def test_EMBL_CCDS_RefSeq(self):
exp = [
CodingSequence(
'CR456855', 'EMBL',
Seq(
'ATGGAGGGTCAACGCTGGCTGCCGCTGGAGGCCAATCCCGAGGTCACCAACCAGTTTCTTAAACAATTAGGTCTACATCCTAACTGGCAATTCGTTGATGTATATGGAATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCTTAA',
IUPACUnambiguousDNA()),
Seq(
'MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'DQ917642', 'EMBL',
Seq(
'ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGAGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGCTGATTTTTCTTTTCAAGTGGCAGCCCGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCCAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTAAGTGTGTTATTGAACTGTACCCATCAGGATGTCCATTTAGGAGAGACATTGTCAGAGTTTAAGGAATTCTCACAAAGTTTTGATGCAGCTATGAAAGGTTTGGCCCTGAGTAATTCGGATGTGATTCGCCAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATGCAAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTACGTTCCTGTGAATGGAAGACTGTACGAATTAGATGGATTAAGAGAAGGACCGATCGATTTAGGTGCATGCAATCAAGATGACTGGATCAGCGCAGTGAGGCCAGTCATAGAAAAAAGGATACAAAAGTACAGTGAAGGTGAAATTCGATTTAACTTAATGGCCATTGTGTCTGACAGGAAAATGATATATGAACAGAAGATAGCAGAGTTACAAAGACAGCTTGCTGAGGAGGAACCCATGGATACAGATCAGGGTAGTAACATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATATAAGATTGAAAACATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAACTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCTCTCGTAGAAAAGGCAAAAGAAAAACAGAATGCGAAGAAGGCACAGGAAACCAAATGA',
IUPACUnambiguousDNA()),
Seq(
'MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDAKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEEPMDTDQGSNMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK',
ExtendedIUPACProtein())),
CodingSequence(
'NM_001270952', 'RefSeq',
Seq(
'ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG',
IUPACUnambiguousDNA()),
Seq(
'MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA',
ExtendedIUPACProtein())),
CodingSequence(
'CCDS73586.1', 'CCDS',
Seq('ATGGATCCTGAACTCCTTAGCATGGTACCAAGACCAGTCTGTGCAGTCTTACTTCTCTTTCCTATTACAGAAAAGTATGAAGTATTCAGAACAGAAGAGGAAGAAAAAATAAAATCTCAGGGACAAGATGTTACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATTGGACTGATTCATGCTATTGCAAACAATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAATTCCTGGAGGAATCTGTGTCAATGAGCCCTGAAGAACGAGCCAGATACCTGGAGAACTATGATGCCATCCGAGTTACTCATGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAGTATAGATGAGAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCGGAAGCCATTTCCAATTAACCATGGTGAAACTAGTGATGAAACTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTATGGAGCGCGACCCTGATGAACTAAGATTTAATGCGATTGCTCTTTCTGCAGCATAG'
),
Seq('MDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA'
)),
CodingSequence(
'CCDS86041.1', 'CCDS',
Seq('ATGACGGGCAATGCCGGGGAGTGGTGCCTCATGGAAAGCGACCCCGGGGTCTTCACCGAGCTCATTAAAGGATTCGGTTGCCGAGGAGCCCAAGTAGAAGAAATATGGAGTTTAGAGCCTGAGAATTTTGAAAAATTAAAGCCAGTTCATGGGTTAATTTTTCTTTTCAAGTGGCAGCCAGGAGAAGAACCAGCAGGCTCTGTGGTTCAGGACTCCCGACTTGACACGATATTTTTTGCTAAGCAGGTAATTAATAATGCTTGTGCTACTCAAGCCATAGTGAGTGTGTTACTGAACTGTACCCACCAGGATGTCCATTTAGGCGAGACATTATCAGAGTTTAAAGAATTTTCACAAAGTTTTGATGCAGCTATGAAAGGCTTGGCACTGAGCAATTCAGATGTGATTCGACAAGTACACAACAGTTTCGCCAGACAGCAAATGTTTGAATTTGATACGAAGACATCAGCAAAAGAAGAAGATGCTTTTCACTTTGTCAGTTATGTTCCTGTTAATGGGAGACTGTATGAATTAGATGGATTAAGAGAAGGACCGATTGATTTAGGTGCATGCAATCAAGATGATTGGATCAGTGCAGTAAGGCCTGTCATAGAAAAAAGGATACAAAAAGACGGGTTTTCACCATGTTGCCCAGGCTGGTCTCAGACTCCTGAGCTCAAGCCATCCGCCTGCCTCGACCTCCCAAAGTGGTACAGTGAAGGTGAAATTCGATTTAATTTAATGGCCATTGTGTCTGACAGAAAAATGATATATGAGCAGAAGATAGCAGAGTTACAAAGACAACTTGCAGAGGAACCCATGGATACAGATCAAGGTAATAGTATGTTAAGTGCTATTCAGTCAGAAGTTGCCAAAAATCAGATGCTTATTGAAGAAGAAGTACAGAAATTAAAAAGATACAAGATTGAGAATATCAGAAGGAAGCATAATTATCTGCCTTTCATTATGGAATTGTTAAAGACTTTAGCAGAACACCAGCAGTTAATACCACTAGTAGAAAAGGCAAAAGAAAAACAGAACGCAAAGAAAGCTCAGGAAACCAAATGA'
),
Seq('MTGNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLDTIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQKDGFSPCCPGWSQTPELKPSACLDLPKWYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGNSMLSAIQSEVAKNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK'
))
]
ids = {
'EMBL': ['CR456855.1', 'DQ917642.1'],
'RefSeq': ['NM_001270952.1'],
'CCDS': ['CCDS73586.1', 'CCDS86041.1']
}
formatter = dba.UrlFormatter()
queries = []
for database, id_list in ids.items():
queries += formatter.format(database, id_list)
loop = asyncio.get_event_loop()
fetcher = dba.Entry_fetcher()
entries = loop.run_until_complete(fetcher.fetch_all(queries))
splitter = dba.EntrySplitter()
entries = splitter.split(entries)
loop.close()
parser = dba.DnaParser()
res = parser.parse(entries)
for item in res:
self.assertTrue(item in exp)
self.assertEqual(len(exp), len(res))
def test_bact_non_standard_start_codon(self):
id_list = ['AH002539']
database = 'EMBL'
exp = CodingSequence(id_list[0], database, eftu1_ecoli_dna_seq,
eftu1_ecoli_protein_seq)
entry = self._fetch_data(database, id_list)[0][1]
res = self.parser.parse_non_eukaryotes(database, entry)
self.assertIn(exp, res) # others will be there - multiple cds
def test_euk_correct_functioning(self):
id_list = ['AJ250042']
database = 'EMBL'
exp = CodingSequence(id_list[0], database, q9uj41_2_dna_seq,
q9uj41_2_protein_seq)
entry = self._fetch_data(database, id_list)[0][1]
res = self.parser.parse(database, BeautifulSoup(entry, 'xml'))
self.assertEqual(res, exp)
def parse(self, database, xml_soup):
'''
Input: Beautifulsoup(xml) of Genbank entry
Output:
entry_id, DNA sequence, Protein sequence
Raises NotAnORF if DNA does not contain a coding sequence (CDS)
'''
is_mrna = bool(xml_soup.find_all('GBSeq_moltype')[0].text.strip() == 'mRNA')
is_dna = bool(xml_soup.find_all('GBSeq_moltype')[0].text.strip() == 'cDNA')
if not (is_dna or is_mrna):
raise NotAnORF
id_ = xml_soup.find_all('GBSeq_locus')[0].text.strip()
features = xml_soup.find_all('GBFeature')
if not features: # entirely unannotated entry - ultra rare
raise SequenceNotFoundError
found = False
for f in features:
if f.GBFeature_key.text.strip() == 'CDS':
loc = f.find_all('GBFeature_location')[0].text
loc = loc
#sometimes format is start...pos2,pos3..stop);
#if pos2 != pos3, or more intervals are indicated, we ignore this entry
if loc.startswith('join('):
loc = loc[5:-1].split('..')
positions = []
for pos in loc:
positions = positions + pos.split(',') #pos2,pos2
positions = list(set(positions))
try:
assert len(positions) == 3
start, stop = positions[0], positions[2]
except (AssertionError, ValueError):
raise NotAnORF
#mostly feature location is simply encoded as start..stop;
else:
start, stop = loc.split('..')
if '<' in start or '>' in stop: # start or stop codon not known
raise NotAnORF
start, stop = int(start), int(stop)
found = True
break
if not found: # not sure this ever happens
raise SequenceNotFoundError
dna_seq = xml_soup.GBSeq_sequence.text.strip().upper()
orf = dna_seq[start-1:stop]
try:
assert orf.startswith('ATG')
assert orf.endswith(('TAA', 'TGA', 'TAG'))
assert len(orf)%3 == 0
except AssertionError:
raise NotAnORF
cds = Seq(orf, IUPACUnambiguousDNA())
return CodingSequence(id_, database, cds, cds.translate(cds=True))
def parse(self, html_soup):
# title: Report for CCDS[id].[version] (current version)
#.[version] is optional.
#" (current version)" might not be present
titlematcher = re.compile(r'Report for CCDS[0-9]*(?:\.[0-9]*)(?:\ \(current version\))?')
id_ = html_soup.find_all(string=titlematcher)[0] #find() does not take kwargs
idmatcher = r'CCDS[0-9]*(?:.[0-9]*)?'
id_ = re.search(idmatcher, id_).group(0)
nucleotides = html_soup.find_all('span', {'id':re.compile('n[0-9]+')})
aminoacids = html_soup.find_all('span', {'id':re.compile('p[0-9]+')})
dna_seq = Seq(''.join([nt.text for nt in nucleotides]),
IUPACUnambiguousDNA())
aa_seq = Seq(''.join([aa.text for aa in aminoacids]), ExtendedIUPACProtein())
assert aa_seq == dna_seq.translate(cds=True)
return CodingSequence(id_, 'CCDS', dna_seq, aa_seq)
def parse_non_eukaryotes(self, database, xml):
xml_soup = BeautifulSoup(xml, 'xml')
id_ = str(xml_soup.find_all('GBSeq_primary-accession')[0].text).strip()
features = xml_soup.find_all('GBFeature')
if not features: # entirely unannotated entry - ultra rare
raise SequenceNotFoundError
found = False
#unlike eukaryotes, there are usually multiple CDS per entry, and they
#might be on complementary strands...
coding_sequences = []
for f in features:
if f.GBFeature_key.text.strip() == 'CDS':
try:
dna_seq = Seq(xml_soup.GBSeq_sequence.text.strip().upper(),
IUPACUnambiguousDNA()) #don't move out of loop...
except AttributeError: #entry does not actually have a normal sequence (e.g. HOPD_ECOLX)
raise SequenceNotFoundError
loc = f.find_all('GBFeature_location')[0].text
start, stop = loc.split('..')
if '<' in start or '>' in stop: # start or stop codon not known
continue
try:
if not 'complement('.upper() in start.upper(): #cds on sense strand
start, stop = int(start), int(stop)
elif 'complement('.upper() in start.upper(): #cds on other strand
#complement([start]..[stop])
start = int(start.split('(')[-1])
stop = int(stop.replace(')', ''))
#reverse complement dna and remap
dna_seq = dna_seq.reverse_complement()
temp = start
start = len(dna_seq) - stop +1
stop = len(dna_seq) - temp +1
except ValueError: #some other abstruse way of indicating starts and stops
continue
orf = dna_seq[start-1:stop]
try:
protein_seq = orf.translate(table=11, cds=True) #note that we use bacterial codon table
coding_sequences.append(CodingSequence(id_, database, orf, protein_seq))
found = True
except TranslationError:
continue #not a good CDS
if not found: # not sure this ever happens
raise NotAnORF
return coding_sequences