omxware package

Subpackages

• omxware.entities package
  • Submodules
  • omxware.entities.Domain module
  • omxware.entities.Entity module
  • omxware.entities.Gene module
  • omxware.entities.Genome module
  • omxware.entities.Genus module
  • omxware.entities.GoTerm module
  • omxware.entities.IprCode module
  • omxware.entities.Protein module
  • omxware.entities.User module
  • Module contents

Submodules

omxware.OmxResponse module

class omxware.OmxResponse.OmxResponse(connecthdr, omx_response: requests.models.Response)

Bases: object

error()

OMXWare Query errors / exceptions

Returns:

returns:str: Error messages

facets()

Get the pre-defined groups/facets for the results requested.

Returns:

return:JSON array with the group names and counts.

message()

OMXWare response comment

Returns:

returns:str: Message

page_index()

Get Response page number

Returns:

returns:str: Response page number

page_size()

Get Response page size

Returns:

returns:str: Response page size

response_time()

Get Response time for the query

Returns:

returns:str: Response time

results(type='list')

Get the results for in the chosen output format

Parameters:

type (str): one of {‘list’, ‘json’, ‘df’, ‘fasta’}

Returns:

‘list’ => OMXWare query results as list ‘json’ => List of OMXWare query results as a json array ‘df’ => List of OMXWare query results as a Pandas data-frame ‘fasta’ => (Only for Genes and/or Proteins) Get results as Fasta

show_facets(name='type', topN=5)

Display the groups / facets from the results. Only to be used in an environments that can display a pandas visualization.

Parameters:

name (str): group name. (e.g: when searching for genes/proteins group name could be ‘genus_name’)

topN (int): top ‘N’ groups

Returns:

Pandas pie chart (visualization)

total_results()

Get total number of results for the query

Returns:

returns:int: Total number of results

type()

Get Response type

Returns:

returns:str: Response type

omxware.omxware module

OMXWare SDK

omxware.omxware.get_token(username, password)

Verify the credentials and get a User Token

Parameters:

param username:OMXWare username. This is different from your IBM Id username type username:str param password:OMXWare password. This is different from your IBM Id’s password type password:str

Returns:

OMXWare user token

Raises:

KeyError: Raises an exception.

class omxware.omxware.omxware(omxware_token, env='public')

Bases: object

PAGE_INDEX_DEFAULT = 1

PAGE_SIZE_DEFAULT = 25

domains(ids=None, sequence=None, genus_names=None, protein_ids=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)

Get OMXWare Domains.

Parameters:

param ids:List of domain ids type ids:[str] param sequence:Domain sequence type sequence:str param genus_names:  List of Genus names type genus_names:  [str] param protein_ids:  List of Protein ids type protein_ids:  [str] param go_terms: type go_terms:[str] param ipr_ids: type ipr_ids:[str] param sequence_length:   type sequence_length:  str param page_number:  (int): Page Number type page_number:  int param page_size:  (int): Results page size type page_size:int

Returns:

return:OmxResponse: Domain

genes(ids=None, sequence=None, gene_name=None, genome_ids=None, genus_names=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)

Get Genes.

Parameters:

param ids:List of gene ids type ids:[str] param sequence:Gene sequence type sequence:str param gene_name:   type gene_name:str param genome_ids:  List of Genome IDs type genome_ids:  [str] param genus_names:  List of Genus names type genus_names:  [str] param go_terms: type go_terms:[str] param ipr_ids: type ipr_ids:[str] param sequence_length:   type sequence_length:  str param classification:  Must only be one of {‘bacteria’, ‘virus’, ‘all’} type classification:  str param collection:  List of Collection names. e.g: ‘covid19’ (collections is a pre-defined set of data tagged by the platform team) type collection:  [str] param page_number:  (int): Page Number type page_number:  int param page_size:  (int): Results page size type page_size:int

Returns:

return:OmxResponse: Gene

genomes(ids=None, genus_names=None, genome_type=None, genome_taxid=None, classification=None, collection=None, created_before=None, created_after=None, modified_before=None, modified_after=None, page_size=25, page_number=1)

Get Genomes by List of Genome ID(s) and/or Genus name(s) .

Parameters:

param ids:List of Genome IDs type ids:[str] param genus_names:  List of Genus names type genus_names:  [str] param genome_type:  List of Genome Types. Must be one of { ‘REFSEQ’, ‘SRA’, ‘GENBANK’ } type genome_type:  [str] param genome_taxid:  List of Genome Tax ids type genome_taxid:  [str] param classification:  Must only be one of {‘bacteria’, ‘virus’, ‘all’} type classification:  str param collection:  List of Collection names. e.g: ‘covid19’ (collections is a pre-defined set of data tagged by the platform team) type collection:  [str] param created_before:  Date - Created / Imported before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type created_before:  [str] param created_after:  Date - Created / Imported after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type created_after:  [str] param modified_before:  Date - Modified before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type modified_before:  [str] param modified_after:  Date - Modified after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type modified_after:  [str] param page_number:  Page Number type page_number:  int param page_size:  Results page size type page_size:int

Returns:

return:OmxResponse: Genome

genus(genus_names=None, page_size=25, page_number=1)

Get Genera by names .

Parameters:

param genus_names:  List of Genus names type genus_names:  [str] param page_number:  Page Number type page_number:  int param page_size:  Results page size type page_size:int

Returns:

return:OmxResponse: Genus

go(ids=None, categories=None, page_size=25, page_number=1)

Get OMXWare GO Terms by List of GO ID(s) and/or Category name(s) .

Parameters:

param ids:List of GO Term IDs type ids:[str] param categories:  List of GO Term Categories. Must be one of { ‘MOLECULAR_FUNCTION’, ‘BIOLOGICAL_PROCESS’, ‘CELLULAR_COMPONENT’ } type categories:  [str] param page_number:  Page Number type page_number:  int param page_size:  Results page size type page_size:int

Returns:

return:OmxResponse: Go

ipr(ids=None, categories=None, page_size=25, page_number=1)

Get OMXWare IPRs by List of IPR Code(s) and/or Category name(s) .

Parameters:

param ids:List of IPR IDs type ids:[str] param categories:  List of IPR Categories. type categories:  [str] param page_number:  Page Number type page_number:  int param page_size:  Results page size type page_size:int

Returns:

return:OmxResponse: Ipr

proteins(ids=None, sequence=None, protein_name=None, genome_ids=None, genus_names=None, domain_ids=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)

Get Proteins.

Parameters:

param ids:List of Protein ids type ids:[str] param sequence:Protein sequence type sequence:str param protein_name:   type protein_name:  str param genome_ids:  List of Genome IDs type genome_ids:  [str] param genus_names:  List of Genus names type genus_names:  [str] param domain_ids:   type domain_ids:  [str] param go_terms: type go_terms:[str] param ipr_ids: type ipr_ids:[str] param sequence_length:   type sequence_length:  str param page_number:  (int): Page Number type page_number:  int param page_size:  (int): Results page size type page_size:int

Returns:

return:OmxResponse: Protein

omxware.omxwaredev module

OMXWare SDK

class omxware.omxwaredev.OmxwareDev(omxware_token, env='public')

Bases: omxware.omxware.omxware

PAGE_INDEX_DEFAULT = 1

PAGE_SIZE_DEFAULT = 25

events(type=None, lastNdays=30, page_size=50000, page_nummber=1)

Get OMXWare User Events

Parameters:

param:type: str: Must be one of { ‘login’, ‘register’ } param:lastNdays: int: last N days to query the events

Returns:

return:OmxResponse : User

genes(ids=None, sequence=None, gene_name=None, genome_ids=None, genus_names=None, go_terms=None, ipr_ids=None, resistant_only=False, sequence_length=None, page_size=25, page_number=1)

Get OMXWare Genes.

Parameters:

param ids:List of gene ids type ids:[str] param sequence:Gene sequence type sequence:str param gene_name:   type gene_name:str param genome_ids:  List of Genome IDs type genome_ids:  [str] param genus_names:  List of Genus names type genus_names:  [str] param go_terms: type go_terms:[str] param ipr_ids: type ipr_ids:[str] param sequence_length:   type sequence_length:  str param page_number:  (int): Page Number type page_number:  int param page_size:  (int): Results page size type page_size:int

Returns:

return:OmxResponse: Gene

genomes(ids=None, genus_names=None, genome_type=None, genome_taxid=None, resistant_only=False, created_before=None, created_after=None, modified_before=None, modified_after=None, page_size=25, page_number=1)

Get OMXWare Genomes by List of Genome ID(s) and/or Genus name(s) .

Parameters:

param ids:List of Genome IDs type ids:[str] param genus_names:  List of Genus names type genus_names:  [str] param genus_names:  List of Genome Types. Must be one of { ‘REFSEQ’, ‘SRA’, ‘GENBANK’ } type genus_names:  [str] param genus_names:  List of Genome Tax ids type genus_names:  [str] param created_before:  Date - Created / Imported before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type created_before:  [str] param created_after:  Date - Created / Imported after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type created_after:  [str] param modified_before:  Date - Modified before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type modified_before:  [str] param modified_after:  Date - Modified after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY type modified_after:  [str] param page_number:  Page Number type page_number:  int param page_size:  Results page size type page_size:int

Returns:

return:OmxResponse: Genome

whoami()

Get OMXWare User info .

Returns:

return:OmxResponse : User

omxware.omxwaredev.get_token(username, password)

Verify the credentials and get a User Token

Parameters:

param username:OMXWare username. This is different from your IBM Id username type username:str param password:OMXWare password. This is different from your IBM Id’s password type password:str

Returns:

OMXWare user token

Raises:

KeyError: Raises an exception.

Module contents

Top-level package for omxware.