omxware.entities package

Submodules

omxware.entities.Domain module

class omxware.entities.Domain.Domain(connecthdr: 'omxware.config.Connection', domain)[source]

Bases: omxware.entities.Entity.Entity

OMXWare Domain Entity Class

genus(page_size=25, page_number=1)[source]

Get all the associated Genera for this Domain

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genus
go(page_size=25, page_number=1)[source]

Get all the associated GO terms for this Domain

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: GO
ipr(page_size=25, page_number=1)[source]

Get all the associated IPR codes for this Domain

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Iprs
proteins(page_size=25, page_number=1)[source]

Get all the associated Proteins for this Domain

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Proteins
sequence()[source]

Get this Domain’s sequence

Returns:
return:str : Domain Sequence
sequence_length()[source]

Get this Domain’s sequence length

Returns:
return:int : Domain Sequence’s length

omxware.entities.Entity module

class omxware.entities.Entity.Entity(connecthdr: 'omxware.config.Connection', etty_obj)[source]

Bases: object

Entity Base Class

configuration()[source]
connection()[source]
id()[source]

ID

Returns:
return:str : OMXWare ID
is_preview_obj()[source]
json()[source]

As Json

Returns:
return:json : json
name()[source]

Name

Returns:
return:str : Name
omx_token()[source]
type()[source]

Type

Returns:
return:str : OMXWare Type

omxware.entities.Gene module

class omxware.entities.Gene.Gene(connecthdr: 'omxware.config.Connection', gene)[source]

Bases: omxware.entities.Entity.Entity

OMXWare Gene Entity Class

genomes(page_size=25, page_number=1)[source]

Get associated Genomes for this Gene

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genomes
genus(page_size=25, page_number=1)[source]

Get all the associated Genera for this Gene

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genus
go(page_size=25, page_number=1)[source]

Get all the associated GO terms for this Gene

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: GO
ipr(page_size=25, page_number=1)[source]

Get all the associated IPRs for this Gene

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Ipr
sequence()[source]

Get this Gene’s sequence

Returns:
return:str : Gene Sequence
sequence_length()[source]

Get this Gene’s sequence length

Returns:
return:int : Gene Sequence’s length

omxware.entities.Genome module

class omxware.entities.Genome.Genome(connecthdr: 'omxware.config.Connection', genome)[source]

Bases: omxware.entities.Entity.Entity

OMXWare Genome Entity Class

genes(page_size=25, page_number=1)[source]

Get OMXWare Genes for the Genome

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genes
genome_type()[source]

Get this Genome’s type. Will be one of { ‘REFSEQ’, ‘SRA’, ‘GENBANK’ }

Returns:
return:str : Genome type
genus(page_size=25, page_number=1)[source]

Get OMXWare Genera the Genome

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genus
metadata(type='biosample')[source]

Get Genome metadata

Parameters:
param type:Genome metadata. Must be one of [‘biosample’]
type type:str
Returns:
OmxResponse: Genome Metadata :return: dict: Genome metadata
proteins(page_size=25, page_number=1)[source]

Get OMXWare Proteins for the Genome

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Proteins
taxid()[source]

Get this Genome’s Tax ID

Returns:
return:str : Tax ID

omxware.entities.Genus module

class omxware.entities.Genus.Genus(connecthdr: 'omxware.config.Connection', genus)[source]

Bases: omxware.entities.Entity.Entity

OMXWare Genus Entity Class

domains(page_size=25, page_number=1)[source]

Get OMXWare Domains for the Genus

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Domains
genes(page_size=25, page_number=1)[source]

Get OMXWare Genes for the Genus

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genes
genomes(page_size=25, page_number=1)[source]

Get OMXWare Genomes for the Genus

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genomes
proteins(page_size=25, page_number=1)[source]

Get OMXWare Proteins for the Genus

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Proteins

omxware.entities.GoTerm module

class omxware.entities.GoTerm.Go(connecthdr: 'omxware.config.Connection', go)[source]

Bases: omxware.entities.Entity.Entity

OMXWare GO Entity Class

category()[source]

Get this GO Term’s category

Returns:
return:str : GO Term category
domains(page_size=25, page_number=1)[source]

Get OMXWare Domains for this GO Term

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Domains
genes(page_size=25, page_number=1)[source]

Get OMXWare Genes for this GO Term

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genes
proteins(page_size=25, page_number=1)[source]

Get OMXWare Proteins for this GO Term

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Proteins

omxware.entities.IprCode module

class omxware.entities.IprCode.Ipr(connecthdr: 'omxware.config.Connection', ipr)[source]

Bases: omxware.entities.Entity.Entity

OMXWare IPR Entity Class

category()[source]

Get this IPR Code’s category

Returns:
return:str : IPR code’s category
description()[source]

Get this IPR Code’s description

Returns:
return:str : IPR code’s description
domains(page_size=25, page_number=1)[source]

Get OMXWare Domains for this IPR code

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Domains
genes(page_size=25, page_number=1)[source]

Get OMXWare Genes for this IPR code

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genes
proteins(page_size=25, page_number=1)[source]

Get OMXWare Proteins for this IPR code

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Proteins

omxware.entities.Protein module

class omxware.entities.Protein.Protein(connecthdr: 'omxware.config.Connection', protein)[source]

Bases: omxware.entities.Entity.Entity

OMXWare Protein Entity Class

domains(page_size=25, page_number=1)[source]

Get all the associated Domains for this Protein

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Domains
genomes(page_size=25, page_number=1)[source]

Get all the associated Genomes for this Protein

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genomes
genus(page_size=25, page_number=1)[source]

Get all the associated Genera for this Protein

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Genus
go(page_size=25, page_number=1)[source]

Get all the associated GO terms for this Protein

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: GO
ipr(page_size=25, page_number=1)[source]

Get all the associated GO terms for this Protein

Parameters:
param page_number:
 Page Number
type page_number:
 int
param page_size:
 Results page size
type page_size:int
Returns:
return:OmxResponse: Ipr
sequence()[source]

Get this Protein’s sequence

Returns:
return:str : Protein Sequence
sequence_length()[source]

Get this Protein’s sequence length

Returns:
return:int : Protein Sequence’s length

omxware.entities.User module

class omxware.entities.User.User(connecthdr: 'omxware.config.Connection', user)[source]

Bases: omxware.entities.Entity.Entity

OMXWare User Entity Class

email()[source]

Get the email for Current user

Returns:str : Email
firstname()[source]

Get the First Name for Current user

Returns:str : First Name
lastname()[source]

Get the Last Name for Current user

Returns:str : Last Name
locale()[source]

Get the locale for Current user

Returns:str : Locale
roles()[source]

Get the roles assigned for Current user

Returns:[str] : User Roles
username()[source]

Get the username for Current user

Returns:str : Username

Module contents