#!/usr/bin/env python """Tests for the MEME parser """ from __future__ import division from cogent.util.unit_test import TestCase, main import string import re from cogent.motif.util import Motif from cogent.core.moltype import DNA from cogent.parse.record import DelimitedSplitter from cogent.parse.record_finder import LabeledRecordFinder from cogent.parse.meme import * __author__ = "Jeremy Widmann" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Jeremy Widmann", "Rob Knight"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "Jeremy Widmann" __email__ = "jermey.widmann@colorado.edu" __status__ = "Production" class MemeTests(TestCase): """Tests for meme module. """ def setUp(self): """Setup function for meme tests. """ #Meme output data: self.meme_file = MEME_FILE.split('\n') self.meme_main = LabeledRecordFinder(lambda x: x.startswith('COMMAND')) self.meme_command = LabeledRecordFinder(lambda x: x.startswith('MOTIF')) self.meme_summary = LabeledRecordFinder(lambda x: x.startswith('SUMMARY')) self.meme_module = LabeledRecordFinder(lambda x: x.startswith('Motif')) self.alphabet_block, self.main_block = \ list(self.meme_main(self.meme_file)) self.cmd_mod_list = list(self.meme_command(self.main_block)) self.command_block = self.cmd_mod_list[0] self.module_blocks = self.cmd_mod_list[1:] self.summary_block = list(self.meme_summary(self.module_blocks[-1]))[1] self.module_data_blocks = [] for module in self.module_blocks: self.module_data_blocks.append(\ list(self.meme_module(module))) #List and Dict for testing dictFromList function self.sample_list = ['key1',1,'key2',2,'key3',3,'key4',4] self.sample_dict = {'key1':1, 'key2':2, 'key3':3, 'key4':4, } #List of command line data self.command_line_list = [ 'model: mod= tcm nmotifs= 3 evt= 1e+100', 'object function= E-value of product of p-values', 'width: minw= 4 maxw= 10 minic= 0.00', 'width: wg= 11 ws= 1 endgaps= yes', 'nsites: minsites= 2 maxsites= 50 wnsites= 0.8', 'theta: prob= 1 spmap= uni spfuzz= 0.5', 'em: prior= dirichlet b= 0.01 maxiter= 20', 'distance= 1e-05', 'data: n= 597 N= 15', 'strands: +', 'sample: seed= 0 seqfrac= 1', ] #List of dicts which contain general info for each module. self.module_info_dicts = [ {'MOTIF':'1', 'width':'10', 'sites':'11', 'llr':'131', 'E-value':'1.3e-019', }, {'MOTIF':'2', 'width':'7', 'sites':'11', 'llr':'88', 'E-value':'2.5e-006', }, {'MOTIF':'3', 'width':'7', 'sites':'6', 'llr':'53', 'E-value':'5.5e-001', }, ] #Summary dict self.summary_dict = {'CombinedP':{ '1': float(3.48e-02), '11': float(3.78e-05), '17': float(2.78e-08), '28': float(3.49e-06), '105': float(3.98e-06), '159': float(1.08e-02), '402-C01': float(4.22e-07), '407-A07': float(7.32e-08), '410-A10': float(4.23e-04), '505-D01': float(5.72e-07), '507-B04-1': float(1.01e-04), '518-D12': float(2.83e-06), '621-H01': float(8.69e-07), '625-H05': float(8.86e-06), '629-C08': float(5.61e-07), } } self.remap_dict = { '11':'11', '1':'1', '407-A07':'407-A07', '17':'17', '159':'159', '505-D01':'505-D01', '28':'28', '507-B04-1':'507-B04-1', '402-C01':'402-C01', '621-H01':'621-H01', '629-C08':'629-C08', '410-A10':'410-A10', '105':'105', '625-H05':'625-H05', '518-D12':'518-D12' } #ModuleInstances and Modules self.ModuleInstances = [ [ModuleInstance('CTATTGGGGC',Location('629-C08',18,28), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('621-H01',45,55), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('505-D01',26,36), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('407-A07',5,15), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('105',0,10), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('28',3,13), float(1.95e-06)), ModuleInstance('CTATTGGGGC',Location('17',16,26), float(1.95e-06)), ModuleInstance('CTATTGGGCC',Location('402-C01',24,34), float(3.30e-06)), ModuleInstance('CTAGTGGGGC',Location('625-H05',2,12), float(5.11e-06)), ModuleInstance('CTAGTGGGCC',Location('11',15,25), float(6.37e-06)), ModuleInstance('CTATTGGGGT',Location('518-D12',0,10), float(9.40e-06)), ], [ModuleInstance('CGTTACG',Location('629-C08',37,44), float(6.82e-05)), ModuleInstance('CGTTACG',Location('621-H01',30,37), float(6.82e-05)), ModuleInstance('CGTTACG',Location('507-B04-1',8,15), float(6.82e-05)), ModuleInstance('CGTTACG',Location('410-A10',7,14), float(6.82e-05)), ModuleInstance('CGTTACG',Location('407-A07',26,33), float(6.82e-05)), ModuleInstance('CGTTACG',Location('17',0,7), float(6.82e-05)), ModuleInstance('TGTTACG',Location('625-H05',32,39), float(1.74e-04)), ModuleInstance('TGTTACG',Location('505-D01',3,10), float(1.74e-04)), ModuleInstance('CATTACG',Location('518-D12',30,37), float(2.14e-04)), ModuleInstance('CGGTACG',Location('402-C01',1,8), float(2.77e-04)), ModuleInstance('TGTTCCG',Location('629-C08',5,12), float(6.45e-04)), ], [ModuleInstance('CTATTGG',Location('629-C08',57,64), float(1.06e-04)), ModuleInstance('CTATTGG',Location('507-B04-1',42,49), float(1.06e-04)), ModuleInstance('CTATTGG',Location('410-A10',27,34), float(1.06e-04)), ModuleInstance('CTATTGG',Location('159',14,21), float(1.06e-04)), ModuleInstance('CTATTGG',Location('1',18,25), float(1.06e-04)), ModuleInstance('CTAATGG',Location('507-B04-1',28,35), float(1.63e-04)), ], ] self.Modules = [] for module, info in zip(self.ModuleInstances, self.module_info_dicts): curr_module_data = {} for instance in module: curr_module_data[(instance.Location.SeqId, instance.Location.Start)] = instance temp_module = Module(curr_module_data, MolType=DNA, Evalue=float(info['E-value']), Llr=int(info['llr'])) self.Modules.append(temp_module) self.ConsensusSequences = ['CTATTGGGGC','CGTTACG','CTATTGG'] def test_get_data_block(self): """getDataBlock should return the main block and the alphabet.""" main_block, alphabet = getDataBlock(self.meme_file) self.assertEqual(main_block,self.main_block) self.assertEqual(alphabet, DNA) def test_get_alphabet(self): """getMolType should return the correct alphabet.""" self.assertEqual(getMolType(self.alphabet_block),DNA) def test_get_command_module_blocks(self): """getCommandModuleBlocks should return the command and module blocks. """ command_block, module_blocks = getCommandModuleBlocks(self.main_block) self.assertEqual(command_block, self.command_block) self.assertEqual(module_blocks, self.module_blocks) def test_get_summary_block(self): """getSummaryBlock should return the MEME summary block.""" self.assertEqual(getSummaryBlock(self.module_blocks[-1]), self.summary_block) def test_dict_from_list(self): """dictFromList should return a dict given a list.""" self.assertEqual(dictFromList(self.sample_list),self.sample_dict) def test_extract_command_line_data(self): """extractCommandLineData should return a dict of command line data.""" self.assertEqual(extractCommandLineData(self.command_block), self.command_line_list) def test_get_module_data_blocks(self): """getModuleDataBlocks should return a list of blocks for each module. """ self.assertEqual(getModuleDataBlocks(self.module_blocks), self.module_data_blocks) def test_extract_module_data(self): """extractModuleData should return a Module object.""" for data, module in zip(self.module_data_blocks,self.Modules): ans = extractModuleData(data,DNA,self.remap_dict) self.assertEqual(ans,module) def test_get_consensus_sequence(self): """getConsensusSequence should return Module's Consensus sequence.""" for data,seq in zip(self.module_data_blocks,self.ConsensusSequences): ans = getConsensusSequence(data[1]) self.assertEqual(ans,seq) def test_get_module_general_info(self): """getModuleGeneralInfo should return a dict of Module info.""" for module, data_dict in zip(self.module_data_blocks, self.module_info_dicts): self.assertEqual(getModuleGeneralInfo(module[0][0]),data_dict) #Test that getModuleGeneralInfo can parse general info line when # motif ID is > 100. MEME changes the format of this line when in this # case. data_line_special = \ 'MOTIF100 width = 50 sites = 2 llr = 273 E-value = 3.1e-007' expected = {'MOTIF':'100','width':'50','sites':'2','llr':'273',\ 'E-value':'3.1e-007'} self.assertEqual(getModuleGeneralInfo(data_line_special),expected) def test_extract_summary_data(self): """extractSummaryData should return a dict of MEME summary data.""" self.assertEqual(extractSummaryData(self.summary_block), self.summary_dict) def test_meme_parser(self): """MemeParser should correctly return a MotifResults object.""" test_motif_results = MotifResults([],[],{}) test_motif_results.Results = self.summary_dict test_motif_results.Results['Warnings']=[] test_motif_results.Parameters = self.command_line_list test_motif_results.Modules = self.Modules ans_motif_results = MemeParser(self.meme_file) self.assertEqual(ans_motif_results.Modules,test_motif_results.Modules) self.assertEqual(ans_motif_results.Results,test_motif_results.Results) self.assertEqual(ans_motif_results.Parameters, test_motif_results.Parameters) MEME_FILE = """ ******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2001/03/03 13:05:22) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.sdsc.edu. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= meme.16346.data ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 26 11 1.0000 25 17 1.0000 26 28 1.0000 26 105 1.0000 21 159 1.0000 21 402-C01 1.0000 34 407-A07 1.0000 34 410-A10 1.0000 34 505-D01 1.0000 49 507-B04-1 1.0000 49 518-D12 1.0000 49 621-H01 1.0000 74 625-H05 1.0000 65 629-C08 1.0000 64 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme meme.16346.data -dna -mod tcm -nmotifs 3 -minw 4 -maxw 10 -evt 1e100 -time 720 -maxsize 60000 -nostatus -maxiter 20 model: mod= tcm nmotifs= 3 evt= 1e+100 object function= E-value of product of p-values width: minw= 4 maxw= 10 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 50 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 20 distance= 1e-05 data: n= 597 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.173 C 0.206 G 0.299 T 0.322 Background letter frequencies (from dataset with add-one prior applied): A 0.173 C 0.207 G 0.298 T 0.322 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 11 llr = 131 E-value = 1.3e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a::::::: pos.-specific C a:::::::29 probability G :::2:aaa8: matrix T :a:8a::::1 bits 2.5 * 2.3 * * 2.0 * * 1.8 * * *** * Information 1.5 *** **** * content 1.3 *** ****** (17.2 bits) 1.0 ********** 0.8 ********** 0.5 ********** 0.3 ********** 0.0 ---------- Multilevel CTATTGGGGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------- 629-C08 19 1.95e-06 TCCGTGAACA CTATTGGGGC GTGTAAGAGC 621-H01 46 1.95e-06 CGCATGCGTG CTATTGGGGC GTCATTTGTC 505-D01 27 1.95e-06 TTGATTGTTG CTATTGGGGC ATTGCCGTAC 407-A07 6 1.95e-06 CGTTA CTATTGGGGC GGGTATTTTC 105 1 1.95e-06 . CTATTGGGGC CGAAATGGTT 28 4 1.95e-06 TCC CTATTGGGGC CAAGGGCTAC 17 17 1.95e-06 GCTACTTGTG CTATTGGGGC 402-C01 25 3.30e-06 CTTAACATTC CTATTGGGCC 625-H05 3 5.11e-06 GC CTAGTGGGGC AGCTGACAGA 11 16 6.37e-06 TGTTAGACAG CTAGTGGGCC 518-D12 1 9.40e-06 . CTATTGGGGT GTTGTATTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 629-C08 2e-06 18_[1]_36 621-H01 2e-06 45_[1]_19 505-D01 2e-06 26_[1]_13 407-A07 2e-06 5_[1]_19 105 2e-06 [1]_11 28 2e-06 3_[1]_13 17 2e-06 16_[1] 402-C01 3.3e-06 24_[1] 625-H05 5.1e-06 2_[1]_53 11 6.4e-06 15_[1] 518-D12 9.4e-06 [1]_39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=11 629-C08 ( 19) CTATTGGGGC 1 621-H01 ( 46) CTATTGGGGC 1 505-D01 ( 27) CTATTGGGGC 1 407-A07 ( 6) CTATTGGGGC 1 105 ( 1) CTATTGGGGC 1 28 ( 4) CTATTGGGGC 1 17 ( 17) CTATTGGGGC 1 402-C01 ( 25) CTATTGGGCC 1 625-H05 ( 3) CTAGTGGGGC 1 11 ( 16) CTAGTGGGCC 1 518-D12 ( 1) CTATTGGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 462 bayes= 6.40183 E= 1.3e-019 -1010 227 -1010 -1010 -1010 -1010 -1010 164 253 -1010 -1010 -1010 -1010 -1010 -71 135 -1010 -1010 -1010 164 -1010 -1010 174 -1010 -1010 -1010 174 -1010 -1010 -1010 174 -1010 -1010 -19 146 -1010 -1010 214 -1010 -182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 11 E= 1.3e-019 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.000000 0.909091 0.000000 0.090909 -------------------------------------------------------------------------------- Time 0.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 7 sites = 11 llr = 88 E-value = 2.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1::9:: pos.-specific C 7:::1a: probability G :91:::a matrix T 3:9a::: bits 2.5 2.3 * 2.0 ** 1.8 *** Information 1.5 **** content 1.3 ******* (11.6 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ******* 0.0 ------- Multilevel CGTTACG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- 629-C08 38 6.82e-05 CGTGTAAGAG CGTTACG TGTTCCGTGA 621-H01 31 6.82e-05 CGAGGGAGTA CGTTACG CATGCGTGCT 507-B04-1 9 6.82e-05 CTTGCACA CGTTACG TGTGAGCCAT 410-A10 8 6.82e-05 CTTTGCT CGTTACG TGGTTGTATG 407-A07 27 6.82e-05 GGTATTTTCC CGTTACG T 17 1 6.82e-05 . CGTTACG CTACTTGTGC 625-H05 33 1.74e-04 ATAGGTCGAC TGTTACG GTTAGCGTTC 505-D01 4 1.74e-04 GCA TGTTACG TGACTTTTGA 518-D12 31 2.14e-04 GTTATTGCGA CATTACG CGTTCTGGTT 402-C01 2 2.77e-04 C CGGTACG GTTTGTCTTA 629-C08 6 6.45e-04 TTACG TGTTCCG TGAACACTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 629-C08 0.00064 5_[2]_25_[2]_20 621-H01 6.8e-05 30_[2]_37 507-B04-1 6.8e-05 8_[2]_34 410-A10 6.8e-05 7_[2]_20 407-A07 6.8e-05 26_[2]_1 17 6.8e-05 [2]_19 625-H05 0.00017 32_[2]_26 505-D01 0.00017 3_[2]_39 518-D12 0.00021 30_[2]_12 402-C01 0.00028 1_[2]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=7 seqs=11 629-C08 ( 38) CGTTACG 1 621-H01 ( 31) CGTTACG 1 507-B04-1 ( 9) CGTTACG 1 410-A10 ( 8) CGTTACG 1 407-A07 ( 27) CGTTACG 1 17 ( 1) CGTTACG 1 625-H05 ( 33) TGTTACG 1 505-D01 ( 4) TGTTACG 1 518-D12 ( 31) CATTACG 1 402-C01 ( 2) CGGTACG 1 629-C08 ( 6) TGTTCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 507 bayes= 6.53743 E= 2.5e-006 -1010 181 -1010 -24 -93 -1010 161 -1010 -1010 -1010 -171 150 -1010 -1010 -1010 164 239 -118 -1010 -1010 -1010 227 -1010 -1010 -1010 -1010 174 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 11 E= 2.5e-006 0.000000 0.727273 0.000000 0.272727 0.090909 0.000000 0.909091 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.000000 1.000000 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 0.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 7 sites = 6 llr = 53 E-value = 5.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a2::: pos.-specific C a:::::: probability G :::::aa matrix T :a:8a:: bits 2.5 * 2.3 * * 2.0 * * 1.8 * * ** Information 1.5 *** *** content 1.3 *** *** (12.7 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ******* 0.0 ------- Multilevel CTATTGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- 629-C08 58 1.06e-04 TCCGTGAACA CTATTGG 507-B04-1 43 1.06e-04 TGGTGTTGCG CTATTGG 410-A10 28 1.06e-04 TTGTATGCCG CTATTGG 159 15 1.06e-04 GACCGTTGGT CTATTGG 1 19 1.06e-04 TTGGATAGTG CTATTGG G 507-B04-1 29 1.63e-04 GAGCCATTCT CTAATGG TGTTGCGCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 629-C08 0.00011 57_[3] 507-B04-1 0.00016 28_[3]_7_[3] 410-A10 0.00011 27_[3] 159 0.00011 14_[3] 1 0.00011 18_[3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=7 seqs=6 629-C08 ( 58) CTATTGG 1 507-B04-1 ( 43) CTATTGG 1 410-A10 ( 28) CTATTGG 1 159 ( 15) CTATTGG 1 1 ( 19) CTATTGG 1 507-B04-1 ( 29) CTAATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 507 bayes= 6.83576 E= 5.5e-001 -923 227 -923 -923 -923 -923 -923 164 253 -923 -923 -923 -6 -923 -923 137 -923 -923 -923 164 -923 -923 174 -923 -923 -923 174 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 6 E= 5.5e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 3.48e-02 26 11 3.78e-05 15_[1(6.37e-06)] 17 2.78e-08 [2(6.82e-05)]_9_[1(1.95e-06)] 28 3.49e-06 3_[1(1.95e-06)]_13 105 3.98e-06 [1(1.95e-06)]_11 159 1.08e-02 21 402-C01 4.22e-07 24_[1(3.30e-06)] 407-A07 7.32e-08 5_[1(1.95e-06)]_11_[2(6.82e-05)]_1 410-A10 4.23e-04 7_[2(6.82e-05)]_20 505-D01 5.72e-07 26_[1(1.95e-06)]_13 507-B04-1 1.01e-04 8_[2(6.82e-05)]_34 518-D12 2.83e-06 [1(9.40e-06)]_39 621-H01 8.69e-07 30_[2(6.82e-05)]_8_[1(1.95e-06)]_19 625-H05 8.86e-06 2_[1(5.11e-06)]_53 629-C08 5.61e-07 18_[1(1.95e-06)]_9_[2(6.82e-05)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: compute-0-2.local ******************************************************************************** """ #run if called from command-line if __name__ == "__main__": main()