def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML, parser=MinimalBlastParser7)
self.assertEqual(len(list(result.keys())), 1)
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML, xml=True)
class BlastXmlResultTests(TestCase):
"""Tests parsing of output of Blast with output mode 7 (XML)."""
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML, xml=True)
def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML, parser=MinimalBlastParser7)
self.assertEqual(len(list(result.keys())), 1)
# make sure whether normal Blast parser still works upon code merge!
def test_parsed_query_sequence(self):
"""The result dict should have one query sequence as a key."""
# The full query sequence is not given in the XML file.
# Thus it is not checked explicitly, only whether there is
# exactly one found.
self.assertEqual(len(list(self.result.keys())), 1)
def test_parsed_iterations(self):
"""The result should have the right number of iterations."""
n_iter = 0
for query_id, hits in self.result.iterHitsByQuery():
n_iter += 1
self.assertEqual(n_iter, 1)
def test_parsed_hsps(self):
"""The result should have the right number of hsps."""
n_hsps = 0
for query_id, hsps in self.result.iterHitsByQuery():
n_hsps += len(hsps)
self.assertEqual(n_hsps, 3)
def test_parse_hit_details(self):
"""The result should have data from hit fields."""
for query in self.result:
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['SUBJECT_ID'],
"gi|148670104|gb|EDL02051.1|")
self.assertEqual(
first_hsp['HIT_DEF'],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]"
)
self.assertEqual(first_hsp['HIT_ACCESSION'], "2001")
self.assertEqual(first_hsp['HIT_LENGTH'], 707)
def test_parse_hsp_details(self):
"""The result should have data from hsp fields."""
for query in self.result:
# should check integers in next version.
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['QUERY ID'], 1)
self.assertEqual(first_hsp['BIT_SCORE'], '1023.46')
self.assertEqual(first_hsp['SCORE'], '2645')
self.assertEqual(first_hsp['E_VALUE'], '0.333')
self.assertEqual(first_hsp['QUERY_START'], '4')
self.assertEqual(first_hsp['QUERY_END'], '18')
self.assertEqual(first_hsp['QUERY_ALIGN'],
'ELEPHANTTHISISAHITTIGER')
self.assertEqual(first_hsp['MIDLINE_ALIGN'], 'ORCA-WHALE')
self.assertEqual(first_hsp['SUBJECT_ALIGN'],
'SEALSTHIS---HIT--GER')
self.assertEqual(first_hsp['SUBJECT_START'], '5')
self.assertEqual(first_hsp['SUBJECT_END'], '19')
self.assertEqual(first_hsp['PERCENT_IDENTITY'], '55')
self.assertEqual(first_hsp['POSITIVE'], '555')
self.assertEqual(first_hsp['GAP_OPENINGS'], 0)
self.assertEqual(first_hsp['ALIGNMENT_LENGTH'], '14')
gap_hsp = self.result[query][0][1]
self.assertEqual(gap_hsp['GAP_OPENINGS'], '33')
def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML,parser=MinimalBlastParser7)
self.assertEqual(len(result.keys()),1)
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML,xml=True)
class BlastXmlResultTests(TestCase):
"""Tests parsing of output of Blast with output mode 7 (XML)."""
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML,xml=True)
def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML,parser=MinimalBlastParser7)
self.assertEqual(len(result.keys()),1)
# make sure whether normal Blast parser still works upon code merge!
def test_parsed_query_sequence(self):
"""The result dict should have one query sequence as a key."""
# The full query sequence is not given in the XML file.
# Thus it is not checked explicitly, only whether there is
# exactly one found.
self.assertEqual(len(self.result.keys()),1)
def test_parsed_iterations(self):
"""The result should have the right number of iterations."""
n_iter = 0
for query_id,hits in self.result.iterHitsByQuery():
n_iter += 1
self.assertEqual(n_iter,1)
def test_parsed_hsps(self):
"""The result should have the right number of hsps."""
n_hsps = 0
for query_id,hsps in self.result.iterHitsByQuery():
n_hsps += len(hsps)
self.assertEqual(n_hsps,3)
def test_parse_hit_details(self):
"""The result should have data from hit fields."""
for query in self.result:
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['SUBJECT_ID'],
"gi|148670104|gb|EDL02051.1|")
self.assertEqual(first_hsp['HIT_DEF'],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]")
self.assertEqual(first_hsp['HIT_ACCESSION'],"2001")
self.assertEqual(first_hsp['HIT_LENGTH'],707)
def test_parse_hsp_details(self):
"""The result should have data from hsp fields."""
for query in self.result:
# should check integers in next version.
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['QUERY ID'],1)
self.assertEqual(first_hsp['BIT_SCORE'],'1023.46')
self.assertEqual(first_hsp['SCORE'],'2645')
self.assertEqual(first_hsp['E_VALUE'],'0.333')
self.assertEqual(first_hsp['QUERY_START'],'4')
self.assertEqual(first_hsp['QUERY_END'],'18')
self.assertEqual(first_hsp['QUERY_ALIGN'],'ELEPHANTTHISISAHITTIGER')
self.assertEqual(first_hsp['MIDLINE_ALIGN'],'ORCA-WHALE')
self.assertEqual(first_hsp['SUBJECT_ALIGN'],'SEALSTHIS---HIT--GER')
self.assertEqual(first_hsp['SUBJECT_START'],'5')
self.assertEqual(first_hsp['SUBJECT_END'],'19')
self.assertEqual(first_hsp['PERCENT_IDENTITY'],'55')
self.assertEqual(first_hsp['POSITIVE'],'555')
self.assertEqual(first_hsp['GAP_OPENINGS'],0)
self.assertEqual(first_hsp['ALIGNMENT_LENGTH'],'14')
gap_hsp = self.result[query][0][1]
self.assertEqual(gap_hsp['GAP_OPENINGS'],'33')