def proteins(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT
):
"""
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
"""
omx = omxware.omxware(self.connection().config().token(), env=self.connection().config().env())
results = omx.proteins(genus_names=self.id(), page_size=page_size, page_number=page_number)
return results
def ipr(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT
):
"""
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
"""
if self._iprcodes is None and self.is_preview_obj():
self.__reload()
if self._iprcodes is None and not self.is_preview_obj():
return None
ipr_list = self._iprcodes
offset = (page_number - 1) * page_size
ids = []
for ipr in ipr_list[offset:page_size]:
if isinstance(ipr, Ipr):
ids.append(ipr.id())
elif isinstance(ipr, str):
ids.append(ipr)
if len(ids) == 0:
return None
omx = omxware.omxware(self.connection().config().token(), env=self.connection().config().env())
results = omx.ipr(ids=ids, page_size=len(ids), page_number=page_number)
return results
def go(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT):
"""
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
"""
if self._goterms is None and self.is_preview_obj():
self.__reload()
if self._goterms is None and not self.is_preview_obj():
return None
go_list = self._goterms
offset = (page_number - 1) * page_size
ids = []
for go in go_list[offset:page_size]:
if isinstance(go, Go):
ids.append(go.id())
elif isinstance(go, str):
ids.append(go)
if len(ids) == 0:
return None
omx = omxware.omxware(self.connection().config().token(),
env=self.connection().config().env())
results = omx.go(ids=ids, page_size=len(ids), page_number=page_number)
return results
def genomes(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT):
"""
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
"""
if (self._genomes is None
or len(self._genomes) == 0) and self.is_preview_obj():
self.__reload()
if self._genomes is None and not self.is_preview_obj():
return None
genome_list = self._genomes
offset = (page_number - 1) * page_size
ids = []
for genome in genome_list[offset:page_size]:
ids.append(genome.id())
if len(ids) == 0:
return None
omx = omxware.omxware(self.connection().config().token(),
env=self.connection().config().env())
results = omx.genomes(ids=ids,
page_size=len(ids),
page_number=page_number)
return results
def proteins(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT):
"""
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
"""
if self._proteins is None and self.is_preview_obj():
self.__reload()
if self._proteins is None and not self.is_preview_obj():
return None
protein_list = self._proteins
offset = (page_number - 1) * page_size
ids = []
for protein in protein_list[offset:page_size]:
ids.append(protein.id())
if len(ids) == 0:
return None
omx = omxware.omxware(self.connection().config().token(),
env=self.connection().config().env())
results = omx.proteins(ids=ids,
page_size=len(ids),
page_number=page_number)
return results
def genes(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT):
"""
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
"""
omx = omxware.omxware(self.connection().config().token(),
env=self.connection().config().env())
results = omx.genes(go_terms=self.id(),
page_size=page_size,
page_number=page_number)
return results
def domains(self,
page_size=Entity._PAGE_SIZE_DEFAULT,
page_number=Entity._PAGE_INDEX_DEFAULT):
"""
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
"""
omx = omxware.omxware(self.connection().config().token(),
env=self.connection().config().env())
results = omx.domains(ipr_ids=self.id(),
page_size=page_size,
page_number=page_number)
return results