PADMet is a python library to manage metabolic networks.
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 3.8 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
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)| 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 |