def test_build_url_retOMA(self):
"""Tests that build URL inserts the variable portions of the url correcly into the base"""
self.lyz.sequence = 'MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV'
self.assertEqual(
constool.build_url(base_url='https://omabrowser.org',
tail='/api/sequence/?query={0}',
variation=[self.lyz.sequence]),
'https://omabrowser.org/api/sequence/?query=MKALIVLGLVLLSVTVQGKVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV'
)
def HOG_to_fasta(self):
"""
Retrieves the fasta file containing the sequences of the proteins in the HOG of the input protein
"""
url = constool.build_url(base_url=self.OMA_BASE_URL,
tail='/oma/hogs/{0}/{1}/fasta/',
variation=[self.id, self.hog_level])
response = requests.get(url)
if response.status_code == 200:
self.HOGs = str(response.text)
return self.HOGs
else:
self.save_status = response.status_code
raise exceptions.RequestException(
'There was an issue querying the database. Status code {0}'.
format(self.save_status))
def update_orthoIDs(self):
"""
Takes the OMA specific ID of a protein species, and returns a list of the
canonical IDs of the orthologs of that protein
Returns:
A list of strings, the canonical IDS for the orthologs of the protein
"""
url = constool.build_url(base_url=self.OMA_BASE_URL,
tail='/api/protein/{0}/orthologs/',
variation=[self.id])
response = requests.get(url, headers=self.HEADERS)
if response.status_code == 200:
self.read_resp_orthoIDs(response)
else:
self.save_status = response.status_code
raise exceptions.RequestException(
'There was an issue querying the database. Status code {0}'.
format(self.save_status))
def ortholog_to_fasta(self):
"""
Takes an OMA specific ID and returns a fasta string of the orthologs assciated
with that protein
Returns:
A single fasta string containing the orthologs of that protein, as
dictated by OMA.Note that when the fasta file is parsed,
the first id is the OMA ID, and the second is the canonical id.
"""
url = constool.build_url(base_url=self.OMA_BASE_URL,
tail='/oma/vps/{0}/fasta/',
variation=[self.id])
response = requests.get(url)
if response.status_code == 200:
self.orthologs = str(response.text)
return self.orthologs
else:
self.save_status = response.status_code
raise exceptions.RequestException(
'There was an issue querying the database. Status code {0}'.
format(self.save_status))
def retrieve_OMAid(self):
"""
Takes a protein sequence and returns the oma id of the best protein
match
Returns:
A string containing the ID of the best protein match for the entered sequence
"""
url = constool.build_url(base_url=self.OMA_BASE_URL,
tail='/api/sequence/?query={0}',
variation=[self.sequence])
response = requests.get(url, headers=self.HEADERS)
if response.status_code == 200:
self.read_resp_protID(response)
if response.status_code == 504:
self.save_status = response.status_code
raise TimeoutError(
'The database timed out. Could not determine the orthologs of your sequence. Status code {0}'
.format(self.save_status))
if response.status_code != 200:
self.save_status = response.status_code
raise exceptions.RequestException(
'There was an issue querying the database. Status code {0}'.
format(self.save_status))
def retrieve_HOG_level(self, root=True):
"""
Retrieve information on the taxonomic levels that the HOG spans through
Args:
root(Boolean): if true, return the deepest level of the HOG. If false, return a list
of the alternative level that the HOG spans through
Returns: The deepest level relating the HOG, or a list of all the levels
"""
url = constool.build_url(base_url=self.OMA_BASE_URL,
tail='/api/hog/{0}/',
variation=[self.id])
response = requests.get(url, headers=self.HEADERS)
if response.status_code == 200:
return self.read_HOGid(response, root)
if response.status_code == 504:
self.save_status = response.status_code
raise TimeoutError(
'The database timed out. Could not determine the orthologs of your sequence. Status code {0}'
.format(self.save_status))
if response.status_code != 200:
self.save_status = response.status_code
raise exceptions.RequestException(
'There was an issue querying the database. Status code {0}'.
format(self.save_status))