disgenet package

Submodules

disgenet.da_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.da_disgenet.DADisgenet(output_file_path, retrieve_by=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Disease Attribute Disgenet
This class is for downloading a Disease Attribute request from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • retrieve_by (str) (Optional) – Configuration params to pass for the retrieval of the association on the REST API, not mandatory, in default is obtained by gene ID (uniprot_entry, source)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • diseaseName (str) - (None) Disease name recognized by the database.

    • disease_id (str) - (None) Disease id or a list of disease ids separated by commas.

    • source (str) - (“ALL”) Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • max_dsi (str) - (None) Max value of DSI range for the gene.

    • min_dsi (str) - (None) Min value of DSI range for the gene.

    • min_dpi (str) - (None) Min value of DPI range for the gene.

    • max_dpi (str) - (None) Max value of DPI range for the gene.

    • max_pli (str) - (None) Max value of pLI range for the gene.

    • min_pli (str) - (None) Min value of pLI range for the gene.

    • format (str) - (“json”) Format output file.

    • limit (str) - (None) Number of disease to retrieve.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (None) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.DADisgenet import DADisgenet

prop = {

‘disease_id’:’disease_id’, ‘source’: ‘source’, ‘min_dsi’: ‘min_dsi’, ‘max_dsi’: ‘max_dsi’, ‘min_dpi’: ‘min_dpi’, ‘max_dpi’: ‘max_dpi’, ‘min_pli’: ‘min_pli’, ‘max_pli’:’max_pli’, ‘format’: ‘format’, ‘limit’: ‘limit’

} DADisgenet(

retrieve_by=’source’, output_file_path=’/path/to/associationsFile’, properties=prop)

Info:
retrieve_by can be:

disease, diseaseName, source, mappings, similarity

launch() → int[source]

Execute the DADisgenet object.

disgenet.da_disgenet.da_disgenet(output_file_path: str, retrieve_by: Optional[str] = None, properties: Optional[dict] = None, **kwargs) → int[source]

Create DADisgenet class and execute the launch() method.

disgenet.da_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.dda_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.dda_disgenet.DDADisgenet(retrieve_by, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Disease Association Disgenet
This class is for downloading a Disease Disease Associations file from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • shared_by (str) – Configuration params to pass for the retrieval of the association on the REST API (gene, uniprot_entry, disease, source, evidences_gene, evidences_disease)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • source (str) - (“ALL”) Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • disease_vocabulary (str) - Disease vocabulary (icd9cm, icd10, mesh, omim, do, efo, nci, hpo, mondo, ordo).

    • pvalue (str) - (None) Pvalue of the disease-disease score range.

    • format (str) - (“json”) Format output file.

    • limit (str) - (“10”) Number of disease to retrieve.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (None) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.dda_disgenet import dda_disgenet

prop = {

‘disease_id’: ‘C0002395’, ‘source’: ‘source’, ‘pvalue’:’pvalue’, ‘vocabulary’:’vocabulary’, ‘format’: ‘format’, ‘limit’: ‘limit’

} dda_disgenet(shared_by=’genes’,

output_file_path=’/path/to/associationsFile’, properties=prop)

Info:

launch() → int[source]

Execute the DDADisgenet object.

disgenet.dda_disgenet.dda_disgenet(retrieve_by: str, output_file_path: str, properties: Optional[dict] = None, **kwargs) → int[source]

Create DDADisgenet class and execute the launch() method.

disgenet.dda_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.ga_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.ga_disgenet.GADisgenet(output_file_path, retrieve_by=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Gene Attribute Disgenet
This class is for downloading a Gene Attribute request from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • retrieve_by (str) – Configuration params to pass for the retrieval of the association on the REST API (gene, uniprot_entry, disease, source, evidences_gene, evidences_disease)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • source (str) - (“ALL”) Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • max_dsi (str) - (None) Max value of DSI range for the gene.

    • min_dsi (str) - (None) Min value of DSI range for the gene.

    • min_dpi (str) - (None) Min value of DPI range for the gene.

    • max_dpi (str) - (None) Max value of DPI range for the gene.

    • max_pli (str) - (None) Max value of pLI range for the gene.

    • min_pli (str) - (None) Min value of pLI range for the gene.

    • format (str) - (“json”) Format output file.

    • limit (str) - (None) Number of disease to retrieve.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • container_path (str) - (None) Path to the binary executable of your container.

    • container_image (str) - (None) Container Image identifier.

    • container_volume_path (str) - (“/data”) Path to an internal directory in the container.

    • container_working_dir (str) - (None) Path to the internal CWD in the container.

    • container_user_id (str) - (None) User number id to be mapped inside the container.

    • container_shell_path (str) - (“/bin/bash”) Path to the binary executable of the container shell.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.ga_disgenet import ga_disgenet

prop = {

‘gene_id’: ‘351’, ‘source’: ‘source’, ‘min_dsi’: ‘min_dsi’, ‘max_dsi’: ‘max_dsi’, ‘min_dpi’: ‘min_dpi’, ‘max_dpi’: ‘max_dpi’, ‘min_pli’: ‘min_pli’, ‘max_pli’:’max_pli’, ‘format’: ‘format’, ‘limit’: ‘limit’

} ga_disgenet(

retrieve_by=’gene’ output_file_path=’/path/to/associationsFile’, properties=prop)

Info:
retrieve_by can be:

gene, uniprot, source

launch() → int[source]

Execute the GADisgenet object.

disgenet.ga_disgenet.ga_disgenet(output_file_path: str, retrieve_by: Optional[str] = None, properties: Optional[dict] = None, **kwargs) → int[source]

Create GADisgenet class and execute the launch() method.

disgenet.ga_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.gda_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.gda_disgenet.GDADisgenet(retrieve_by, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Gene Disease Association Disgenet
This class is for downloading a Gene Disease Associations file from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • retrieve_by (str) – Configuration params to pass for the retrieval of the association on the REST API (gene, uniprot_entry, disease, source, evidences_gene, evidences_disease)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • gene_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.

    • disease (str) - Disease id or a list of disease separated by commas.

    • disease_type (str) - Disease, phenotype, group.

    • source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • disease_vocabulary (str) - Disease vocabulary (icd9cm, icd10, mesh, omim, do, efo, nci, hpo, mondo, ordo).

    • disease_class * - MeSh disease classes.

    • min_score (str) - Min value of the gene-disease score range.

    • max_score (str) - Max value of the gene-disease score range.

    • min_ei (str) - Min value of evidence index score range.

    • max_ei (str) - Max value of evidence index score range.

    • max_dsi (str) - Max value of DSI range for the gene.

    • min_dsi (str) - Min value of DSI range for the gene.

    • max_pli (str) - Max value of pLI range for the gene.

    • min_pli (str) - Min value of pLI range for the gene.

    • format (str) - Format output file.

    • limit (str) - Number of GDAs to retrieve.

    • min_year (str) - The year of the earliest publications.

    • max_year (str) - The year of the latest publicatons.

    • offset (str) - Starting offset of the page.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.gda_disgenet import gda_disgenet

prop = {

‘gene_id’: ‘gene_id’, ‘disease_id’: ‘disease_id’, ‘uniprot_id’: ‘uniprot_id’, ‘source’: ‘source’, ‘min_score’: ‘min_score’, ‘max_score’: ‘max_score’, ‘min_ei’: ‘min_ei’, ‘max_ei’: ‘max_ei’, ‘type’: ‘disease_type’, ‘disease_class’: ‘disease_class’, ‘min_dsi’: ‘min_dsi’, ‘max_dsi’: ‘max_dsi’, ‘min_dpi’: ‘min_dpi’, ‘max_dpi’: ‘max_dpi’, ‘min_pli’: ‘min_pli’, ‘max_pli’:’max_pli’, ‘format’: ‘format’, ‘limit’: ‘limit’, ‘min_year’:’min_year’, ‘max_year’:’max_year’, ‘offset’:’offset’

} gda_disgenet(retrieve_by=’gene’,

output_file_path=’output_gene_351’, properties=prop)

Info:

retrieve_by can be:

gene, uniprot, source, evidences

launch() → int[source]

Execute the GDADisgenet object.

disgenet.gda_disgenet.gda_disgenet(retrieve_by: str, output_file_path: str, properties: Optional[dict] = None, **kwargs) → int[source]

Create GDADisgenet class and execute the launch() method.

disgenet.gda_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.va_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.va_disgenet.VADisgenet(output_file_path, retrieve_by=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Variant Attribute Disgenet
This class is for downloading a Variant Attribute request from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • retrieve_by (str) – Configuration params to pass for the retrieval of the association on the REST API, not mandatory, in default is obtained by gene ID (uniprot_entry, source)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • gene_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.

    • variant_id (str) - Uniprot id or a list of variant ids separated by commas.

    • source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • max_dsi (str) - Max value of DSI range for the gene.

    • min_dsi (str) - Min value of DSI range for the gene.

    • min_dpi (str) - Min value of DPI range for the gene.

    • max_dpi (str) - Max value of DPI range for the gene.

    • max_pli (str) - Max value of pLI range for the gene.

    • min_pli (str) - Min value of pLI range for the gene.

    • format (str) - Format output file.

    • limit (str) - Number of disease to retrieve.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.ga_disgenet import ga_disgenet

prop = {

‘variant_id’: ‘variant_id’, ‘source’: ‘source’, ‘min_dsi’: ‘min_dsi’, ‘max_dsi’: ‘max_dsi’, ‘min_dpi’: ‘min_dpi’, ‘max_dpi’: ‘max_dpi’, ‘min_pli’: ‘min_pli’, ‘max_pli’:’max_pli’, ‘format’: ‘format’, ‘limit’: ‘limit’

} va_disgenet(

retrieve_by=”variant”, output_file_path=’/path/to/associationsFile’, properties=prop)

Info:

launch() → int[source]

Execute the VADisgenet object.

disgenet.va_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.va_disgenet.va_disgenet(output_file_path: str, retrieve_by: Optional[str] = None, properties: Optional[dict] = None, **kwargs) → int[source]

Create VADisgenet class and execute the launch() method.

disgenet.vda_disgenet module

Module containing the BioBBs DisGeNET class and the command line interface.

class disgenet.vda_disgenet.VDADisgenet(retrieve_by, output_file_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_disgenet Variant Association Disgenet
This class is for downloading a Varinat Disease Associations file from DisGeNET database.
Wrapper for the DisGeNET database https://www.disgenet.org and the DisGeNET REST API ´https://www.disgenet.org/api/´ for downloading available collections of genes and variants associated data to human diseases.
Parameters

  • retrieve_by (str) – Configuration params to pass for the retrieval of the association on the REST API (variant, disease, source)

  • output_file_path (str) – Path to the output file, that can be in format TSV, JSON or XML.

  • properties (dict - Python dict containing the properties for the API interrogation, considering also the credentials of the user to the database) –

    • gene_id (str) - Number identification for a gene or a list of genes separated by commas recognized by the database.

    • variant_id (*str) - Variant id for the gene or a list of variant ids separated by commas recognized by the database.

    • disease_id (str) - Disease id or a list of disease separated by commas.

    • type (str) - Disease, phenotype, group.

    • source (str) - Source of the associations (CURATED, INFERRED, ANIMAL_MODELS, ALL, BEFREE, CGI, CLINGEN, CLINVAR, CTD_human, CTD_mouse, CTD_rat, GENOMICS_ENGLAND, GWASCAT, GWASDB, HPO, LHGDN, MGD, ORPHANET, PSYGENET, RGD, UNIPROT).

    • disease_class * - MeSh disease classes.

    • min_score (str) - Min value of the gene-disease score range.

    • max_score (str) - Max value of the gene-disease score range.

    • min_ei (str) - Min value of evidence index score range.

    • max_ei (str) - Max value of evidence index score range.

    • max_dsi (str) - Max value of DSI range for the gene.

    • min_dsi (str) - Min value of DSI range for the gene.

    • max_pli (str) - Max value of pLI range for the gene.

    • min_pli (str) - Min value of pLI range for the gene.

    • format (str) - Format output file.

    • limit (str) - Number of GDAs to retrieve.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_disgenet.disgenet.vda_disgenet import vda_disgenet

prop = {

‘variant_id’: ‘variant_id’, ‘disease_id’: ‘disease_id’, ‘source’: ‘source’, ‘min_score’: ‘min_score’, ‘max_score’: ‘max_score’, ‘min_ei’: ‘min_ei’, ‘max_ei’: ‘max_ei’, ‘type’: ‘disease_type’, ‘disease_class’: ‘disease_class’, ‘min_dsi’: ‘min_dsi’, ‘max_dsi’: ‘max_dsi’, ‘min_dpi’: ‘min_dpi’, ‘max_dpi’: ‘max_dpi’, ‘min_pli’: ‘min_pli’, ‘max_pli’:’max_pli’, ‘format’: ‘format’, ‘limit’: ‘limit’ ‘min_year’:’min_year’, ‘max_year’:’max_year’, ‘offset’:’offset’

} vda_disgenet(retrieve_by=’variant’,

output_file_path=’/path/to/associationsFile’, properties=prop)

Info:
retrieve_by can be:

variant, gene, disease, source, evidences

launch() → int[source]

Execute the VDADisgenet object.

disgenet.vda_disgenet.main()[source]

Command line execution of this building block. Please check the command line documentation.

disgenet.vda_disgenet.vda_disgenet(retrieve_by: str, output_file_path: str, properties: Optional[dict] = None, **kwargs) → int[source]

Create VDADisgenet class and execute the launch() method.