Command Line Interface

Napistu CLI

The main Napistu CLI provides commands for data ingestion, integration, consensus building, and more.

Main Command

napistu

The Napistu CLI

Usage

napistu [OPTIONS] COMMAND [ARGS]...

consensus

Command line tools to create a consensus model from SBML_dfs

Usage

napistu consensus [OPTIONS] COMMAND [ARGS]...

check

Check a consensus model for potential issues

Usage

napistu consensus check [OPTIONS] SBML_DFS_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

create

Create a consensus model from a list of SBML_dfs

Usage

napistu consensus create [OPTIONS] [SBML_DFS_URIS]... OUTPUT_MODEL_URI

Options

-n, --nondogmatic: Run in non-dogmatic mode (trying to merge genes and proteins)?

--ignore-mergeability: Ignore issues which will prevent merging across models

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URIS: Optional argument(s)

OUTPUT_MODEL_URI: Required argument

exporter

Command line tools to export a consensus model to various formats

Usage

napistu exporter [OPTIONS] COMMAND [ARGS]...

export_napistu_graph

Export the consensus model as an igraph object

Usage

napistu exporter export_napistu_graph [OPTIONS] SBML_DFS_URI OUTPUT_URI

Options

-a, --graph_attrs_spec_uri <graph_attrs_spec_uri>: File specifying reaction and/or species attributes to add to the graph

-f, --format <format>: Output format: gml, edgelist, pickle

-g, --wiring_approach <wiring_approach>: bipartite or regulatory

-w, --weighting_strategy <weighting_strategy>: Approach to adding weights to the network

-d, --directed <directed>: Directed or undirected graph?

-r, --reverse <reverse>: Reverse edges so they flow from effects to causes?

-x, --drop_reactions_when <drop_reactions_when>

When to drop reactions as network vertices: ‘same_tier’ (default), ‘edgelist’, or ‘always’

Options:: same_tier | edgelist | always

--deduplicate_edges: Deduplicate edges so 0-1 edges connect each vertex.

Arguments

SBML_DFS_URI: Required argument

OUTPUT_URI: Required argument

export_precomputed_distances

Export precomputed distances for the igraph object

Usage

napistu exporter export_precomputed_distances [OPTIONS] GRAPH_URI OUTPUT_URI

Options

-f, --format <format>: Input igraph format: gml, edgelist, pickle

-s, --max_steps <max_steps>: The max number of steps between pairs of species to save a distance

-q, --max_score_q <max_score_q>: Retain up to the “max_score_q” quantiles of all scores (small scores are better)

-p, --partition_size <partition_size>: The number of species to process together when computing distances

-w, --weight_vars <weight_vars>: One or more variables defining edge weights to use when calculating weighted shortest paths.

Arguments

GRAPH_URI: Required argument

OUTPUT_URI: Required argument

export_smbl_dfs_tables

Export the consensus model as a collection of table

Usage

napistu exporter export_smbl_dfs_tables [OPTIONS] SBML_DFS_URI OUTPUT_URI

Options

-m, --model-prefix <model_prefix>: Model prefix for files?

-n, --nondogmatic: Run in non-dogmatic mode (trying to merge genes and proteins)?

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

--overwrite: Overwrite existing files.

Arguments

SBML_DFS_URI: Required argument

OUTPUT_URI: Required argument

helpers

Various helper functions

Usage

napistu helpers [OPTIONS] COMMAND [ARGS]...

copy_uri

Copy a uri representing a file or folder from one location to another

Usage

napistu helpers copy_uri [OPTIONS] INPUT_URI OUTPUT_URI

Options

--is-file <is_file>: Is the input a file?

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

INPUT_URI: Required argument

OUTPUT_URI: Required argument

summarize_sbml_dfs

Display a summary of an SBML_dfs object

Usage

napistu helpers summarize_sbml_dfs [OPTIONS] SBML_DFS_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

validate_assets

Validate assets for consistency

Loads an SBML_dfs object and optionally validates it against other assets: - NapistuGraph: Network representation of the SBML_dfs - Precomputed distances: Distance matrix between vertices in the graph - Identifiers DataFrame: Systematic identifiers for compartmentalized species

At least one optional asset must be provided for validation to occur.

Usage

napistu helpers validate_assets [OPTIONS] SBML_DFS_URI

Options

-g, --napistu_graph_uri <napistu_graph_uri>: URI to NapistuGraph pickle file

-d, --precomputed_distances_uri <precomputed_distances_uri>: URI to precomputed distances parquet file

-i, --identifiers_df_uri <identifiers_df_uri>: URI to identifiers DataFrame TSV file

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

validate_sbml_dfs

Validate a sbml_dfs object

Usage

napistu helpers validate_sbml_dfs [OPTIONS] SBML_DFS_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

importer

Tools to import sbml_dfs directly from other sources

Usage

napistu importer [OPTIONS] COMMAND [ARGS]...

sbml

Import sbml_dfs from a sbml file

Usage

napistu importer sbml [OPTIONS] INPUT_URI OUTPUT_MODEL_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

INPUT_URI: Required argument

OUTPUT_MODEL_URI: Required argument

sbml_dfs

Import sbml_dfs from an uri, eg another GCS bucket

Usage

napistu importer sbml_dfs [OPTIONS] INPUT_URI SBML_DFS_URI OUTPUT_MODEL_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

INPUT_URI: Required argument

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

ingestion

Command line tools to retrieve raw data.

Usage

napistu ingestion [OPTIONS] COMMAND [ARGS]...

bigg

Usage

napistu ingestion bigg [OPTIONS] BASE_FOLDER

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

BASE_FOLDER: Required argument

gtex-rnaseq-expression

Usage

napistu ingestion gtex-rnaseq-expression [OPTIONS] TARGET_URI

Options

--url <url>: URL to download the gtex file from.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

TARGET_URI: Required argument

intact

Download IntAct PSI-MI XML files for a specific species.

OUTPUT_DIR_PATH: Local directory to create and unzip files into ORGANISMAL_SPECIES: The species name (e.g., “Homo sapiens”) to work with

Usage

napistu ingestion intact [OPTIONS] OUTPUT_DIR_PATH ORGANISMAL_SPECIES

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

OUTPUT_DIR_PATH: Required argument

ORGANISMAL_SPECIES: Required argument

proteinatlas_subcell

Usage

napistu ingestion proteinatlas_subcell [OPTIONS] TARGET_URI

Options

--url <url>: URL to download the zipped protein atlas subcellular localization tsv from.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

TARGET_URI: Required argument

reactome

Usage

napistu ingestion reactome [OPTIONS] BASE_FOLDER

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

BASE_FOLDER: Required argument

reactome_fi

Download Reactome Functional Interactions (FI) dataset as a TSV file.

Usage

napistu ingestion reactome_fi [OPTIONS] TARGET_URI

Options

--url <url>: URL to download the Reactome FI data from. If not provided, uses default URL.

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

TARGET_URI: Required argument

string_aliases

Usage

napistu ingestion string_aliases [OPTIONS] ORGANISMAL_SPECIES TARGET_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

ORGANISMAL_SPECIES: Required argument

TARGET_URI: Required argument

string_db

Usage

napistu ingestion string_db [OPTIONS] ORGANISMAL_SPECIES TARGET_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

ORGANISMAL_SPECIES: Required argument

TARGET_URI: Required argument

trrust

Usage

napistu ingestion trrust [OPTIONS] TARGET_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

TARGET_URI: Required argument

integrate

Command line tools to integrate raw models into a single SBML_dfs model

Usage

napistu integrate [OPTIONS] COMMAND [ARGS]...

bigg

Integrates bigg models based on a pw_index

Usage

napistu integrate bigg [OPTIONS] PW_INDEX_URI ORGANISMAL_SPECIES
                       OUTPUT_MODEL_URI

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

PW_INDEX_URI: Required argument

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

dogmatic_scaffold

Dogmatic Scaffold

Parameters

organismal_speciesstr: Species to use
output_model_uristr: output uri of model in sbml dfs format
preferred_methodstr: Preferred method to use for identifier expansion
allow_fallbackbool: Allow fallback to other methods if preferred method fails

Example call: > cpr integrate dogmatic_scaffold ./test.pickle

Usage

napistu integrate dogmatic_scaffold [OPTIONS] ORGANISMAL_SPECIES
                                    OUTPUT_MODEL_URI

Options

-p, --preferred-method <preferred_method>: Preferred method to use for identifier expansion

-a, --allow-fallback <allow_fallback>: Allow fallback to other methods if preferred method fails

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

intact

Converts IntAct PSI-MI XML files to SBML_dfs model.

INTACT_XML_DIR: Directory containing the IntAct PSI-MI XML files ORGANISMAL_SPECIES: The species name (e.g., “Homo sapiens”) to work with OUTPUT_MODEL_URI: Output URI for the SBML_dfs model OVERWRITE: Overwrite existing files?

Usage

napistu integrate intact [OPTIONS] INTACT_XML_DIR ORGANISMAL_SPECIES
                         OUTPUT_MODEL_URI

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

INTACT_XML_DIR: Required argument

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

omnipath

Downloads OmniPath data and formats interactions as an SBML_dfs model.

ORGANISMAL_SPECIES: The species name (e.g., “Homo sapiens”) to work with OUTPUT_MODEL_URI: Output URI for the SBML_dfs model PREFERRED_METHOD: Preferred Genodexito method for identifier mapping (default: bioconductor). ALLOW_FALLBACK: Allow fallback to other Genodexito methods if preferred method fails (default: True). OVERWRITE: Overwrite existing files?

Usage

napistu integrate omnipath [OPTIONS] ORGANISMAL_SPECIES OUTPUT_MODEL_URI

Options

-p, --preferred-method <preferred_method>: Preferred method to use for identifier expansion

-a, --allow-fallback <allow_fallback>: Allow fallback to other methods if preferred method fails

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

reactome

Integrates reactome models based on a pw_index

Usage

napistu integrate reactome [OPTIONS] PW_INDEX_URI ORGANISMAL_SPECIES
                           OUTPUT_MODEL_URI

Options

--overwrite: Overwrite existing files.

-p, --permissive: Can parsing failures in submodels throw warnings instead of exceptions?

-v, --verbose: Include detailed logs?

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

PW_INDEX_URI: Required argument

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

reactome_fi

Converts Reactome FI TSV to SBML_dfs model

Usage

napistu integrate reactome_fi [OPTIONS] REACTOME_FI_URI OUTPUT_MODEL_URI

Options

-p, --preferred-method <preferred_method>: Preferred method to use for identifier expansion

-a, --allow-fallback <allow_fallback>: Allow fallback to other methods if preferred method fails

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

REACTOME_FI_URI: Required argument

OUTPUT_MODEL_URI: Required argument

string_db

Converts STRING database to the sbml_dfs format

Usage

napistu integrate string_db [OPTIONS] STRING_DB_URI STRING_ALIASES_URI
                            ORGANISMAL_SPECIES OUTPUT_MODEL_URI

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

STRING_DB_URI: Required argument

STRING_ALIASES_URI: Required argument

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

trrust

Converts TRRUST csv to SBML_dfs model

Usage

napistu integrate trrust [OPTIONS] TRRUST_CSV_URI OUTPUT_MODEL_URI

Options

--overwrite: Overwrite existing files.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

TRRUST_CSV_URI: Required argument

OUTPUT_MODEL_URI: Required argument

refine

Command line tools to refine a consensus model

Usage

napistu refine [OPTIONS] COMMAND [ARGS]...

add_reactome_entity_sets

Add reactome entity sets to a consensus model

The entity set csv is classically exported from the neo4j reactome database.

Usage

napistu refine add_reactome_entity_sets [OPTIONS] SBML_DFS_URI ENTITY_SET_CSV
                                        OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

ENTITY_SET_CSV: Required argument

OUTPUT_MODEL_URI: Required argument

add_reactome_identifiers

Add reactome identifiers to a consensus model

The crossref csv is classically exported from the neo4j reactome database.

Usage

napistu refine add_reactome_identifiers [OPTIONS] SBML_DFS_URI CROSSREF_CSV
                                        OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

CROSSREF_CSV: Required argument

OUTPUT_MODEL_URI: Required argument

add_transportation_reactions

Add transportation reactions to a consensus model

Usage

napistu refine add_transportation_reactions [OPTIONS] SBML_DFS_URI
                                            OUTPUT_MODEL_URI

Options

-e, --exchange-compartment <exchange_compartment>: Exchange compartment for new transport reactions.

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

apply_manual_curations

Apply manual curations to a consensus model

The curation dir is a directory containing the manual curations Check napistu.modify.curation.curate_sbml_dfs for more information.

Usage

napistu refine apply_manual_curations [OPTIONS] SBML_DFS_URI CURATION_DIR
                                      OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

CURATION_DIR: Required argument

OUTPUT_MODEL_URI: Required argument

drop_cofactors

Remove reaction species acting as cofactors

Usage

napistu refine drop_cofactors [OPTIONS] SBML_DFS_URI OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

expand_identifiers

Expand identifiers of a model

Parameters

sbml_dfs_uristr: sbml_dfs_uri (str): uri of model in sbml dfs format
organismal_speciesstr: Species to use
output_model_uristr: output uri of model in sbml dfs format
ontologiesset[str]: ontologies to add or update

Example call: > napistu refine expand_identifiers gs://<uri> ./test.pickle -o ensembl_gene

Usage

napistu refine expand_identifiers [OPTIONS] SBML_DFS_URI ORGANISMAL_SPECIES
                                  OUTPUT_MODEL_URI

Options

-o, --ontologies <ontologies>: Ontologies to add or complete

-p, --preferred-method <preferred_method>: Preferred method to use for identifier expansion

-a, --allow-fallback <allow_fallback>: Allow fallback to other methods if preferred method fails

Arguments

SBML_DFS_URI: Required argument

ORGANISMAL_SPECIES: Required argument

OUTPUT_MODEL_URI: Required argument

filter_gtex_tissue

Filter model by the gtex tissue expression

This uses zfpkm values derived from gtex to filter the model.

Usage

napistu refine filter_gtex_tissue [OPTIONS] SBML_DFS_URI GTEX_FILE_URI TISSUE
                                  OUTPUT_MODEL_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

GTEX_FILE_URI: Required argument

TISSUE: Required argument

OUTPUT_MODEL_URI: Required argument

filter_hpa_compartments

Filter an interaction network using the human protein atlas

This uses loads the human proteome atlas and removes reactions (including interactions) containing genes which are not colocalized.

Only interactions between genes in the same compartment are kept.

Usage

napistu refine filter_hpa_compartments [OPTIONS] SBML_DFS_URI HPA_FILE_URI
                                       OUTPUT_MODEL_URI

Options

-v, --verbosity <verbosity>

Set the logging verbosity level for napistu.

Options:: DEBUG | INFO | WARNING | ERROR | CRITICAL

Arguments

SBML_DFS_URI: Required argument

HPA_FILE_URI: Required argument

OUTPUT_MODEL_URI: Required argument

infer_uncompartmentalized_species_location

Infer Uncompartmentalized Species Location

If the compartment of a subset of compartmentalized species was not specified, infer an appropriate compartment from other members of reactions they particpate in

Usage

napistu refine infer_uncompartmentalized_species_location [OPTIONS]
                                                          SBML_DFS_URI
                                                          OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

merge_model_compartments

Take a compartmentalized mechanistic model and merge all of the compartments.

Usage

napistu refine merge_model_compartments [OPTIONS] SBML_DFS_URI
                                        OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

name_compartmentalized_species

Name Compartmentalized Species

Rename compartmentalized species if they have the same name as their species

Usage

napistu refine name_compartmentalized_species [OPTIONS] SBML_DFS_URI
                                              OUTPUT_MODEL_URI

Arguments

SBML_DFS_URI: Required argument

OUTPUT_MODEL_URI: Required argument

stats

Various functions to calculate network statistics

The statistics are saved as json files

Usage

napistu stats [OPTIONS] COMMAND [ARGS]...

igraph_network

Calculate statistics for an igraph object

Usage

napistu stats igraph_network [OPTIONS] INPUT_URI OUTPUT_URI

Arguments

INPUT_URI: Required argument

OUTPUT_URI: Required argument

sbml_dfs_network

Calculate statistics for a sbml_dfs object

Usage

napistu stats sbml_dfs_network [OPTIONS] SBML_DFS_URI OUTPUT_URI

Arguments

SBML_DFS_URI: Required argument

OUTPUT_URI: Required argument

This will automatically generate documentation for all commands, subcommands, arguments, and options.

MCP Server CLI

The MCP server CLI provides commands for starting and managing MCP servers.