__ in __init__.py but it will also use the import in this file. So if you use a pip install with this version, the package that will be installed by pip will be imported before being installed leading to an import error (it is explained in the point 1 of the versioning page of python).

To avoid this issue, if you have a version of setuptools < 46.4.0 you should upgrade setuptools with pip install --upgrade setuptools.

Padmet classes scripts (handling PADMet format) and most of the padmet utils scripts require:

• biopython to handle fasta files.
• cobra to handle sbml files and make Flux Balance Analysis.
• docopt for the command-line.
• lxml to handle XML file.
• python-libsbml to handle sbml files.

These 5 dependencies are installed with padmet.

For the padmet utils scripts (to use the PADMet format and the command-line):

• seaborn to create data visualization.
• matplotlib to create data visualization.
• networkx for network analysis (in visu_* scripts).
• igraph for network analysis (in visu_* scripts).
• tzlocal: required by rpy2.
• rpy2 to interface R and Python.
• scipy to create dendrogram (in dendrogram_reactions_distance).
• pandas to use dataframe of reaction presence/asbence.
• sklearn to visualize similarity between metabolic networks using MDS.
• gevent to handle issue when downloading files (in biggAPI_to_padmet).
• requests to download files (in biggAPI_to_padmet).
• grequests to asynchronously download files (in biggAPI_to_padmet).
• supervenn to create Venn diagram of reactions between multiple organisms (in dendrogram_reactions_distance).

Contrary to the 5 first depedencies, you have to install these packages with a pip install if you want to use them.

Scripts that need to install one of these optional dependencies:

• biggAPI_to_padmet.py: gevent, requests and grequests
• dendrogram_reactions_distance.py: matplotlib, seaborn, scipy, supervenn, rpy2 (with 'ape' and 'pvclust'), tzlocal and pandas
• visu_network.py: python-igraph
• visu_path.py: matplotlib, networkx and seaborn
• visu_similarity_gsmn.py: matplotlib, pandas and scikit-learn

pip install padmet

PADMet can be used either with an entrypoint (padmet -h) or by making an import in python (import padmet).

There is a documentation in construction.

usage:
    padmet <command> [<args>...]

options:
    -h --help     Show help.
    -v     Verbose.

The subcommands are:

utils:
    gbr    Extract 'AND' and 'OR' from gene string

connection:
    biggAPI_to_padmet    Create PADMet file from BIGG API
    check_orthology_input    Check proteomes for AuReMe
    check_orthology_input    Check proteomes for AuReMe
    enhanced_meneco_output    Extract meneco output and add reaction informations
    extract_orthofinder    Extract result from OrthoFinder and creates SBML outputs
    extract_rxn_with_gene_assoc    Extract from a SBML the reactions with gene association
    gbk_to_faa    Extract the proteome from a genbank file
    gene_to_targets    From a list of genes and a PADMet extract the targets linked to each gene
    get_metacyc_ontology    From a PADMet Ref file of MetaCyc create an XML ontology file
    metexploreviz_export    Create a metexploreviz JSON to visualize metabolic network from padmet or sbml
    modelSeed_to_padmet    Create a PADMet file from modelSeed reactions and pathways files
    padmet_to_asp    Convert PADMet to ASP
    padmet_to_matrix    Create a a stoichiometry matrix from a PADMet file
    padmet_to_padmet    Merge multiple PADMets into one PADMet file
    padmet_to_tsv    Convert a PADMet file into AskOmics compatible tsv files
    pgdb_to_padmet    Create PADMet from dat files
    sbml_to_curation    Extract reaction(s) from SBML file into an AuReMe compatible form
    sbml_to_padmet    Convert a SBML file into a PADMet file
    sbml_to_sbml    Convert a SBML file into another SBML (level change)
    sbmlGenerator    Create a SBML file using a PADMet file
    wikiGenerator    Create Wiki files using a PADMet file

exploration:
    compare_padmet    Compare n PADMet files
    compare_sbml    Compare n SBML files
    compare_sbml_padmet    Compare a SBML file with a PADMet file
    convert_sbml_db    Use MetaNetX to convert a SBML from one database to another database
    dendrogram_reactions_distance    Create a reaction absence/presence dendrogram using reactions.tsv file (from compare_padmet)
    flux_analysis    Run Flux Balance Analysis on a defined reaction
    get_pwy_from_rxn    Return Pathway using a list of reactions from a PADMet Ref file
    padmet_stats    Compute stats on a PADMet file
    pathway_production    Show the input/output of pathways from multiple PADMet
    prot2genome    Perfoms the structural annotation of AuCoMe
    report_network    Creates reports for a PADMet file
    visu_network    Allows to visualize a PADMet or SBML network
    visu_path    Allows to visualize a pathway in PADMet network
    visu_similarity_gsmn    Visualize similarity between metabolic networks using MDS

management:
    manual_curation    Update a PADMet Spec by filling specific forms
    padmet_compart    For a given PADMet file, check and update compartment
    padmet_medium    For a given set of compounds, create 2 reactions for each compounds to maintain consistency of the network for flux analysis.
    relation_curation    Manually curate PADMet relation

See 'padmet <command> -h' for more information on a specific command.

from padmet.utils.connection.pgdb_to_padmet import from_pgdb_to_padmet

padmet_instance = from_pgdb_to_padmet(pgdb_folder, extract_gene=True)