padmet 5.0.3

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.

PADMet

PADMet is a python library to manage metabolic networks.

Table of contents

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

Description

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

License

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

Requirements

Padmet requires Python. It is tested on Python 3.8 and 3.9 (with GitHub Actions). Due to dependencies (like biopython or docopt) it is recommended to use these versions and not version below 3.8.

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

Installation

Installation with pip

pip install padmet

Use

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.

Entrypoint

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.

Python import

from padmet.utils.connection.pgdb_to_padmet import from_pgdb_to_padmet

padmet_instance = from_pgdb_to_padmet(pgdb_folder, extract_gene=True)

Corresponding functions

script	function to import	command-line
biggAPI_to_padmet	from padmet.utils.connection.biggAPI_to_padmet import biggAPI_to_padmet	padmet biggAPI_to_padmet
check_orthology_input	from padmet.utils.connection.check_orthology_input import check_orthology_input	padmet check_orthology_input
enhanced_meneco_output	from padmet.utils.connection.enhanced_meneco_output import check_orthology_input	padmet enhanced_meneco_output
extract_orthofinder	from padmet.utils.connection.extract_orthofinder import orthogroups_to_sbml	padmet extract_orthofinder
extract_orthofinder	from padmet.utils.connection.extract_orthofinder import orthologue_to_sbml	padmet extract_orthofinder
extract_rxn_with_gene_assoc	from padmet.utils.connection.extract_rxn_with_gene_assoc import extract_rxn_with_gene_assoc	padmet extract_rxn_with_gene_assoc
gbk_to_faa	from padmet.utils.connection.gbk_to_faa import gbk_to_faa	padmet gbk_to_faa
gene_to_targets	from padmet.utils.connection.gene_to_targets import gene_to_targets	padmet gene_to_targets
get_metacyc_ontology	from padmet.utils.connection.get_metacyc_ontology import metacyc_to_ontology	padmet get_metacyc_ontology
metexploreviz_export	from padmet.utils.connection.metexploreviz_export import metexploreviz_export	padmet metexploreviz_export
modelSeed_to_padmet	from padmet.utils.connection.modelSeed_to_padmet import modelSeed_to_padmet	padmet modelSeed_to_padmet
padmet_to_asp	from padmet.utils.connection.padmet_to_asp import padmet_to_asp	padmet padmet_to_asp
padmet_to_matrix	from padmet.utils.connection.padmet_to_matrix import padmet_to_matrix	padmet padmet_to_matrix
padmet_to_padmet	from padmet.utils.connection.padmet_to_padmet import padmet_to_padmet	padmet padmet_to_padmet
padmet_to_tsv	from padmet.utils.connection.padmet_to_tsv import padmet_to_tsv	padmet padmet_to_tsv
pgdb_to_padmet	from padmet.utils.connection.pgdb_to_padmet import from_pgdb_to_padmet	padmet pgdb_to_padmet
sbmlGenerator	from padmet.utils.connection.sbmlGenerator import padmet_to_sbml	padmet sbmlGenerator
sbml_to_curation_form	from padmet.utils.connection.sbml_to_curation_form import sbml_to_curation	padmet sbml_to_curation_form
sbml_to_padmet	from padmet.utils.connection.sbml_to_padmet import sbml_to_padmetSpec	padmet sbml_to_padmet
sbml_to_sbml	from padmet.utils.connection.sbml_to_sbml import from_sbml_to_sbml	padmet sbml_to_sbml
wikiGenerator	from padmet.utils.connection.wikiGenerator import wikiGenerator	padmet wikiGenerator
compare_padmet	from padmet.utils.exploration.compare_padmet import compare_padmet	padmet compare_padmet
compare_sbml	from padmet.utils.exploration.compare_sbml import compare_sbml	padmet compare_sbml
compare_sbml_padmet	from padmet.utils.exploration.compare_sbml_padmet import compare_sbml_padmet	padmet compare_sbml_padmet
convert_sbml_db	from padmet.utils.exploration.convert_sbml_db import map_sbml	padmet convert_sbml_db
dendrogram_reactions_distance	from padmet.utils.exploration.dendrogram_reactions_distance import reaction_figure_creation	padmet dendrogram_reactions_distance
flux_analysis	from padmet.utils.exploration.flux_analysis import flux_analysis	padmet flux_analysis
get_pwy_from_rxn	from padmet.utils.exploration.get_pwy_from_rxn import get_pwy_from_rxn	padmet get_pwy_from_rxn
padmet_stats	from padmet.utils.exploration.padmet_stats import compute_stats	padmet padmet_stats
pathway_production	from padmet.utils.exploration.pathway_production import pathway_production	padmet pathway_production
prot2genome	from padmet.utils.exploration.prot2genome import fromAucome	padmet prot2genome
report_network	padmetSpec.network_report(output_dir, padmetRef_file, verbose)	padmet report_network
visu_network	from padmet.utils.exploration.visu_network import create_compounds_graph	padmet visu_network
visu_path	from padmet.utils.exploration.visu_path import visu_path	padmet visu_path
visu_similarity_gsmn	from padmet.utils.exploration.visu_similarity_gsmn import visu_similarity_gsmn	padmet visu_similarity_gsmn
manual_curation		padmet manual_curation
padmet_compart		padmet padmet_compart
padmet_medium	from padmet.utils.exploration.padmet_medium import manage_medium	padmet padmet_medium
relation_curation	from padmet.utils.exploration.relation_curation import get_relations	padmet relation_curation