microberx.DataFiles

This is a module that provides functions to load and process data for the MicrobeRX tool.

The module requires the following packages: pandas, importlib_resources

The module contains the following functions:

  • load_reaction_rules: Load the reaction rules from a compressed tab-separated file.

  • load_human_evidences: Load the human evidences from a compressed tab-separated file.

  • load_microbes_evidences: Load the microbes evidences from a compressed tab-separated file.

  • load_microbes_reactions: Load the microbes reactions from a compressed tab-separated file.

  • load_microbes_data: Load the microbes data from a compressed tab-separated file.

Functions

load_reaction_rules()

Load the reaction rules from a compressed tab-separated file.

load_evidences()

Load the human evidences from a compressed tab-separated file.

load_microbes_reactions()

Load the microbes reactions from a compressed tab-separated file.

load_microbes_data()

Load the microbes data from a compressed tab-separated file.

Module Contents

microberx.DataFiles.load_reaction_rules()[source]

Load the reaction rules from a compressed tab-separated file.

Returns:

A dataframe containing the reaction rules, with columns:

  • num_atoms : Number of atoms to match in the query to perfom a prediction.

  • rule : SMARTS string of the single reactant reaction rule (SRRR).

  • reaction_id : Reaction_id in unified MetaNetX v4.0 id or AGORA2.

  • substrate : MetaNetX id of the Real subtrate of the SRRR.

  • substrate_map : Atom mappeed SMARTS of the of the Real subtrate of the SRRR.

  • product : MetaNetX id of the Main real subtrate of the SRRR.

  • product_map : Atom mappeed SMARTS of Main real product of the SRRR.

Return type:

pandas.DataFrame

microberx.DataFiles.load_evidences()[source]

Load the human evidences from a compressed tab-separated file.

Returns:

A dataframe containing the human evidences, with columns:

  • source : The unique identifier of the source coming from the metabolic reconstruction.

  • name : Name of the biotransformations, can match with enzyme name.

  • ec : Enzyme Commission number for the biotransformation.

  • mnx_id : Unified id from MetaNetX v4.0.

  • organisms_count : Number of organims where this souce id has been found.

  • xrefs : coss-references to other reaction databases.

  • origin : Tells if the reaction is coming from human or gut microbes.

  • complexes_count : Numer of genes or complexes found in the metabolic network for this biotransformation.

Return type:

pandas.DataFrame

microberx.DataFiles.load_microbes_reactions()[source]

Load the microbes reactions from a compressed tab-separated file.

Returns:

A dataframe containing the microbes reactions.

  • index: strain name of all gut microbes included in microbeRX (source: AGORA2).

  • columns : source name of biotransformation from the metabolic reconstructions.

  • data : any cell contains information about the genes or complexes that have been annotated for each organims and biotransformation.

Return type:

pandas.DataFrame

microberx.DataFiles.load_microbes_data()[source]

Load the microbes data from a compressed tab-separated file.

Returns:

A dataframe containing the microbes data, with columns:

  • microbe_name

  • Strain

  • Species

  • Genus

  • Family

  • Order

  • Class

  • Phylum

  • Kingdom

  • Host

  • NCBI Taxonomy ID

  • Cultured

  • Ecosystem

  • Ecosystem Category

  • Ecosystem Subtype

  • Ecosystem Type

  • Gram Staining

  • Oxygen Requirement

  • Motility

Return type:

pandas.DataFrame