mgnipy.emgapi_v2_client.api.assemblies package

Contains endpoint functions for accessing the API

Submodules

mgnipy.emgapi_v2_client.api.assemblies.get_assembly module

mgnipy.emgapi_v2_client.api.assemblies.get_assembly.sync_detailed(accession, *, client)

Get assembly by accession

Get detailed information about a specific assembly.

Parameters:

• accession (str )

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[AssemblyDetail]

Return type:

Response[AssemblyDetail]

mgnipy.emgapi_v2_client.api.assemblies.get_assembly.sync(accession, *, client)

Get assembly by accession

Get detailed information about a specific assembly.

Parameters:

• accession (str )

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

AssemblyDetail

Return type:

AssemblyDetail | None

async mgnipy.emgapi_v2_client.api.assemblies.get_assembly.asyncio_detailed(accession, *, client)

Get assembly by accession

Get detailed information about a specific assembly.

Parameters:

• accession (str )

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[AssemblyDetail]

Return type:

Response[AssemblyDetail]

async mgnipy.emgapi_v2_client.api.assemblies.get_assembly.asyncio(accession, *, client)

Get assembly by accession

Get detailed information about a specific assembly.

Parameters:

• accession (str )

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

AssemblyDetail

Return type:

AssemblyDetail | None

mgnipy.emgapi_v2_client.api.assemblies.list_additional_contained_genomes_for_assembly module

mgnipy.emgapi_v2_client.api.assemblies.list_additional_contained_genomes_for_assembly.sync_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List additional contained genomes for an assembly

Return additional contained genomes (and their metrics) discovered for this assembly.

Accessible at /assemblies/{accession}/additional-contained-genomes.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema]

Return type:

Response[NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema]

mgnipy.emgapi_v2_client.api.assemblies.list_additional_contained_genomes_for_assembly.sync(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List additional contained genomes for an assembly

Return additional contained genomes (and their metrics) discovered for this assembly.

Accessible at /assemblies/{accession}/additional-contained-genomes.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema

Return type:

NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema | None

async mgnipy.emgapi_v2_client.api.assemblies.list_additional_contained_genomes_for_assembly.asyncio_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List additional contained genomes for an assembly

Return additional contained genomes (and their metrics) discovered for this assembly.

Accessible at /assemblies/{accession}/additional-contained-genomes.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema]

Return type:

Response[NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema]

async mgnipy.emgapi_v2_client.api.assemblies.list_additional_contained_genomes_for_assembly.asyncio(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List additional contained genomes for an assembly

Return additional contained genomes (and their metrics) discovered for this assembly.

Accessible at /assemblies/{accession}/additional-contained-genomes.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema

Return type:

NinjaPaginationResponseSchemaAdditionalContainedGenomeSchema | None

mgnipy.emgapi_v2_client.api.assemblies.list_analyses_for_assembly module

mgnipy.emgapi_v2_client.api.assemblies.list_analyses_for_assembly.sync_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List analyses for an assembly

Return MGnify analyses (MGYAs) that were generated from this assembly.

Accessible at /assemblies/{accession}/analyses.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

mgnipy.emgapi_v2_client.api.assemblies.list_analyses_for_assembly.sync(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List analyses for an assembly

Return MGnify analyses (MGYAs) that were generated from this assembly.

Accessible at /assemblies/{accession}/analyses.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaMGnifyAnalysis

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysis | None

async mgnipy.emgapi_v2_client.api.assemblies.list_analyses_for_assembly.asyncio_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List analyses for an assembly

Return MGnify analyses (MGYAs) that were generated from this assembly.

Accessible at /assemblies/{accession}/analyses.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

Return type:

Response[NinjaPaginationResponseSchemaMGnifyAnalysis]

async mgnipy.emgapi_v2_client.api.assemblies.list_analyses_for_assembly.asyncio(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List analyses for an assembly

Return MGnify analyses (MGYAs) that were generated from this assembly.

Accessible at /assemblies/{accession}/analyses.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaMGnifyAnalysis

Return type:

NinjaPaginationResponseSchemaMGnifyAnalysis | None

mgnipy.emgapi_v2_client.api.assemblies.list_assemblies module

mgnipy.emgapi_v2_client.api.assemblies.list_assemblies.sync_detailed(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all assemblies available in MGnify

Each assembly represents a collection of contigs generated by assembling sequencing reads from an

MGnify or run

Parameters:

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAssembly]

Return type:

Response[NinjaPaginationResponseSchemaAssembly]

mgnipy.emgapi_v2_client.api.assemblies.list_assemblies.sync(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all assemblies available in MGnify

Each assembly represents a collection of contigs generated by assembling sequencing reads from an

MGnify or run

Parameters:

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAssembly

Return type:

NinjaPaginationResponseSchemaAssembly | None

async mgnipy.emgapi_v2_client.api.assemblies.list_assemblies.asyncio_detailed(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all assemblies available in MGnify

Each assembly represents a collection of contigs generated by assembling sequencing reads from an

MGnify or run

Parameters:

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaAssembly]

Return type:

Response[NinjaPaginationResponseSchemaAssembly]

async mgnipy.emgapi_v2_client.api.assemblies.list_assemblies.asyncio(*, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List all assemblies available in MGnify

Each assembly represents a collection of contigs generated by assembling sequencing reads from an

MGnify or run

Parameters:

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaAssembly

Return type:

NinjaPaginationResponseSchemaAssembly | None

mgnipy.emgapi_v2_client.api.assemblies.list_genome_links_for_assembly module

mgnipy.emgapi_v2_client.api.assemblies.list_genome_links_for_assembly.sync_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List genome/MAG links for an assembly

Return genome links (e.g. MAG associations) for a specific assembly.

Accessible at /assemblies/{accession}/genome-links.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema]

Return type:

Response[NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema]

mgnipy.emgapi_v2_client.api.assemblies.list_genome_links_for_assembly.sync(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List genome/MAG links for an assembly

Return genome links (e.g. MAG associations) for a specific assembly.

Accessible at /assemblies/{accession}/genome-links.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema

Return type:

NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema | None

async mgnipy.emgapi_v2_client.api.assemblies.list_genome_links_for_assembly.asyncio_detailed(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List genome/MAG links for an assembly

Return genome links (e.g. MAG associations) for a specific assembly.

Accessible at /assemblies/{accession}/genome-links.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

Response[NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema]

Return type:

Response[NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema]

async mgnipy.emgapi_v2_client.api.assemblies.list_genome_links_for_assembly.asyncio(accession, *, client, page=1, page_size=<mgnipy.emgapi_v2_client.types.Unset object>)

List genome/MAG links for an assembly

Return genome links (e.g. MAG associations) for a specific assembly.

Accessible at /assemblies/{accession}/genome-links.

Parameters:

• accession (str )

• page (int | Unset) – Default: 1.

• page_size (int | None | Unset)

• client (AuthenticatedClient | Client)

Raises:

• errors.UnexpectedStatus – If the server returns an undocumented status code and Client.raise_on_unexpected_status is True.

• httpx.TimeoutException – If the request takes longer than Client.timeout.

Returns:

NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema

Return type:

NinjaPaginationResponseSchemaGenomeAssemblyLinkSchema | None