def test_aseqIdFromMD5Hex(self):
fixtures = [
['yg8A8H8N-4x1Ezf8WW-YbA', 'ca0f00f07f0dfb8c751337fc596f986c'],
['naytI0dLM_rK2kaC1m3ZSQ', '9dacad23474b33facada4682d66dd949'],
['GS8z3QwN5MzpxU0aTuxuaA', '192f33dd0c0de4cce9c54d1a4eec6e68'] ]
for fixture in fixtures:
aseqId, md5hex = fixture
actual = SeqDepot.aseqIdFromMD5Hex(md5hex)
self.assertEqual(aseqId, actual)
#upper-case
actual = SeqDepot.aseqIdFromMD5Hex(md5hex.upper())
self.assertEqual(aseqId, actual)
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_aseqIdFromMD5Hex(self):
fixtures = [
['yg8A8H8N-4x1Ezf8WW-YbA', 'ca0f00f07f0dfb8c751337fc596f986c'],
['naytI0dLM_rK2kaC1m3ZSQ', '9dacad23474b33facada4682d66dd949'],
['GS8z3QwN5MzpxU0aTuxuaA', '192f33dd0c0de4cce9c54d1a4eec6e68']
]
for fixture in fixtures:
aseqId, md5hex = fixture
actual = SeqDepot.aseqIdFromMD5Hex(md5hex)
self.assertEqual(aseqId, actual)
#upper-case
actual = SeqDepot.aseqIdFromMD5Hex(md5hex.upper())
self.assertEqual(aseqId, actual)
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_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_isValidFieldString(self):
fixtures = [
[1, ''],
[1, None],
[1, 's'],
[1, 'l'],
[0, '@'],
[0, '_!@#$'],
[0, '1234567'],
[0, '1A'],
[1, 'A1'],
[1, 's,l'],
[1, 's(l)'],
[0, 's()'],
[1, 's(l),s(l)'],
[1, 'a,b(c|d|e)'],
[1, 'a,b(c),d(e|f)'],
[0, 'a,b(c),d(e|@)'],
[0, 'a,b(c),d(@|f)'],
[0, 'a,b(@),d(e|f)'],
[0, 'a,b(c),d( |f)'],
[0, ' s'] ]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.isValidFieldString(inp)
if expect:
assert(actual)
else:
assert(not actual)
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_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_cleanSequence(self):
fixtures = [['', ''], ['ABC', 'A B C'], ['abc', 'a b c'],
['ABC', ' ABC '], ['ABC', "\n\r\t\f ABC"],
['A@B@C', "A9B#C"]]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.cleanSequence(inp)
self.assertEqual(expect, actual)
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_aseqIdFromSequence(self):
fixtures = [
['yg8A8H8N-4x1Ezf8WW-YbA', 'MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATTAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML'],
['naytI0dLM_rK2kaC1m3ZSQ', 'MNNEPLRPDPDRLLEQTAAPHRGKLKVFFGACAGVGKTWAMLAEAQRLRAQGLDIVVGVVETHGRKDTAAMLEGLAVLPLKRQAYRGRHISEFDLDAALARRPALILMDELAHSNAPGSRHPKRWQDIEELLEAGIDVFTTVNVQHLESLNDVVSGVTGIQVRETVPDPFFDAADDVVLVDLPPDDLRQRLKEGKVYIAGQAERAIEHFFRKGNLIALRELALRRTADRVDEQMRAWRGHPGEEKVWHTRDAILLCIGHNTGSEKLVRAAARLASRLGSVWHAVYVETPALHRLPEKKRRAILSALRLAQELGAETATLSDPAEEKAVVRYAREHNLGKIILGRPASRRWWRRETFADRLARIAPDLDQVLVALDEPPARTINNAPDNRSFKDKWRVQIQGCVVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARYREQRTRHLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTLTASEEQARMASEREQIRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNLKKEWLTLEEVVGSALQMLEPGLSSPINLSLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQTAPELEEFHEDM'],
['GS8z3QwN5MzpxU0aTuxuaA', 'MSGLRPALSTFIFLLLITGGVYPLLTTVLGQWWFPWQANGSLIREGDTVRGSALIGQNFTGNGYFHGRPSATAEMPYNPQASGGSNLAVSNPELDKLIAARVAALRAANPDASASVPVELVTASASGLDNNITPQAAAWQIPRVAKARNLSVEQLTQLIAKYSQQPLVKYIGQPVVNIVELNLALDKLDE'] ]
for fixture in fixtures:
aseqId, sequence = fixture
actual = SeqDepot.aseqIdFromSequence(sequence)
self.assertEqual(aseqId,actual)
def test_MD5HexFromAseqId(self):
fixtures = [
['ca0f00f07f0dfb8c751337fc596f986c', 'yg8A8H8N-4x1Ezf8WW-YbA'],
['9dacad23474b33facada4682d66dd949', 'naytI0dLM_rK2kaC1m3ZSQ'],
['192f33dd0c0de4cce9c54d1a4eec6e68', 'GS8z3QwN5MzpxU0aTuxuaA']
]
for fixture in fixtures:
md5hex, aseqId = fixture
actual = SeqDepot.MD5HexFromAseqId(aseqId)
self.assertEqual(md5hex, actual)
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_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_cleanSequence(self):
fixtures = [
['', ''],
['ABC', 'A B C'],
['abc', 'a b c'],
['ABC', ' ABC '],
['ABC', "\n\r\t\f ABC"],
['A@B@C', "A9B#C"]]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.cleanSequence(inp)
self.assertEqual(expect, actual)
def test_isValidAseqId(self):
fixtures = [[1,
'yg8A8H8N-4x1Ezf8WW-YbA'], [0, 'yg8A8H8N-4x1Ezf8WW-Yb'],
[0, 'yg8A8H8N-4x1Ezf8WW-YbAA'], [0, None], [0, ''],
[0, 'yg8A8H8N-4x1Ezf8WW-Yb@']]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.isValidAseqId(inp)
if expect:
assert (actual)
else:
assert (not actual)
def test_isValidFieldString(self):
fixtures = [[1, ''], [1, None], [1, 's'], [1, 'l'], [0, '@'],
[0, '_!@#$'], [0, '1234567'], [0, '1A'], [1, 'A1'],
[1, 's,l'], [1, 's(l)'], [0, 's()'], [1, 's(l),s(l)'],
[1, 'a,b(c|d|e)'], [1, 'a,b(c),d(e|f)'],
[0, 'a,b(c),d(e|@)'], [0, 'a,b(c),d(@|f)'],
[0, 'a,b(@),d(e|f)'], [0, 'a,b(c),d( |f)'], [0, ' s']]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.isValidFieldString(inp)
if expect:
assert (actual)
else:
assert (not actual)
def test_isValidAseqId(self):
fixtures = [
[1, 'yg8A8H8N-4x1Ezf8WW-YbA'],
[0, 'yg8A8H8N-4x1Ezf8WW-Yb'],
[0, 'yg8A8H8N-4x1Ezf8WW-YbAA'],
[0, None],
[0, ''],
[0, 'yg8A8H8N-4x1Ezf8WW-Yb@'] ]
for fixture in fixtures:
expect, inp = fixture
actual = SeqDepot.isValidAseqId(inp)
if expect:
assert(actual)
else:
assert( not actual)
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_aseqIdFromSequence(self):
fixtures = [
[
'yg8A8H8N-4x1Ezf8WW-YbA',
'MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATTAPDPLVKFSDVTVDLAARVIHRGEEEVHLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQDPARPRHFITETGIGYRFML'
],
[
'naytI0dLM_rK2kaC1m3ZSQ',
'MNNEPLRPDPDRLLEQTAAPHRGKLKVFFGACAGVGKTWAMLAEAQRLRAQGLDIVVGVVETHGRKDTAAMLEGLAVLPLKRQAYRGRHISEFDLDAALARRPALILMDELAHSNAPGSRHPKRWQDIEELLEAGIDVFTTVNVQHLESLNDVVSGVTGIQVRETVPDPFFDAADDVVLVDLPPDDLRQRLKEGKVYIAGQAERAIEHFFRKGNLIALRELALRRTADRVDEQMRAWRGHPGEEKVWHTRDAILLCIGHNTGSEKLVRAAARLASRLGSVWHAVYVETPALHRLPEKKRRAILSALRLAQELGAETATLSDPAEEKAVVRYAREHNLGKIILGRPASRRWWRRETFADRLARIAPDLDQVLVALDEPPARTINNAPDNRSFKDKWRVQIQGCVVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARYREQRTRHLYEMSKALAVGRSPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALERLTLTASEEQARMASEREQIRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNLKKEWLTLEEVVGSALQMLEPGLSSPINLSLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQTAPELEEFHEDM'
],
[
'GS8z3QwN5MzpxU0aTuxuaA',
'MSGLRPALSTFIFLLLITGGVYPLLTTVLGQWWFPWQANGSLIREGDTVRGSALIGQNFTGNGYFHGRPSATAEMPYNPQASGGSNLAVSNPELDKLIAARVAALRAANPDASASVPVELVTASASGLDNNITPQAAAWQIPRVAKARNLSVEQLTQLIAKYSQQPLVKYIGQPVVNIVELNLALDKLDE'
]
]
for fixture in fixtures:
aseqId, sequence = fixture
actual = SeqDepot.aseqIdFromSequence(sequence)
self.assertEqual(aseqId, actual)
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_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_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')
