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#!/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 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__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()
|
