diff --git a/.gitignore b/.gitignore index 246d4e4..b5a389a 100755 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ *.pyc /src/sh/*.sh *.swp +/emp-env + diff --git a/config/conf.json b/config/conf.json index a02bba0..22747db 100755 --- a/config/conf.json +++ b/config/conf.json @@ -10,7 +10,7 @@ "hg_th" : "0.05", "permuted_datasets_folder" : "../../data/emp_test/permuted_datasets", "permuted_solutions_folder" : "../../data/emp_test/permuted_solutions", - "true_solutions_folder" : "../../emp_test/true_solutions", + "true_solutions_folder" : "../../data/emp_test/true_solutions", "report_folder" : "../../data/emp_test/report", "n_start" : "0", "n_end" : "1010", diff --git a/data/emp_test/networks/dip.dip_louvain_slices.pkl b/data/emp_test/networks/dip.dip_louvain_slices.pkl new file mode 100644 index 0000000..a70a133 Binary files /dev/null and b/data/emp_test/networks/dip.dip_louvain_slices.pkl differ diff --git a/data/emp_test/networks/dip_louvain_slices.txt b/data/emp_test/networks/dip_louvain_slices.txt new file mode 100644 index 0000000..0707f98 --- /dev/null +++ b/data/emp_test/networks/dip_louvain_slices.txt @@ -0,0 +1,205 @@ +# of cc after modularity optimization: 449 +cc #0: n=34 +[ENSG00000073614, ENSG00000139687, ENSG00000103479, ENSG00000066336, ENSG00000120690, ENSG00000032219, ENSG00000116731, ENSG00000282899, ENSG00000198176, ENSG00000114126, ENSG00000080839, ENSG00000101412, ENSG00000116478, ENSG00000205250, ENSG00000133740, ENSG00000112242, ENSG00000281221, ENSG00000179348, ENSG00000185551, ENSG00000156802, ENSG00000124151, ENSG00000148335, ENSG00000119335, ENSG00000180198, ENSG00000126012, ENSG00000141646, ENSG00000174197, ENSG00000169016, ENSG00000198945, ENSG00000100395, ENSG00000163159, ENSG00000112983, ENSG00000142453, ENSG00000196776] +cc #1: n=29 +[ENSG00000112592, ENSG00000028277, ENSG00000100811, ENSG00000120656, ENSG00000147133, ENSG00000273841, ENSG00000106290, ENSG00000137947, ENSG00000103168, ENSG00000185591, ENSG00000064995, ENSG00000197780, ENSG00000166337, ENSG00000143190, ENSG00000023608, ENSG00000104976, ENSG00000158773, ENSG00000145391, ENSG00000178913, ENSG00000130699, ENSG00000130816, ENSG00000137413, ENSG00000150281, ENSG00000175832, ENSG00000148835, ENSG00000165632, ENSG00000107175, ENSG00000137504, ENSG00000064313] +cc #2: n=16 +[ENSG00000110395, ENSG00000111057, ENSG00000157483, ENSG00000141968, ENSG00000177885, ENSG00000157404, ENSG00000096696, ENSG00000186081, ENSG00000170421, ENSG00000205420, ENSG00000185651, ENSG00000213658, ENSG00000033327, ENSG00000166233, ENSG00000177628, ENSG00000186847] +cc #3: n=21 +[ENSG00000167193, ENSG00000172164, ENSG00000152818, ENSG00000101400, ENSG00000179841, ENSG00000154229, ENSG00000114302, ENSG00000078018, ENSG00000170776, ENSG00000221823, ENSG00000138814, ENSG00000101096, ENSG00000107263, ENSG00000196262, ENSG00000050820, ENSG00000095370, ENSG00000137936, ENSG00000116473, ENSG00000150760, ENSG00000173517, ENSG00000131196] +cc #4: n=25 +[ENSG00000145675, ENSG00000100368, ENSG00000164400, ENSG00000113525, ENSG00000164399, ENSG00000198223, ENSG00000091181, ENSG00000185291, ENSG00000119535, ENSG00000082175, ENSG00000116809, ENSG00000091831, ENSG00000131788, ENSG00000140009, ENSG00000033800, ENSG00000114062, ENSG00000121879, ENSG00000162676, ENSG00000105647, ENSG00000151090, ENSG00000108342, ENSG00000126351, ENSG00000175745, ENSG00000163346, ENSG00000075711] +cc #5: n=27 +[ENSG00000171105, ENSG00000169047, ENSG00000140443, ENSG00000160691, ENSG00000179295, ENSG00000141738, ENSG00000213281, ENSG00000100030, ENSG00000254647, ENSG00000121351, ENSG00000143761, ENSG00000105443, ENSG00000196396, ENSG00000115290, ENSG00000106070, ENSG00000010310, ENSG00000159224, ENSG00000115263, ENSG00000171497, ENSG00000008256, ENSG00000119912, ENSG00000124216, ENSG00000163629, ENSG00000117461, ENSG00000188130, ENSG00000070159, ENSG00000085832] +cc #6: n=35 +[ENSG00000166913, ENSG00000108312, ENSG00000137693, ENSG00000170027, ENSG00000138175, ENSG00000109103, ENSG00000102931, ENSG00000213465, ENSG00000126016, ENSG00000074219, ENSG00000124813, ENSG00000196781, ENSG00000170836, ENSG00000101335, ENSG00000132356, ENSG00000126460, ENSG00000108953, ENSG00000134308, ENSG00000128245, ENSG00000154803, ENSG00000217128, ENSG00000181929, ENSG00000125398, ENSG00000197905, ENSG00000166025, ENSG00000205476, ENSG00000152104, ENSG00000114019, ENSG00000132471, ENSG00000007866, ENSG00000163001, ENSG00000144827, ENSG00000088854, ENSG00000125691, ENSG00000175970] +cc #7: n=28 +[ENSG00000132155, ENSG00000174775, ENSG00000157764, ENSG00000164045, ENSG00000101224, ENSG00000164924, ENSG00000169032, ENSG00000134057, ENSG00000149554, ENSG00000143344, ENSG00000266094, ENSG00000078061, ENSG00000115904, ENSG00000104375, ENSG00000089220, ENSG00000160271, ENSG00000135723, ENSG00000106605, ENSG00000102882, ENSG00000163291, ENSG00000158186, ENSG00000115234, ENSG00000161905, ENSG00000114978, ENSG00000169220, ENSG00000158796, ENSG00000054654, ENSG00000141068] +cc #8: n=18 +[ENSG00000129152, ENSG00000071564, ENSG00000122180, ENSG00000162367, ENSG00000167705, ENSG00000075785, ENSG00000198728, ENSG00000145687, ENSG00000157216, ENSG00000127152, ENSG00000104903, ENSG00000169744, ENSG00000143013, ENSG00000118513, ENSG00000155256, ENSG00000121454, ENSG00000048540, ENSG00000105538] +cc #9: n=27 +[ENSG00000149136, ENSG00000143799, ENSG00000253729, ENSG00000196419, ENSG00000004700, ENSG00000079246, ENSG00000174405, ENSG00000152422, ENSG00000187736, ENSG00000169621, ENSG00000131778, ENSG00000203812, ENSG00000197903, ENSG00000181218, ENSG00000092201, ENSG00000129484, ENSG00000115163, ENSG00000215301, ENSG00000136153, ENSG00000072609, ENSG00000133112, ENSG00000164508, ENSG00000185130, ENSG00000173614, ENSG00000148362, ENSG00000134684, ENSG00000077463] +cc #10: n=20 +[ENSG00000100393, ENSG00000005339, ENSG00000185697, ENSG00000118260, ENSG00000172977, ENSG00000099783, ENSG00000083312, ENSG00000135486, ENSG00000134323, ENSG00000126456, ENSG00000128604, ENSG00000124766, ENSG00000105610, ENSG00000089280, ENSG00000182944, ENSG00000276833, ENSG00000133794, ENSG00000107485, ENSG00000108840, ENSG00000073861] +cc #11: n=22 +[ENSG00000072310, ENSG00000125686, ENSG00000155111, ENSG00000112237, ENSG00000132964, ENSG00000099917, ENSG00000042429, ENSG00000133398, ENSG00000133997, ENSG00000198911, ENSG00000184634, ENSG00000105085, ENSG00000008838, ENSG00000124641, ENSG00000102145, ENSG00000179588, ENSG00000104973, ENSG00000108510, ENSG00000112282, ENSG00000175221, ENSG00000180182, ENSG00000156603] +cc #12: n=21 +[ENSG00000196628, ENSG00000283060, ENSG00000039068, ENSG00000173482, ENSG00000044115, ENSG00000168036, ENSG00000050405, ENSG00000100211, ENSG00000138795, ENSG00000189283, ENSG00000148737, ENSG00000111424, ENSG00000115738, ENSG00000114346, ENSG00000161800, ENSG00000182568, ENSG00000104885, ENSG00000078403, ENSG00000066032, ENSG00000163110, ENSG00000135837] +cc #13: n=30 +[ENSG00000097007, ENSG00000150093, ENSG00000213949, ENSG00000164171, ENSG00000113721, ENSG00000126561, ENSG00000145715, ENSG00000100311, ENSG00000197461, ENSG00000134853, ENSG00000150630, ENSG00000037280, ENSG00000112715, ENSG00000102755, ENSG00000099250, ENSG00000075213, ENSG00000118257, ENSG00000119630, ENSG00000099942, ENSG00000128052, ENSG00000115414, ENSG00000138448, ENSG00000161638, ENSG00000076356, ENSG00000137801, ENSG00000171345, ENSG00000198959, ENSG00000108821, ENSG00000115221, ENSG00000145431] +cc #14: n=36 +[ENSG00000149311, ENSG00000107643, ENSG00000101773, ENSG00000159692, ENSG00000092330, ENSG00000147601, ENSG00000128513, ENSG00000102977, ENSG00000104320, ENSG00000188486, ENSG00000020922, ENSG00000132604, ENSG00000166848, ENSG00000235291, ENSG00000147316, ENSG00000113522, ENSG00000048392, ENSG00000185122, ENSG00000118655, ENSG00000051382, ENSG00000139197, ENSG00000172482, ENSG00000009954, ENSG00000178971, ENSG00000257949, ENSG00000166340, ENSG00000107960, ENSG00000158161, ENSG00000166313, ENSG00000070814, ENSG00000068654, ENSG00000125630, ENSG00000117877, ENSG00000025156, ENSG00000081177, ENSG00000175029] +cc #15: n=20 +[ENSG00000171791, ENSG00000087088, ENSG00000143384, ENSG00000100290, ENSG00000143514, ENSG00000107262, ENSG00000158828, ENSG00000030110, ENSG00000171552, ENSG00000015475, ENSG00000086758, ENSG00000002330, ENSG00000258643, ENSG00000213585, ENSG00000177272, ENSG00000124486, ENSG00000153094, ENSG00000185345, ENSG00000116688, ENSG00000171109] +cc #16: n=33 +[ENSG00000102871, ENSG00000067182, ENSG00000168040, ENSG00000026103, ENSG00000137275, ENSG00000204490, ENSG00000028137, ENSG00000231408, ENSG00000231314, ENSG00000121858, ENSG00000173530, ENSG00000269335, ENSG00000213341, ENSG00000104365, ENSG00000003402, ENSG00000142867, ENSG00000064012, ENSG00000198286, ENSG00000117560, ENSG00000104814, ENSG00000092098, ENSG00000125826, ENSG00000179526, ENSG00000151929, ENSG00000172175, ENSG00000118503, ENSG00000113712, ENSG00000103056, ENSG00000204628, ENSG00000135002, ENSG00000051523, ENSG00000007952, ENSG00000165168] +cc #17: n=15 +[ENSG00000137752, ENSG00000115594, ENSG00000184216, ENSG00000139946, ENSG00000174516, ENSG00000172936, ENSG00000134070, ENSG00000150455, ENSG00000137033, ENSG00000115602, ENSG00000197329, ENSG00000198001, ENSG00000103313, ENSG00000255221, ENSG00000255501] +cc #18: n=22 +[ENSG00000125538, ENSG00000111321, ENSG00000102245, ENSG00000101017, ENSG00000131323, ENSG00000127191, ENSG00000189403, ENSG00000100324, ENSG00000135341, ENSG00000055208, ENSG00000197442, ENSG00000273936, ENSG00000175104, ENSG00000185043, ENSG00000034152, ENSG00000154310, ENSG00000064393, ENSG00000081189, ENSG00000196083, ENSG00000247077, ENSG00000145365, ENSG00000006062] +cc #19: n=33 +[ENSG00000165025, ENSG00000071242, ENSG00000101336, ENSG00000011422, ENSG00000254087, ENSG00000162434, ENSG00000134352, ENSG00000105397, ENSG00000142166, ENSG00000136244, ENSG00000160712, ENSG00000159110, ENSG00000000938, ENSG00000188379, ENSG00000095752, ENSG00000137070, ENSG00000122756, ENSG00000242689, ENSG00000113594, ENSG00000128342, ENSG00000099985, ENSG00000120242, ENSG00000171855, ENSG00000147873, ENSG00000197919, ENSG00000276211, ENSG00000010810, ENSG00000176105, ENSG00000163814, ENSG00000122861, ENSG00000010671, ENSG00000205726, ENSG00000185436] +cc #20: n=34 +[ENSG00000164305, ENSG00000124491, ENSG00000106211, ENSG00000110958, ENSG00000120868, ENSG00000132906, ENSG00000101966, ENSG00000184047, ENSG00000109846, ENSG00000160202, ENSG00000167207, ENSG00000196954, ENSG00000107731, ENSG00000067141, ENSG00000074527, ENSG00000065320, ENSG00000182168, ENSG00000138794, ENSG00000165806, ENSG00000111348, ENSG00000187323, ENSG00000118785, ENSG00000106100, ENSG00000104312, ENSG00000110218, ENSG00000102837, ENSG00000213139, ENSG00000139370, ENSG00000110446, ENSG00000165416, ENSG00000273992, ENSG00000160505, ENSG00000132357, ENSG00000104518] +cc #21: n=32 +[ENSG00000135679, ENSG00000141510, ENSG00000147889, ENSG00000198625, ENSG00000078900, ENSG00000181019, ENSG00000077721, ENSG00000168564, ENSG00000104881, ENSG00000073282, ENSG00000178568, ENSG00000096717, ENSG00000197548, ENSG00000078747, ENSG00000140939, ENSG00000166167, ENSG00000134107, ENSG00000133961, ENSG00000163565, ENSG00000143499, ENSG00000158941, ENSG00000100605, ENSG00000137393, ENSG00000168411, ENSG00000107404, ENSG00000161202, ENSG00000112578, ENSG00000135451, ENSG00000102921, ENSG00000122257, ENSG00000268606, ENSG00000196470] +cc #22: n=12 +[ENSG00000110448, ENSG00000182866, ENSG00000197635, ENSG00000196839, ENSG00000081237, ENSG00000106546, ENSG00000080824, ENSG00000068745, ENSG00000198821, ENSG00000007168, ENSG00000115085, ENSG00000015676] +cc #23: n=17 +[ENSG00000078142, ENSG00000126581, ENSG00000135249, ENSG00000086827, ENSG00000174442, ENSG00000184445, ENSG00000196455, ENSG00000126775, ENSG00000198382, ENSG00000026025, ENSG00000151779, ENSG00000122694, ENSG00000177425, ENSG00000168818, ENSG00000097033, ENSG00000184432, ENSG00000153071] +cc #24: n=22 +[ENSG00000153187, ENSG00000124181, ENSG00000066468, ENSG00000113578, ENSG00000140285, ENSG00000068078, ENSG00000138685, ENSG00000075388, ENSG00000138675, ENSG00000077782, ENSG00000186895, ENSG00000160867, ENSG00000162344, ENSG00000070193, ENSG00000118972, ENSG00000102908, ENSG00000111241, ENSG00000102678, ENSG00000157227, ENSG00000107831, ENSG00000111679, ENSG00000134072] +cc #25: n=32 +[ENSG00000174791, ENSG00000143322, ENSG00000105974, ENSG00000073756, ENSG00000075624, ENSG00000105971, ENSG00000188536, ENSG00000169877, ENSG00000164867, ENSG00000102119, ENSG00000276045, ENSG00000108518, ENSG00000177469, ENSG00000077522, ENSG00000157388, ENSG00000167323, ENSG00000160991, ENSG00000175938, ENSG00000170011, ENSG00000080709, ENSG00000144935, ENSG00000041353, ENSG00000106976, ENSG00000239672, ENSG00000100243, ENSG00000160293, ENSG00000168497, ENSG00000170955, ENSG00000138741, ENSG00000079805, ENSG00000243678, ENSG00000125733] +cc #26: n=18 +[ENSG00000015285, ENSG00000158092, ENSG00000115935, ENSG00000130340, ENSG00000163466, ENSG00000115091, ENSG00000138071, ENSG00000162704, ENSG00000111229, ENSG00000241553, ENSG00000241685, ENSG00000106299, ENSG00000130429, ENSG00000242498, ENSG00000107554, ENSG00000111880, ENSG00000107854, ENSG00000136950] +cc #27: n=12 +[ENSG00000142627, ENSG00000169242, ENSG00000099617, ENSG00000116106, ENSG00000125266, ENSG00000184349, ENSG00000243364, ENSG00000044524, ENSG00000137845, ENSG00000165458, ENSG00000146904, ENSG00000108947] +cc #28: n=35 +[ENSG00000146648, ENSG00000177463, ENSG00000105976, ENSG00000109758, ENSG00000163481, ENSG00000109332, ENSG00000131508, ENSG00000138798, ENSG00000157168, ENSG00000065361, ENSG00000163235, ENSG00000141736, ENSG00000166145, ENSG00000019991, ENSG00000276920, ENSG00000110330, ENSG00000074319, ENSG00000185359, ENSG00000147010, ENSG00000114423, ENSG00000163743, ENSG00000228405, ENSG00000130939, ENSG00000101213, ENSG00000136738, ENSG00000116285, ENSG00000276701, ENSG00000109321, ENSG00000174808, ENSG00000101197, ENSG00000023445, ENSG00000169783, ENSG00000229058, ENSG00000166598, ENSG00000136235] +cc #29: n=17 +[ENSG00000028528, ENSG00000130779, ENSG00000101367, ENSG00000204843, ENSG00000131558, ENSG00000090989, ENSG00000113645, ENSG00000112685, ENSG00000129515, ENSG00000114520, ENSG00000167552, ENSG00000183785, ENSG00000183311, ENSG00000084764, ENSG00000101162, ENSG00000258947, ENSG00000171100] +cc #30: n=23 +[ENSG00000179218, ENSG00000230254, ENSG00000223481, ENSG00000117394, ENSG00000127022, ENSG00000171564, ENSG00000187555, ENSG00000226173, ENSG00000171862, ENSG00000165029, ENSG00000090054, ENSG00000172057, ENSG00000104738, ENSG00000100596, ENSG00000172296, ENSG00000165389, ENSG00000196542, ENSG00000169914, ENSG00000058056, ENSG00000198947, ENSG00000138160, ENSG00000112200, ENSG00000124299] +cc #31: n=10 +[ENSG00000131876, ENSG00000183431, ENSG00000189091, ENSG00000099995, ENSG00000198783, ENSG00000021776, ENSG00000240682, ENSG00000076924, ENSG00000084072, ENSG00000104897] +cc #32: n=15 +[ENSG00000142192, ENSG00000118271, ENSG00000175899, ENSG00000087085, ENSG00000130203, ENSG00000064300, ENSG00000134259, ENSG00000198400, ENSG00000134243, ENSG00000163956, ENSG00000157193, ENSG00000147852, ENSG00000146072, ENSG00000186088, ENSG00000030582] +cc #33: n=19 +[ENSG00000221869, ENSG00000185379, ENSG00000196584, ENSG00000144554, ENSG00000140525, ENSG00000108384, ENSG00000126215, ENSG00000175054, ENSG00000164053, ENSG00000100865, ENSG00000196497, ENSG00000231002, ENSG00000104517, ENSG00000162585, ENSG00000158169, ENSG00000187741, ENSG00000112039, ENSG00000163312, ENSG00000182185] +cc #34: n=29 +[ENSG00000112658, ENSG00000125651, ENSG00000099817, ENSG00000196235, ENSG00000213246, ENSG00000188342, ENSG00000108469, ENSG00000102978, ENSG00000144231, ENSG00000163882, ENSG00000005075, ENSG00000060069, ENSG00000168002, ENSG00000105258, ENSG00000164880, ENSG00000109111, ENSG00000108506, ENSG00000102786, ENSG00000109606, ENSG00000104613, ENSG00000185049, ENSG00000188986, ENSG00000138785, ENSG00000204356, ENSG00000160563, ENSG00000158711, ENSG00000187531, ENSG00000106459, ENSG00000104343] +cc #35: n=12 +[ENSG00000111358, ENSG00000163161, ENSG00000104884, ENSG00000110768, ENSG00000276910, ENSG00000134899, ENSG00000049167, ENSG00000225830, ENSG00000272047, ENSG00000153767, ENSG00000154767, ENSG00000221974] +cc #36: n=38 +[ENSG00000100526, ENSG00000170312, ENSG00000145386, ENSG00000110092, ENSG00000173207, ENSG00000123374, ENSG00000105810, ENSG00000135446, ENSG00000118971, ENSG00000250506, ENSG00000105173, ENSG00000124762, ENSG00000132646, ENSG00000134058, ENSG00000129355, ENSG00000140326, ENSG00000105486, ENSG00000168496, ENSG00000116717, ENSG00000130222, ENSG00000099860, ENSG00000152669, ENSG00000163918, ENSG00000175305, ENSG00000112576, ENSG00000111276, ENSG00000058091, ENSG00000152942, ENSG00000049541, ENSG00000133119, ENSG00000111445, ENSG00000077514, ENSG00000105401, ENSG00000102098, ENSG00000117020, ENSG00000160193, ENSG00000037897, ENSG00000105193] +cc #37: n=14 +[ENSG00000197122, ENSG00000112164, ENSG00000137486, 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ENSG00000107371, ENSG00000077348, ENSG00000172795, ENSG00000272886, ENSG00000038358, ENSG00000179151, ENSG00000151065, ENSG00000126070, ENSG00000189266, ENSG00000105939, ENSG00000274829, ENSG00000114127, ENSG00000075914, ENSG00000035681] +cc #79: n=14 +[ENSG00000108055, ENSG00000164754, ENSG00000129810, ENSG00000118007, ENSG00000101972, ENSG00000062650, ENSG00000072501, ENSG00000083642, ENSG00000121892, ENSG00000135476, ENSG00000101146, ENSG00000110713, ENSG00000146670, ENSG00000137497] +cc #80: n=32 +[ENSG00000170759, ENSG00000140941, ENSG00000161011, ENSG00000130294, ENSG00000148498, ENSG00000034713, ENSG00000170296, ENSG00000113368, ENSG00000160789, ENSG00000023287, ENSG00000163820, ENSG00000197769, ENSG00000175224, ENSG00000123395, ENSG00000101460, ENSG00000177169, ENSG00000197386, ENSG00000197102, ENSG00000174996, ENSG00000154153, ENSG00000139112, ENSG00000144567, ENSG00000141699, ENSG00000221944, ENSG00000161970, ENSG00000153904, ENSG00000184828, ENSG00000156515, ENSG00000102981, ENSG00000111725, ENSG00000084073, ENSG00000176619] +cc #81: n=45 +[ENSG00000137841, ENSG00000136238, ENSG00000149269, ENSG00000070831, ENSG00000067560, ENSG00000114993, ENSG00000140575, ENSG00000175220, ENSG00000132694, ENSG00000061676, ENSG00000273749, ENSG00000183918, ENSG00000117090, ENSG00000254999, ENSG00000112290, ENSG00000158195, ENSG00000102606, ENSG00000129675, ENSG00000122223, ENSG00000170558, ENSG00000134516, ENSG00000155849, ENSG00000128340, ENSG00000138443, ENSG00000038382, ENSG00000198855, ENSG00000163154, ENSG00000129219, ENSG00000181790, ENSG00000166441, ENSG00000170854, ENSG00000169564, ENSG00000131051, ENSG00000088986, ENSG00000105254, ENSG00000079739, ENSG00000148303, ENSG00000100650, ENSG00000161547, ENSG00000197451, ENSG00000196935, ENSG00000138698, ENSG00000111300, ENSG00000173801, ENSG00000124126] +cc #82: n=27 +[ENSG00000128191, ENSG00000175387, ENSG00000166949, ENSG00000069869, ENSG00000187608, ENSG00000113360, ENSG00000163877, ENSG00000088247, ENSG00000110911, ENSG00000131507, ENSG00000049759, ENSG00000108854, ENSG00000101665, ENSG00000170365, ENSG00000108654, ENSG00000198742, ENSG00000124571, ENSG00000113658, ENSG00000141622, ENSG00000136603, ENSG00000157933, ENSG00000137834, ENSG00000182179, ENSG00000144579, ENSG00000175215, ENSG00000144677, ENSG00000184979] +cc #83: n=12 +[ENSG00000113575, ENSG00000105568, ENSG00000073711, ENSG00000140807, ENSG00000102572, ENSG00000172757, ENSG00000106683, ENSG00000143093, ENSG00000104695, ENSG00000128578, ENSG00000142149, ENSG00000110497] +cc #84: n=25 +[ENSG00000100985, ENSG00000274442, ENSG00000197157, ENSG00000148346, ENSG00000167118, ENSG00000142544, ENSG00000174177, ENSG00000275051, ENSG00000182134, ENSG00000124217, ENSG00000135655, ENSG00000170242, ENSG00000037474, ENSG00000110169, ENSG00000155827, ENSG00000162231, ENSG00000030066, ENSG00000070061, ENSG00000142864, ENSG00000159228, ENSG00000124207, ENSG00000144028, ENSG00000134759, ENSG00000134014, ENSG00000102144] +cc #85: n=18 +[ENSG00000188906, ENSG00000142208, ENSG00000103266, ENSG00000276155, ENSG00000059728, ENSG00000108443, ENSG00000117676, ENSG00000101109, ENSG00000151748, ENSG00000140992, ENSG00000150907, ENSG00000109971, ENSG00000004478, ENSG00000166033, ENSG00000159445, ENSG00000119487, ENSG00000040199, ENSG00000151694] +cc #86: n=18 +[ENSG00000197746, ENSG00000178607, ENSG00000165280, ENSG00000070010, ENSG00000113194, ENSG00000071537, ENSG00000135506, ENSG00000198833, ENSG00000159461, ENSG00000088833, ENSG00000162298, ENSG00000100350, ENSG00000077232, ENSG00000184787, ENSG00000051108, ENSG00000185104, ENSG00000167286, ENSG00000044574] +cc #87: n=21 +[ENSG00000175793, ENSG00000061273, ENSG00000092199, ENSG00000129351, ENSG00000159216, ENSG00000067955, ENSG00000134086, ENSG00000103363, ENSG00000154582, ENSG00000122566, ENSG00000166266, ENSG00000120948, ENSG00000167005, ENSG00000111605, ENSG00000204842, ENSG00000049768, ENSG00000282947, ENSG00000143365, ENSG00000070495, ENSG00000146963, ENSG00000048052] +cc #88: n=26 +[ENSG00000131462, ENSG00000137807, ENSG00000182923, ENSG00000175455, ENSG00000112877, ENSG00000078674, ENSG00000142731, ENSG00000137822, ENSG00000103995, ENSG00000151849, ENSG00000076382, ENSG00000123473, ENSG00000046651, ENSG00000141577, ENSG00000101639, ENSG00000174799, ENSG00000136861, ENSG00000083535, ENSG00000198920, ENSG00000075702, ENSG00000127914, ENSG00000206457, ENSG00000143702, ENSG00000126001, ENSG00000058453, ENSG00000114416] +cc #89: n=23 +[ENSG00000170248, ENSG00000101421, ENSG00000076201, ENSG00000254505, ENSG00000249915, ENSG00000138180, ENSG00000164695, ENSG00000182149, ENSG00000255112, ENSG00000130724, ENSG00000115561, ENSG00000131981, ENSG00000124356, ENSG00000131165, ENSG00000086065, ENSG00000162819, ENSG00000119541, ENSG00000083937, ENSG00000132612, ENSG00000166140, ENSG00000175203, ENSG00000172243, ENSG00000072694] +cc #90: n=15 +[ENSG00000106263, ENSG00000130811, ENSG00000104408, ENSG00000100129, ENSG00000084623, ENSG00000149100, ENSG00000280606, ENSG00000178982, ENSG00000100353, ENSG00000147677, ENSG00000184110, ENSG00000107581, ENSG00000104131, ENSG00000173812, ENSG00000173674] +cc #91: n=23 +[ENSG00000118046, ENSG00000135932, ENSG00000131023, ENSG00000134602, ENSG00000114209, ENSG00000115694, ENSG00000136280, ENSG00000001631, ENSG00000266173, ENSG00000112062, ENSG00000153233, ENSG00000123358, ENSG00000104765, ENSG00000151729, ENSG00000180900, ENSG00000116141, ENSG00000150457, ENSG00000181788, ENSG00000198909, ENSG00000105953, ENSG00000197444, ENSG00000154447, ENSG00000172985] +cc #92: n=28 +[ENSG00000196591, ENSG00000112511, ENSG00000106462, ENSG00000102054, ENSG00000178691, ENSG00000113648, ENSG00000099284, ENSG00000170004, ENSG00000149480, ENSG00000162521, ENSG00000008083, ENSG00000074266, ENSG00000108799, ENSG00000139154, ENSG00000278677, ENSG00000129195, ENSG00000261992, ENSG00000151612, ENSG00000167491, ENSG00000057935, ENSG00000178951, ENSG00000100888, ENSG00000080603, ENSG00000198604, ENSG00000168795, ENSG00000236104, ENSG00000119574, ENSG00000119866] +cc #93: n=38 +[ENSG00000101945, ENSG00000089902, ENSG00000004487, ENSG00000167034, ENSG00000198900, ENSG00000238134, ENSG00000088305, ENSG00000165392, ENSG00000047315, ENSG00000105851, ENSG00000166501, ENSG00000123143, ENSG00000143379, ENSG00000181090, ENSG00000271303, ENSG00000117450, ENSG00000135365, ENSG00000066044, ENSG00000084093, ENSG00000088930, ENSG00000163946, ENSG00000196199, ENSG00000134283, ENSG00000120802, ENSG00000153922, ENSG00000237190, ENSG00000231129, ENSG00000196961, ENSG00000104979, ENSG00000089737, ENSG00000146729, ENSG00000068796, ENSG00000100714, ENSG00000101333, ENSG00000116560, ENSG00000112081, ENSG00000119231, ENSG00000197343] +cc #94: n=11 +[ENSG00000088832, ENSG00000198793, ENSG00000164327, ENSG00000141564, ENSG00000167965, ENSG00000115207, ENSG00000148308, ENSG00000077235, ENSG00000112146, ENSG00000100726, ENSG00000101407] +cc #95: n=14 +[ENSG00000155876, ENSG00000116954, ENSG00000083750, ENSG00000149357, ENSG00000116586, ENSG00000177058, ENSG00000188186, ENSG00000134248, ENSG00000159720, ENSG00000185896, ENSG00000147416, ENSG00000100150, ENSG00000114388, ENSG00000103148] +cc #96: n=13 +[ENSG00000177707, ENSG00000110400, ENSG00000143217, ENSG00000137154, ENSG00000130202, ENSG00000073008, ENSG00000100632, ENSG00000102309, ENSG00000112110, ENSG00000174444, ENSG00000008988, ENSG00000122406, ENSG00000149273] +cc #97: n=12 +[ENSG00000182400, ENSG00000054116, ENSG00000007255, ENSG00000169710, ENSG00000084774, ENSG00000153339, ENSG00000160218, ENSG00000168538, ENSG00000171853, ENSG00000113597, ENSG00000196655, ENSG00000170043] +cc #98: n=11 +[ENSG00000076053, ENSG00000147874, ENSG00000249115, ENSG00000213397, ENSG00000214367, ENSG00000131351, ENSG00000152240, ENSG00000137814, ENSG00000092036, ENSG00000139350, ENSG00000060138] +cc #99: n=10 +[ENSG00000168090, ENSG00000198612, ENSG00000111652, ENSG00000141030, ENSG00000169727, ENSG00000166200, ENSG00000138663, ENSG00000121022, ENSG00000144524, ENSG00000119917] +cc #100: n=18 +[ENSG00000120438, ENSG00000179941, ENSG00000181004, ENSG00000125124, ENSG00000125863, ENSG00000138686, ENSG00000174483, ENSG00000122507, ENSG00000140463, ENSG00000160050, ENSG00000163093, ENSG00000165533, ENSG00000166226, ENSG00000163468, ENSG00000150753, ENSG00000115484, ENSG00000156261, ENSG00000113966] +cc #101: n=18 +[ENSG00000147162, ENSG00000117533, ENSG00000149823, ENSG00000135823, ENSG00000104915, ENSG00000206286, ENSG00000151532, ENSG00000099940, ENSG00000118640, ENSG00000136874, ENSG00000004766, ENSG00000141252, ENSG00000143952, ENSG00000140859, ENSG00000156709, ENSG00000124222, ENSG00000117758, ENSG00000049245] diff --git a/data/emp_test/networks/dip_original.dip_louvain_slices.pkl b/data/emp_test/networks/dip_original.dip_louvain_slices.pkl new file mode 100644 index 0000000..e8c350f Binary files /dev/null and b/data/emp_test/networks/dip_original.dip_louvain_slices.pkl differ diff --git a/data/emp_test/networks/dip_original.sif.pkl b/data/emp_test/networks/dip_original.sif.pkl new file mode 100644 index 0000000..7d57e6a Binary files /dev/null and b/data/emp_test/networks/dip_original.sif.pkl differ diff --git a/src/emp/generate_permuted_solutions.py b/src/emp/generate_permuted_solutions.py index e5bc0b0..1e4d056 100755 --- a/src/emp/generate_permuted_solutions.py +++ b/src/emp/generate_permuted_solutions.py @@ -69,6 +69,8 @@ def main(): params=[ [empirical_dist_iteration, [dataset_file, x, algo, network_file, go_folder, permuted_datasets_folder, permuted_solutions_folder, additional_args]] for x in np.arange(int(n_start), int(n_end)) if override_permutations or not permutation_solution_exists(dataset_name, algo, x, permuted_solutions_folder)] print("about to start generation of {} permuted solutions".format(len(params))) p.map(func_star, params) + # for a in params: + # a[0](*a[1]) break_loop=True except (Exception, MemoryError, OSError) as e: diff --git a/src/runners/abstract_runner.py b/src/runners/abstract_runner.py index 5733eef..0129c9d 100755 --- a/src/runners/abstract_runner.py +++ b/src/runners/abstract_runner.py @@ -71,3 +71,4 @@ def main(self, dataset_file_name, network_file_name, go_folder, output_folder, * print(f'about to run algo with the following parameters: {os.path.abspath(dataset_file_name)}, {os.path.abspath(network_file_name)}, {os.path.abspath(output_folder)}, {kwargs}') modules, all_bg_genes = self.run(os.path.abspath(dataset_file_name), os.path.abspath(network_file_name), os.path.abspath(output_folder), **kwargs) + self.build_all_reports(self.ALGO_NAME, modules, all_bg_genes, os.path.abspath(go_folder), os.path.abspath(os.path.join(output_folder, "report"))) diff --git a/src/utils/network.py b/src/utils/network.py index a973532..f012f8a 100755 --- a/src/utils/network.py +++ b/src/utils/network.py @@ -197,13 +197,12 @@ def build_all_reports(algo_name, modules, all_bg_genes, go_folder, output_folder modules_summary = manager.list() params=[] - # p=multiprocessing.Pool(3) + p=multiprocessing.Pool(3) for i, module in enumerate(modules): - # params.append([module_report, [algo_name, i, module, all_bg_genes[i], score_file_name, network_file_name, dataset_name, all_hg_reports, - # modules_summary]]) - module_report(algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary) + params.append([module_report, [algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary]]) + # module_report(algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary) - # p.map(func_star, params) + p.map(func_star, params) modules_summary=list(modules_summary) all_hg_reports=list(all_hg_reports)