def setUp(self):
# load all the motifs by hand.
self.motif_matrices = [
('zfp4_yrk_3p', [[250, 130, 0, 0, 20, 0, 0, 40, 50],
[100, 50, 0, 0, 0, 0, 10, 0, 0],
[10, 200, 380, 380, 0, 380, 150, 340, 0],
[20, 0, 0, 0, 360, 0, 220, 0, 330]]),
('ttgR', [[7.5, 44.5, 0.0, 0.0, 2.5, 47.5, 8.5],
[21.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[3.5000000000000004, 0.0, 0.0, 50.0, 0.0, 0.0, 0.0],
[18.0, 5.5, 50.0, 0.0, 47.5, 2.5, 43.0]]),
('cdaR', [[35, 4, 0, 3, 28, 7, 42, 49, 31, 23],
[1, 7, 0, 57, 20, 46, 5, 1, 6, 5],
[2, 0, 59, 0, 0, 0, 5, 1, 2, 25],
[22, 49, 1, 0, 12, 7, 8, 9, 21, 7]]),
('p22_cI', [[80, 113, 0, 0, 0, 468, 581, 396, 35],
[68, 20, 581, 0, 0, 35, 0, 10, 0],
[160, 0, 0, 0, 0, 0, 0, 10, 0],
[273, 448, 0, 581, 581, 78, 0, 165, 546]]),
('rpol_10', [[23, 373, 105, 210, 210, 0], [43, 0, 66, 51, 97, 19],
[19, 3, 51, 55, 37, 11], [316, 25, 179, 85, 57,
371]]),
('zfp7_ZP10165', [[50, 0, 0, 50, 0, 0, 0, 0, 50, 0, 50],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 50, 50, 50, 0, 50, 0],
[0, 50, 50, 0, 50, 0, 0, 0, 0, 0, 0]]),
('zfp1_efnba2_3p', [[3, 6, 0, 0, 6, 112, 0, 0, 6],
[15, 112, 0, 0, 112, 0, 6, 118, 0],
[100, 0, 118, 118, 0, 0, 112, 0, 112],
[0, 0, 0, 0, 0, 6, 0, 0, 0]]),
('lacI', [[30, 30, 0, 65, 200, 10, 100, 100, 60, 130],
[30, 100, 0, 165, 30, 230, 30, 30, 30, 30],
[200, 100, 0, 10, 10, 10, 30, 30, 40, 40],
[0, 30, 260, 20, 20, 10, 100, 100, 130, 60]]),
('tetR', [[120, 40, 300, 100, 220, 100, 190, 50],
[200, 0, 20, 45, 100, 20, 50, 70],
[20, 300, 50, 20, 20, 200, 100, 150],
[50, 50, 20, 225, 50, 70, 50, 120]]),
('933W_cI', [[985, 548, 1544, 0, 0, 1252, 0, 149],
[0, 801, 0, 0, 0, 20, 1680, 0],
[11, 33, 184, 1728, 0, 0, 0, 1393],
[732, 346, 0, 0, 1728, 456, 48, 186]]),
('zfp6_ZP10363', [[0, 0, 0, 50, 0, 50, 0, 0, 0, 50, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 50, 0, 0, 50, 0, 0, 50, 50, 0, 50],
[50, 0, 50, 0, 0, 0, 50, 0, 0, 0, 0]]),
('zfp5_ZN0024', [[50, 0, 50, 0, 0, 0, 50, 0, 0, 50, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50],
[0, 50, 0, 50, 0, 50, 0, 50, 50, 0, 0],
[0, 0, 0, 0, 50, 0, 0, 0, 0, 0, 0]]),
('434_cI', [[621, 80, 186, 0, 0, 0, 0], [0, 76, 68, 30, 0, 0, 0],
[0, 375, 0, 0, 0, 659, 0],
[38, 128, 405, 629, 659, 0, 659]]),
('zfp2_dab2_3p', [[8, 178, 108, 0, 70, 158, 0, 150, 0],
[0, 0, 0, 0, 0, 0, 0, 20, 8],
[170, 0, 50, 178, 108, 20, 178, 0, 170],
[0, 0, 20, 0, 0, 0, 0, 8, 0]]),
('acuR', [[0.0, 0.0, 0.0, 0.0, 25.0, 21.0, 17.5, 34.5],
[0.0, 0.0, 50.0, 2.0, 7.5, 0.0, 0.0, 0.0],
[50.0, 0.0, 0.0, 0.0, 0.0, 11.5, 0.0, 2.0],
[0.0, 50.0, 0.0, 48.0, 17.5, 17.5, 32.5, 13.5]]),
('rpol_35', [[42, 18, 18, 173, 142, 134, 116],
[0, 0, 6, 135, 140, 50, 90],
[0, 72, 244, 0, 40, 72, 82],
[359, 311, 133, 93, 79, 145, 113]]),
('zfp8_ZP10457', [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50],
[50, 0, 0, 0, 0, 0, 0, 0, 0, 50, 0],
[0, 0, 0, 0, 50, 0, 0, 50, 50, 0, 0],
[0, 50, 50, 50, 0, 50, 50, 0, 0, 0, 0]]),
('lambda_cI', [[50, 170, 45, 85, 30, 110, 0, 300],
[310, 50, 0, 0, 0, 0, 0, 0],
[50, 190, 365, 5, 380, 195, 0, 65],
[0, 0, 0, 320, 0, 105, 410, 45]]),
('rpol_10_ext', [[0, 0, 100, 23, 373, 105, 210, 210, 0],
[60, 0, 100, 43, 0, 66, 51, 97, 19],
[140, 240, 100, 19, 3, 51, 55, 37, 11],
[200, 160, 100, 316, 25, 179, 85, 57, 371]])
]
# load all thresholds by hand
self.thresholds = [
1.0699545943859903, 0.7897693125951122, 0.6726083744651952,
1.2680761835227123, 1.2225352937342997, 0.9676501362039236,
0.87457893821108, 0.8775565485963774, 0.7705603886602805,
1.4143797568075485, 0.9676501362039236, 0.9676501362039236,
1.2748406244294834, 1.024286840459233, 0.6836163375410198,
1.4530032582649177, 0.9676501362039236, 1.1239104755269196,
2.6755385519992174
]
# generate the moodssearch object.
self.moodssearch_obj_fwd = MOODS.MOODSSearch(
[x[1] for x in self.motif_matrices], self.thresholds,
MOODS.flatbg(), 7, True, False)
self.moodssearch_obj_both = MOODS.MOODSSearch(
[x[1] for x in self.motif_matrices], self.thresholds,
MOODS.flatbg(), 7, True, True)
#apFAB46 sequence
self.apFAB46_seq = ('AAAAAGACAATGAAAAGCTTAGTCATGGCGCGCCAAAAAGAGTATTG'
'ACTTCGCATCTTTTTGTACCTATAATAGATTCATTGCTA')
#These are the proper hits.
self.apFAB46_hits = {
'434_cI': [(57, 4.688399966083337), (-6, 3.3910215941638624)],
'933W_cI': [(-61, 4.046026313566105)],
'acuR': [(54, 2.0456700959741143), (-69, 3.325251483672279),
(-34, 2.045670095974115), (-0.0, 7.348975004033191)],
'cdaR': [(29, 3.0419647953759767), (-16, 0.7214691456808224)],
'lacI': [(-57, 1.8194505679247397), (-40, 1.288724504297107)],
'lambda_cI': [(39, 1.9439365463638196)],
'p22_cI': [],
'rpol_10': [(5, 2.0391667799057487), (67, 5.8335347738270835),
(72, 3.2805992559471626), (-68, 4.930825591137652),
(-54, 1.3544349004462848), (-40, 2.4522945494642174),
(-38, 3.1644672601697525), (-15, 3.193650492100148),
(-9, 1.7285308122946124)],
'rpol_10_ext': [(-40, 3.263862791624584)],
'rpol_35': [(9, 2.494746699845068), (44, 4.673608724636109),
(57, 2.1790487168281887), (58, 2.226020656779173),
(60, 2.779856657750668), (61, 1.54573352717996),
(75, 1.6937781338634328), (-79, 1.524973502802859),
(-74, 2.3203399149336397), (-32, 1.8592143421105267),
(-19, 2.55933983358448), (-9, 3.369439254870037),
(-8, 3.834192305019384), (-3, 4.054157145090022),
(-2, 1.7887495239839581)],
'tetR': [(0, 2.35082455257586), (4, 2.301877909267698),
(9, 0.853460927069236), (10, 2.155196197307788),
(33, 1.1931970179468807), (34, 3.1110648177773217),
(66, 1.533984872075769), (69, 2.8253186216029587),
(73, 1.9382219304721406), (-75, 1.129366669586711),
(-64, 2.4065472341224545), (-55, 1.1931970179468807),
(-54, 2.8883371533478757), (-17, 1.282891279146519)],
'ttgR': [(8, 3.09623693618527), (59, 1.1998476766957555),
(-75, 4.694180469193636), (-71, 2.2452537163828197)],
'zfp1_efnba2_3p': [],
'zfp2_dab2_3p': [],
'zfp4_yrk_3p': [],
'zfp5_ZN0024': [],
'zfp6_ZP10363': [],
'zfp7_ZP10165': [],
'zfp8_ZP10457': []
}
# hits computed by the moods search object
self.raw_hits = self.moodssearch_obj_both.search(self.apFAB46_seq)
def setUp(self):
# load all the motifs by hand.
self.motif_matrices = [
('zfp4_yrk_3p',
[[250, 130, 0, 0, 20, 0, 0, 40, 50],
[100, 50, 0, 0, 0, 0, 10, 0, 0],
[10, 200, 380, 380, 0, 380, 150, 340, 0],
[20, 0, 0, 0, 360, 0, 220, 0, 330]]),
('ttgR',
[[7.5, 44.5, 0.0, 0.0, 2.5, 47.5, 8.5],
[21.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[3.5000000000000004, 0.0, 0.0, 50.0, 0.0, 0.0, 0.0],
[18.0, 5.5, 50.0, 0.0, 47.5, 2.5, 43.0]]),
('cdaR',
[[35, 4, 0, 3, 28, 7, 42, 49, 31, 23],
[1, 7, 0, 57, 20, 46, 5, 1, 6, 5],
[2, 0, 59, 0, 0, 0, 5, 1, 2, 25],
[22, 49, 1, 0, 12, 7, 8, 9, 21, 7]]),
('p22_cI',
[[80, 113, 0, 0, 0, 468, 581, 396, 35],
[68, 20, 581, 0, 0, 35, 0, 10, 0],
[160, 0, 0, 0, 0, 0, 0, 10, 0],
[273, 448, 0, 581, 581, 78, 0, 165, 546]]),
('rpol_10',
[[23, 373, 105, 210, 210, 0],
[43, 0, 66, 51, 97, 19],
[19, 3, 51, 55, 37, 11],
[316, 25, 179, 85, 57, 371]]),
('zfp7_ZP10165',
[[50, 0, 0, 50, 0, 0, 0, 0, 50, 0, 50],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 50, 50, 50, 0, 50, 0],
[0, 50, 50, 0, 50, 0, 0, 0, 0, 0, 0]]),
('zfp1_efnba2_3p',
[[3, 6, 0, 0, 6, 112, 0, 0, 6],
[15, 112, 0, 0, 112, 0, 6, 118, 0],
[100, 0, 118, 118, 0, 0, 112, 0, 112],
[0, 0, 0, 0, 0, 6, 0, 0, 0]]),
('lacI',
[[30, 30, 0, 65, 200, 10, 100, 100, 60, 130],
[30, 100, 0, 165, 30, 230, 30, 30, 30, 30],
[200, 100, 0, 10, 10, 10, 30, 30, 40, 40],
[0, 30, 260, 20, 20, 10, 100, 100, 130, 60]]),
('tetR',
[[120, 40, 300, 100, 220, 100, 190, 50],
[200, 0, 20, 45, 100, 20, 50, 70],
[20, 300, 50, 20, 20, 200, 100, 150],
[50, 50, 20, 225, 50, 70, 50, 120]]),
('933W_cI',
[[985, 548, 1544, 0, 0, 1252, 0, 149],
[0, 801, 0, 0, 0, 20, 1680, 0],
[11, 33, 184, 1728, 0, 0, 0, 1393],
[732, 346, 0, 0, 1728, 456, 48, 186]]),
('zfp6_ZP10363',
[[0, 0, 0, 50, 0, 50, 0, 0, 0, 50, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 50, 0, 0, 50, 0, 0, 50, 50, 0, 50],
[50, 0, 50, 0, 0, 0, 50, 0, 0, 0, 0]]),
('zfp5_ZN0024',
[[50, 0, 50, 0, 0, 0, 50, 0, 0, 50, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50],
[0, 50, 0, 50, 0, 50, 0, 50, 50, 0, 0],
[0, 0, 0, 0, 50, 0, 0, 0, 0, 0, 0]]),
('434_cI',
[[621, 80, 186, 0, 0, 0, 0],
[0, 76, 68, 30, 0, 0, 0],
[0, 375, 0, 0, 0, 659, 0],
[38, 128, 405, 629, 659, 0, 659]]),
('zfp2_dab2_3p',
[[8, 178, 108, 0, 70, 158, 0, 150, 0],
[0, 0, 0, 0, 0, 0, 0, 20, 8],
[170, 0, 50, 178, 108, 20, 178, 0, 170],
[0, 0, 20, 0, 0, 0, 0, 8, 0]]),
('acuR',
[[0.0, 0.0, 0.0, 0.0, 25.0, 21.0, 17.5, 34.5],
[0.0, 0.0, 50.0, 2.0, 7.5, 0.0, 0.0, 0.0],
[50.0, 0.0, 0.0, 0.0, 0.0, 11.5, 0.0, 2.0],
[0.0, 50.0, 0.0, 48.0, 17.5, 17.5, 32.5, 13.5]]),
('rpol_35',
[[42, 18, 18, 173, 142, 134, 116],
[0, 0, 6, 135, 140, 50, 90],
[0, 72, 244, 0, 40, 72, 82],
[359, 311, 133, 93, 79, 145, 113]]),
('zfp8_ZP10457',
[[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50],
[50, 0, 0, 0, 0, 0, 0, 0, 0, 50, 0],
[0, 0, 0, 0, 50, 0, 0, 50, 50, 0, 0],
[0, 50, 50, 50, 0, 50, 50, 0, 0, 0, 0]]),
('lambda_cI',
[[50, 170, 45, 85, 30, 110, 0, 300],
[310, 50, 0, 0, 0, 0, 0, 0],
[50, 190, 365, 5, 380, 195, 0, 65],
[0, 0, 0, 320, 0, 105, 410, 45]]),
('rpol_10_ext',
[[0, 0, 100, 23, 373, 105, 210, 210, 0],
[60, 0, 100, 43, 0, 66, 51, 97, 19],
[140, 240, 100, 19, 3, 51, 55, 37, 11],
[200, 160, 100, 316, 25, 179, 85, 57, 371]])
]
# load all thresholds by hand
self.thresholds = [
1.0699545943859903,
0.7897693125951122,
0.6726083744651952,
1.2680761835227123,
1.2225352937342997,
0.9676501362039236,
0.87457893821108,
0.8775565485963774,
0.7705603886602805,
1.4143797568075485,
0.9676501362039236,
0.9676501362039236,
1.2748406244294834,
1.024286840459233,
0.6836163375410198,
1.4530032582649177,
0.9676501362039236,
1.1239104755269196,
2.6755385519992174
]
# generate the moodssearch object.
self.moodssearch_obj_fwd = MOODS.MOODSSearch(
[x[1] for x in self.motif_matrices],
self.thresholds,
MOODS.flatbg(),
7,
True,
False)
self.moodssearch_obj_both = MOODS.MOODSSearch(
[x[1] for x in self.motif_matrices],
self.thresholds,
MOODS.flatbg(),
7,
True,
True)
#apFAB46 sequence
self.apFAB46_seq = ('AAAAAGACAATGAAAAGCTTAGTCATGGCGCGCCAAAAAGAGTATTG'
'ACTTCGCATCTTTTTGTACCTATAATAGATTCATTGCTA')
#These are the proper hits.
self.apFAB46_hits = {
'434_cI': [(57, 4.688399966083337), (-6, 3.3910215941638624)],
'933W_cI': [(-61, 4.046026313566105)],
'acuR': [(54, 2.0456700959741143),
(-69, 3.325251483672279),
(-34, 2.045670095974115),
(-0.0, 7.348975004033191)],
'cdaR': [(29, 3.0419647953759767), (-16, 0.7214691456808224)],
'lacI': [(-57, 1.8194505679247397), (-40, 1.288724504297107)],
'lambda_cI': [(39, 1.9439365463638196)],
'p22_cI': [],
'rpol_10': [(5, 2.0391667799057487),
(67, 5.8335347738270835),
(72, 3.2805992559471626),
(-68, 4.930825591137652),
(-54, 1.3544349004462848),
(-40, 2.4522945494642174),
(-38, 3.1644672601697525),
(-15, 3.193650492100148),
(-9, 1.7285308122946124)],
'rpol_10_ext': [(-40, 3.263862791624584)],
'rpol_35': [(9, 2.494746699845068),
(44, 4.673608724636109),
(57, 2.1790487168281887),
(58, 2.226020656779173),
(60, 2.779856657750668),
(61, 1.54573352717996),
(75, 1.6937781338634328),
(-79, 1.524973502802859),
(-74, 2.3203399149336397),
(-32, 1.8592143421105267),
(-19, 2.55933983358448),
(-9, 3.369439254870037),
(-8, 3.834192305019384),
(-3, 4.054157145090022),
(-2, 1.7887495239839581)],
'tetR': [(0, 2.35082455257586),
(4, 2.301877909267698),
(9, 0.853460927069236),
(10, 2.155196197307788),
(33, 1.1931970179468807),
(34, 3.1110648177773217),
(66, 1.533984872075769),
(69, 2.8253186216029587),
(73, 1.9382219304721406),
(-75, 1.129366669586711),
(-64, 2.4065472341224545),
(-55, 1.1931970179468807),
(-54, 2.8883371533478757),
(-17, 1.282891279146519)],
'ttgR': [(8, 3.09623693618527),
(59, 1.1998476766957555),
(-75, 4.694180469193636),
(-71, 2.2452537163828197)],
'zfp1_efnba2_3p': [],
'zfp2_dab2_3p': [],
'zfp4_yrk_3p': [],
'zfp5_ZN0024': [],
'zfp6_ZP10363': [],
'zfp7_ZP10165': [],
'zfp8_ZP10457': []}
# hits computed by the moods search object
self.raw_hits = self.moodssearch_obj_both.search(self.apFAB46_seq)