def test_readFastaSequence(self):
sd = SeqDepot.new()
fixtures = [
[""">""", [['', '']]],
[""">1""", [['1', '']]],
[""">1\n""", [['1', '']]],
[""">1\nA""", [['1', 'A']]],
[""">1\nAB""", [['1', 'AB']]],
[""">1\nAB\n""", [['1', 'AB']]],
[""">1\nAB\nC""", [['1', 'ABC']]],
[""">1\nAB\nCD\n""", [['1', 'ABCD']]],
[""">1\nA\n>""", [['1', 'A'], ['', '']]],
[""">1\nA\n>2""", [['1', 'A'], ['2', '']]],
[""">1\nA\n>2\n""", [['1', 'A'], ['2', '']]],
[""">1\nA\n>2\nA""", [['1', 'A'], ['2', 'A']]],
[""">1\nA\n>2\nB\n""", [['1', 'A'], ['2', 'B']]],
[""">1\nA\n>2\nB\n>""", [['1', 'A'], ['2', 'B'], ['', '']]],
# Trim leading and trailing whitespace
["""> 1 \nA\n""", [['1', 'A']]],
# Invalid symbols
[""">!@#$\n12345678900""", [['!@#$', '@@@@@@@@@@@']]],
# Skip empty lines
[
"""\n\n>1\nAB\n\n\tCD\n\n>2\n\nEF""",
[['1', 'ABCD'], ['2', 'EF']]
],
[
""">Ecoli CheY\r\nABCDEF\r\n>Ecoli CheA\r\nGHI\r\nJKL\r\n""",
[['Ecoli CheY', 'ABCDEF'], ['Ecoli CheA', 'GHIJKL']]
]
]
for fixture in fixtures:
sd = SeqDepot.new()
fasta, expect = fixture
actual = []
fh = io.StringIO(fasta)
seq = sd.readFastaSequence(fh)
while seq:
actual.append(seq)
seq = sd.readFastaSequence(fh)
self.assertEqual(len(expect), len(actual))
i = 0
for i in range(len(expect)):
self.assertEqual(expect[i][0], actual[i][0])
self.assertEqual(expect[i][1], actual[i][1])
def test_isToolDone(self):
sd = SeqDepot.new()
fixtures = [
[0, '', ''],
[0, 'bob', ''],
[0, None, None],
[0, 'pfam26', None],
[0, None, 'TTT'],
[1, 'agfam1', 'T'],
[1, 'agfam1', 'd'],
[0, 'agfam1', '-'],
[0, 'ecf', 'TTT'],
[1, 'ecf', 'TTdT'],
[1, 'ecf', 'TTdd'],
[1, 'ecf', 'TTdd-'],
[1, 'ecf', 'TTdd-T'],
[0, 'tigrfam', '------------------'],
[1, 'tigrfam', '-----------------T'] ]
i = 0
for fixture in fixtures:
expect, toolId, status = fixture
i += 1
if expect:
assert(sd.isToolDone(toolId, status))
else:
assert(not sd.isToolDone(toolId, status))
def test_findOne(self):
sd = SeqDepot.new()
ids = 'naytI0dLM_rK2kaC1m3ZSQ'
seq = 'MNNEPLRPDPDRLLEQTAAPHRGKLKVFFGACAGVGKTWAMLAEAQRLRAQGLDIVVGVVETHGRKDTAAMLEGLAVLPLKRQAYRGRHISEFDLDAALARRPALILMDELAHSNAPGSRHPKRWQDIEELLEAGIDVFTTVNVQHLESLNDVVSGVTGIQVRETVPDPFFDAADDVVLVDLPPDDLRQRLKEGKVYIAGQAERAIEHFFRKGNLIALRELALRRTADRVDEQMRAWRGHPGEEKVWHTRDAILLCIGHNTGSEKLVRAAARLASRLGSVWHAVYVETPALHRLPEKKRRAILSALRLAQELGAETATLSDPAEEKAVVRYAREHNLGKIILGRPASRRWWRRETFADRLARIAPDLDQVLVALDEPPARTINNAPDNRSFKDKWRVQIQGCVVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARYREQRTRHLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTLTASEEQARMASEREQIRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNLKKEWLTLEEVVGSALQMLEPGLSSPINLSLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQTAPELEEFHEDM'
obj = sd.findOne(ids, {'fields' : 's,l'})
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
self.assertEqual(seq, obj['s'])
obj = sd.findOne(ids)
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
self.assertEqual(seq, obj['s'])
# Attempt to get gis
obj = sd.findOne(ids, {'fields' : 'x(gi)'})
assert(obj['x']['gi'])
assert(len(obj['x']['gi']) > 0)
# Search via GI, PDB, UniProt, and MD5_Hex
fixtures = { 'gi' : 1651302, 'uni':'B1X6M6_ECODH', 'md5_hex' : '9dacad23474b33facada4682d66dd949' }
for fixture in list(fixtures.keys()):
obj = sd.findOne(fixtures[fixture], {'fields' : 'l', 'type' : fixture})
assert(obj);
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
# now by pdb
obj = sd.findOne('4dpk', {'fields' : 'l', 'type' :'pdb'})
assert(obj)
self.assertEqual(359, obj['l']);
self.assertEqual('-0tNbPaXZtNA2gGW668Kqg', obj['id'])
def test_find(self):
sd = SeqDepot.new()
results = sd.find(['naytI0dLM_rK2kaC1m3ZSQ', 'GS8z3QwN5MzpxU0aTuxuaA']);
self.assertEqual(2, len(results));
self.assertEqual(894, results[0]['data']['l']);
results = sd.find('naytI0dLM_rK2kaC1m3ZSQ', {'labelToolData' : 1})
def test_find(self):
sd = SeqDepot.new()
results = sd.find(['naytI0dLM_rK2kaC1m3ZSQ', 'GS8z3QwN5MzpxU0aTuxuaA'])
self.assertEqual(2, len(results))
self.assertEqual(894, results[0]['data']['l'])
results = sd.find('naytI0dLM_rK2kaC1m3ZSQ', {'labelToolData': 1})
def test_toolNames(self):
sd = SeqDepot.new()
toolNames = sd.toolNames()
checks = {}
for name in toolNames:
checks[name] = 1
assert (checks['das'])
assert (checks['tigrfam'])
def test_toolNames(self):
sd = SeqDepot.new()
toolNames = sd.toolNames()
checks = {}
for name in toolNames:
checks[name] = 1
assert(checks['das'])
assert(checks['tigrfam'])
def test_readFastaSequence(self):
sd = SeqDepot.new()
fixtures = [
[""">""", [['', '']]],
[""">1""", [['1', '']]],
[""">1\n""", [['1', '']]],
[""">1\nA""", [['1', 'A']]],
[""">1\nAB""", [['1', 'AB']]],
[""">1\nAB\n""", [['1', 'AB']]],
[""">1\nAB\nC""", [['1', 'ABC']]],
[""">1\nAB\nCD\n""", [['1', 'ABCD']]],
[""">1\nA\n>""", [['1', 'A'], ['', '']]],
[""">1\nA\n>2""", [['1', 'A'], ['2', '']]],
[""">1\nA\n>2\n""", [['1', 'A'], ['2', '']]],
[""">1\nA\n>2\nA""", [['1', 'A'], ['2', 'A']]],
[""">1\nA\n>2\nB\n""", [['1', 'A'], ['2', 'B']]],
[""">1\nA\n>2\nB\n>""", [['1', 'A'], ['2', 'B'], ['', '']]],
# Trim leading and trailing whitespace
["""> 1 \nA\n""", [['1', 'A']]],
# Invalid symbols
[""">!@#$\n12345678900""", [['!@#$', '@@@@@@@@@@@']]],
# Skip empty lines
["""\n\n>1\nAB\n\n\tCD\n\n>2\n\nEF""", [['1', 'ABCD'], ['2', 'EF']]],
[""">Ecoli CheY\r\nABCDEF\r\n>Ecoli CheA\r\nGHI\r\nJKL\r\n""", [['Ecoli CheY', 'ABCDEF'], ['Ecoli CheA', 'GHIJKL']]] ]
for fixture in fixtures:
sd = SeqDepot.new()
fasta, expect = fixture
actual = []
fh = io.StringIO(fasta)
seq = sd.readFastaSequence(fh)
while seq:
actual.append(seq)
seq = sd.readFastaSequence(fh)
self.assertEqual(len(expect), len(actual))
i = 0
for i in range(len(expect)):
self.assertEqual(expect[i][0], actual[i][0])
self.assertEqual(expect[i][1], actual[i][1])
def test_toolFields(self):
sd = SeqDepot.new()
self.assertIsNone(sd.toolFields('bob'))
assert(sd.toolFields('das'))
names = sd.toolFields('das')
self.assertEqual(5, len(names))
self.assertEqual('start', names[0])
self.assertEqual('stop', names[1])
self.assertEqual('peak', names[2])
self.assertEqual('peak_score', names[3])
self.assertEqual('evalue', names[4])
def getSeqDepot(seq):
"""Fetch seqdepot annotation for sequence"""
import SeqDepot
sd = SeqDepot.new()
aseqid = sd.aseqIdFromSequence(seq)
try:
result = sd.findOne(aseqid)
except Exception, e:
print e
result=None
def test_toolFields(self):
sd = SeqDepot.new()
self.assertIsNone(sd.toolFields('bob'))
assert (sd.toolFields('das'))
names = sd.toolFields('das')
self.assertEqual(5, len(names))
self.assertEqual('start', names[0])
self.assertEqual('stop', names[1])
self.assertEqual('peak', names[2])
self.assertEqual('peak_score', names[3])
self.assertEqual('evalue', names[4])
def test_isToolDone(self):
sd = SeqDepot.new()
fixtures = [[0, '', ''], [0, 'bob', ''], [0, None, None],
[0, 'pfam26', None], [0, None, 'TTT'], [1, 'agfam1', 'T'],
[1, 'agfam1', 'd'], [0, 'agfam1', '-'], [0, 'ecf', 'TTT'],
[1, 'ecf', 'TTdT'], [1, 'ecf', 'TTdd'],
[1, 'ecf', 'TTdd-'], [1, 'ecf', 'TTdd-T'],
[0, 'tigrfam', '------------------'],
[1, 'tigrfam', '-----------------T']]
i = 0
for fixture in fixtures:
expect, toolId, status = fixture
i += 1
if expect:
assert (sd.isToolDone(toolId, status))
else:
assert (not sd.isToolDone(toolId, status))
def test_findOne(self):
sd = SeqDepot.new()
ids = 'naytI0dLM_rK2kaC1m3ZSQ'
seq = 'MNNEPLRPDPDRLLEQTAAPHRGKLKVFFGACAGVGKTWAMLAEAQRLRAQGLDIVVGVVETHGRKDTAAMLEGLAVLPLKRQAYRGRHISEFDLDAALARRPALILMDELAHSNAPGSRHPKRWQDIEELLEAGIDVFTTVNVQHLESLNDVVSGVTGIQVRETVPDPFFDAADDVVLVDLPPDDLRQRLKEGKVYIAGQAERAIEHFFRKGNLIALRELALRRTADRVDEQMRAWRGHPGEEKVWHTRDAILLCIGHNTGSEKLVRAAARLASRLGSVWHAVYVETPALHRLPEKKRRAILSALRLAQELGAETATLSDPAEEKAVVRYAREHNLGKIILGRPASRRWWRRETFADRLARIAPDLDQVLVALDEPPARTINNAPDNRSFKDKWRVQIQGCVVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARYREQRTRHLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTLTASEEQARMASEREQIRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNLKKEWLTLEEVVGSALQMLEPGLSSPINLSLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQTAPELEEFHEDM'
obj = sd.findOne(ids, {'fields': 's,l'})
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
self.assertEqual(seq, obj['s'])
obj = sd.findOne(ids)
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
self.assertEqual(seq, obj['s'])
# Attempt to get gis
obj = sd.findOne(ids, {'fields': 'x(gi)'})
assert (obj['x']['gi'])
assert (len(obj['x']['gi']) > 0)
# Search via GI, PDB, UniProt, and MD5_Hex
fixtures = {
'gi': 1651302,
'uni': 'B1X6M6_ECODH',
'md5_hex': '9dacad23474b33facada4682d66dd949'
}
for fixture in list(fixtures.keys()):
obj = sd.findOne(fixtures[fixture], {
'fields': 'l',
'type': fixture
})
assert (obj)
self.assertEqual(len(seq), obj['l'])
self.assertEqual(ids, obj['id'])
# now by pdb
obj = sd.findOne('4dpk', {'fields': 'l', 'type': 'pdb'})
assert (obj)
self.assertEqual(359, obj['l'])
self.assertEqual('-0tNbPaXZtNA2gGW668Kqg', obj['id'])
def test_tools(self):
sd = SeqDepot.new()
tools = sd.tools()
assert(tools['das']);
assert(tools['ecf']);
def test_tools(self):
sd = SeqDepot.new()
tools = sd.tools()
assert (tools['das'])
assert (tools['ecf'])
def test_saveImage(self):
sd = SeqDepot.new()
assert(sd.saveImage(3355692, None, {'type' : 'gi'}))
assert(os.path.isfile('3355692.png'))
assert(os.path.getsize('3355692.png') > 24)
os.remove('3355692.png')
def test_saveImage(self):
sd = SeqDepot.new()
assert (sd.saveImage(3355692, None, {'type': 'gi'}))
assert (os.path.isfile('3355692.png'))
assert (os.path.getsize('3355692.png') > 24)
os.remove('3355692.png')
