def test_regularity(dataset):
choice_sets, choices, person_df = dataset.load()
unique_choice_sets, idx = np.unique(choice_sets, axis=0, return_inverse=True)
tests = 0
for i, j in combinations(range(len(unique_choice_sets)), 2):
c1, c2 = unique_choice_sets[i], unique_choice_sets[j]
if all(c1 * c2 == c2):
c1, c2 = c2, c1
i, j = j, i
if any(c1 * c2 != c1):
continue
c1_counts = np.bincount(choices[idx == i, 0], minlength=len(c1))
c2_counts = np.bincount(choices[idx == j, 0], minlength=len(c1))
c1_tot = np.sum(c1_counts)
c2_tot = np.sum(c2_counts)
c1_prop = c1_counts / c1_tot
c2_prop = c2_counts / c2_tot
c1_names = [dataset.item_names[k] for k in range(len(c1)) if c1[k] == 1]
c2_names = [dataset.item_names[k] for k in range(len(c1)) if c2[k] == 1]
for k in range(len(c1)):
if c1[k] == 1:
tests += 1
oddsratio, pvalue = stats.fisher_exact(
[[c1_counts[k], c1_tot - c1_counts[k]], [c2_counts[k], c2_tot - c2_counts[k]]])
if c1_prop[k] < c2_prop[k] and pvalue < 0.05:
print(f'{dataset.item_names[k]} (p={pvalue:.2g}])\n'
f'\t{c1_prop[k]:.2f} ({c1_tot} samples) in {c1_names} \n'
f'\t{c2_prop[k]:.2f} ({c2_tot} samples) in {c2_names} ')
def FisherScoreCutoff(posScores, negScores):
"""Define the upper and lower 5 percent bounds of the distribution of scores,
then increase the score cutoff by 1/100 the difference between the two scores at a time
compute the Fishter p-value for each score cutoff and record the best one """
#posScores=sorted(posScores,reverse=True)
negScores = sorted(negScores, reverse=True)
contingencyTable = [[0, 0], [0, 0]]
scoreCutoff = negScores[len(negScores) / 100]
posCount = 0
negCount = 0
for i in range(len(posScores)):
if posScores[i] >= scoreCutoff:
posCount += 1
for j in range(len(negScores)):
if negScores[j] >= scoreCutoff:
negCount += 1
contingencyTable[0][0] = posCount
contingencyTable[0][1] = len(posScores) - posCount
contingencyTable[1][0] = negCount
contingencyTable[1][1] = len(negScores) - negCount
ob, p_value = stats.fisher_exact(contingencyTable)
return p_value, scoreCutoff, contingencyTable[0] + contingencyTable[1]
'''upperBound=negScores[len(negScores)/10000]
lowerBound=negScores[len(negScores)/100*50]
print "Lower index",len(negScores)/100*50
print len(posScores),len(negScores)
print "UPPER LOWER",upperBound,lowerBound
intervalnum=100
interval=(upperBound-lowerBound)/intervalnum
print "INTERVAL",interval
bestcuttoff=-100.0
bestpvalue=1.0
contingencyTable=[[0,0],[0,0]]
besttable=contingencyTable
for i in range(intervalnum):
scoreCutoff=lowerBound+interval*i
if scoreCutoff >upperBound:
break
posCount=0
negCount=0
for j in range(len(posScores)):
if posScores[j]>=scoreCutoff:
posCount+=1
for j in range(len(negScores)):
if negScores[j]>=scoreCutoff:
negCount+=1
contingencyTable[0][0]=posCount
contingencyTable[0][1]=len(posScores)-posCount
contingencyTable[1][0]=negCount
contingencyTable[1][1]=len(negScores)-negCount
ob,p_value=stats.fisher_exact(contingencyTable)
#print p_value,scoreCutoff,contingencyTable
if p_value<bestpvalue:
bestpvalue=p_value
bestcuttoff=scoreCutoff
besttable=contingencyTable[0]+contingencyTable[1]
return bestpvalue,bestcuttoff,besttable'''
return
def generate_rules_for_class(self, general_summary, class_name):
special_summary = []
for summary_detail in general_summary:
if summary_detail[1][class_name] > 0:
special_summary.append(summary_detail)
'''
Compute p-value
'''
item_set = string_2_itemset(summary_detail[0])
satisfy_rule = self.freq_itemset_dict.get_frequency(
summary_detail[0])
no_satisfy_rule = self.freq_itemset_dict.ntransactions - satisfy_rule
correct_predict = self.lookup_frequency(item_set, class_name)
incorrect_predict = satisfy_rule - correct_predict
belong_to_class = self.freq_itemset_dict.get_frequency(
class_name)
no_rule_belong_to_class = belong_to_class - correct_predict
contingency_matrix = np.array(
[[correct_predict, incorrect_predict],
[
no_rule_belong_to_class,
no_satisfy_rule - no_rule_belong_to_class
]])
_, p_value = stats.fisher_exact(contingency_matrix)
summary_detail[1]['p-value'] = p_value
return special_summary
def main():
posfile = argv[1]
negfile = argv[2]
fastafile = argv[3]
outfile = argv[4]
totalseq = len(open(fastafile).read().split(">")) - 1
posdict = {}
file = open(posfile)
file.readline()
for line in file:
tmp = line.strip().split('\t')
if tmp[0] not in posdict:
posdict[tmp[0]] = {}
posdict[tmp[0]][tmp[1]] = 1
negdict = {}
file = open(negfile)
file.readline()
for line in file:
tmp = line.strip().split('\t')
if tmp[0] not in negdict:
negdict[tmp[0]] = {}
negdict[tmp[0]][tmp[1]] = 1
lines = []
pvalues = []
#enrichments = []
for motif in posdict:
if motif not in negdict:
print "ERROR, not the same set of motifs"
break
posnum = len(posdict[motif])
negnum = len(negdict[motif])
enrichment, pvalue = stats.fisher_exact([[posnum, totalseq - posnum], [negnum, totalseq - negnum]])
pvalues += [pvalue]
#enrichments = [enrichment]
line = [motif, str(posnum), str(totalseq - posnum), str(negnum), str(totalseq - negnum), str(enrichment), str(pvalue)]
line = '\t'.join(line)
lines += [line]
sortedindex = sorted(range(len(pvalues)), key = lambda x: pvalues[x])
lines = [lines[x] for x in sortedindex]
target = open(outfile,'w')
for line in lines:
target.write(line+'\n')
target.close()
return
def fisher_exact_two_groups(dataset, target_col, protected_col):
"""
Performs a Fisher exact test on a 2x2 contingency table as in scipy.stats.fisher_exact_two_groups()
@param dataset:
@param target_col: name of the column that contains the classifier results
@param protected_col: name of the column that contains the protection status
@return: odds ratio and related p-value
"""
positive_protected = dataset.count_classification_and_category(target_col, protected_col, group=1, accepted=1)
negative_protected = dataset.count_classification_and_category(target_col, protected_col, group=1, accepted=0)
positive_nonprotected = dataset.count_classification_and_category(target_col, protected_col, group=0, accepted=1)
negative_nonprotected = dataset.count_classification_and_category(target_col, protected_col, group=0, accepted=0)
contingency_table = [[positive_protected, negative_protected], [positive_nonprotected, negative_nonprotected]]
return stats.fisher_exact(contingency_table)
def test_discrete(a, b):
# multiple classes, Fisher's exact test, followed by Bonferonni correction
# returns the smallest p-value for all tested classes
all_categories = set(flatten(a))
pvalues = []
for category in all_categories:
# calculate number of items with this category
a1, a0 = get_counts(a, category)
b1, b0 = get_counts(b, category)
# we are only interested in enrichment, so right_tail
oddsratio, pvalue = stats.fisher_exact([[a1, a0], [b1, b0]],
alternative="greater")
pvalues.append((pvalue, category))
# fisher's exact test plus bonferroni correction of number of tests
min_pvalue, min_category = min(pvalues)
min_pvalue *= len(pvalues)
return min_pvalue, min_category
def test_discrete(a, b):
# multiple classes, Fisher's exact test, followed by Bonferonni correction
# returns the smallest p-value for all tested classes
all_categories = set(flatten(a))
pvalues = []
for category in all_categories:
# calculate number of items with this category
a1, a0 = get_counts(a, category)
b1, b0 = get_counts(b, category)
# we are only interested in enrichment, so right_tail
oddsratio, pvalue = stats.fisher_exact([[a1, a0], [b1, b0]],
alternative="greater")
pvalues.append((pvalue, category))
# fisher's exact test plus bonferroni correction of number of tests
min_pvalue, min_category = min(pvalues)
min_pvalue *= len(pvalues)
return min_pvalue, min_category
def TestPatternInNegSeq(posPatternCovLis, posSeqCnt, negSeqFn, allKmerSet):
patternSet = set()
patternCnt = len(posPatternCovLis)
initPatternSet = map(lambda x:x[0], posPatternCovLis)
negSeqLis, negSeqCnt, _, _ = BioinfoComm.loadSinglelineSeq(negSeqFn)
negKmer2seqIdSet = BioinfoComm.FetchCovInSeqLisMutliKmer(negSeqLis, allKmerSet)
negKmer2seqIdInt = BioinfoComm.formatCovId(negKmer2seqIdSet, negSeqCnt)
for pattern, posCov in posPatternCovLis:
posUncov = posSeqCnt - posCov
negCov, _, negKmer2seqIdInt = BioinfoComm.FetchPatternCov(pattern, negSeqLis, negKmer2seqIdInt)
negUncov = negSeqCnt - negCov
dataTable = [[posCov, posUncov], [negCov, negUncov]]
_, rawPValue = stats.fisher_exact(dataTable)
adjustedPvalue = min(rawPValue * patternCnt, 1)
if adjustedPvalue < 0.05: patternSet.add(pattern)
INFO('pattern before negative filter')
INFO(initPatternSet)
INFO('pattern after negative filter')
INFO(patternSet)
return patternSet
def pvalue_calculation(infile):
sample = ((infile.split('_tenmers'))[0]).replace('donor', 'd')
with open(allseqs_background) as inF:
for line in inF:
if 'seqs' in line:
index_sample = ((line.strip()).split('\t')).index(sample)
else:
linea = line.split('\t')
all_background = float(linea[index_sample])
with open(allseqs_snatched) as inF:
for line in inF:
if 'seqs' in line:
index_sample = ((line.strip()).split('\t')).index(sample)
else:
linea = line.split('\t')
all_snatched = float(linea[index_sample])
out = ('fishers_output_%s.txt')%(sample)
o = open(out, 'w')
with open(infile, 'r') as inF:
for line in inF:
linea = (line.strip()).split('\t')
sequence = linea[0]
snatch = float(linea[2])
unsnatch = float(linea[1])
A = snatch
B = unsnatch
C = all_snatched - snatch
D = all_background - unsnatch
oddsratio, pvalue = stats.fisher_exact([[A, B], [C,D]])
outlist = [sequence, str(A), str(B), str(C), str(D), str(pvalue), str(oddsratio), '\n']
output = '\t'.join(outlist)
o.write(output)
def FisherScoreCutoff(posScores,negScores): """Define the upper and lower 5 percent bounds of the distribution of scores, then increase the score cutoff by 1/100 the difference between the two scores at a time compute the Fishter p-value for each score cutoff and record the best one """ #posScores=sorted(posScores,reverse=True) negScores=sorted(negScores,reverse=True) contingencyTable=[[0,0],[0,0]] scoreCutoff=negScores[len(negScores)/100] posCount=0 negCount=0 for i in range(len(posScores)): if posScores[i]>=scoreCutoff: posCount+=1 for j in range(len(negScores)): if negScores[j]>=scoreCutoff: negCount+=1 contingencyTable[0][0]=posCount contingencyTable[0][1]=len(posScores)-posCount contingencyTable[1][0]=negCount contingencyTable[1][1]=len(negScores)-negCount ob,p_value=stats.fisher_exact(contingencyTable) return p_value,scoreCutoff,contingencyTable[0]+contingencyTable[1] '''upperBound=negScores[len(negScores)/10000] lowerBound=negScores[len(negScores)/100*50] print "Lower index",len(negScores)/100*50 print len(posScores),len(negScores) print "UPPER LOWER",upperBound,lowerBound intervalnum=100 interval=(upperBound-lowerBound)/intervalnum print "INTERVAL",interval bestcuttoff=-100.0 bestpvalue=1.0 contingencyTable=[[0,0],[0,0]] besttable=contingencyTable for i in range(intervalnum): scoreCutoff=lowerBound+interval*i if scoreCutoff >upperBound: break posCount=0 negCount=0 for j in range(len(posScores)): if posScores[j]>=scoreCutoff: posCount+=1 for j in range(len(negScores)): if negScores[j]>=scoreCutoff: negCount+=1 contingencyTable[0][0]=posCount contingencyTable[0][1]=len(posScores)-posCount contingencyTable[1][0]=negCount contingencyTable[1][1]=len(negScores)-negCount ob,p_value=stats.fisher_exact(contingencyTable) #print p_value,scoreCutoff,contingencyTable if p_value<bestpvalue: bestpvalue=p_value bestcuttoff=scoreCutoff besttable=contingencyTable[0]+contingencyTable[1] return bestpvalue,bestcuttoff,besttable''' return
def main():
usage = 'usage: %prog anchor_results.txt anchor_results_null.txt\n'\
'Requires two input arguments:\n'\
'1) Interesting anchor results, output from run_anchor_batch.py\n'\
'2) Null anchor results, output from run_anchor_batch.py\n'
parser = OptionParser(usage=usage)
parser.add_option('-1',
'--exon_label1',
dest='exon_label1',
default='Exon label 1',
help='Exon label of anchor_results.txt.')
parser.add_option('-2',
'--exon_label2',
dest='exon_label2',
default='Exon label 2',
help='Exon label of anchor_results_null.txt')
parser.add_option(
'-t',
'--title',
dest='title',
default='Fraction of exons with predicted binding regions',
help='Title of plot.')
(options, args) = parser.parse_args()
if len(args) != 2:
print 'Two arguments need to be specified in command line.\n'
print usage
sys.exit()
anchor_results_path = args[0]
anchor_results_null_path = args[1]
exon_label1 = options.exon_label1
exon_label2 = options.exon_label2
mytitle = options.title
# init dic with keys and empty lists
anchor_dic = {}
for key in ['binding', 'non_binding', 'total']:
anchor_dic[key] = []
for results in [anchor_results_path, anchor_results_null_path]:
binding_count, total_count = count_anchor_results(results)
non_binding_count = total_count - binding_count
for key, val in zip(['binding', 'non_binding', 'total'],
[binding_count, non_binding_count, total_count]):
anchor_dic[key].append(val)
oddsratio, pvalue = \
fisher_exact([anchor_dic['binding'], anchor_dic['non_binding']])
print 'oddsratio: %s\npvalue: %s' % (oddsratio, pvalue)
# plot distributions (from plot_meme_motif_null_comparison.py)
mylabels = [exon_label1, exon_label2]
# Plot bargraphs
frac_binding = float(anchor_dic['binding'][0]) / anchor_dic['total'][0]
frac_binding_null = float(
anchor_dic['binding'][1]) / anchor_dic['total'][1]
myvals = [frac_binding, frac_binding_null]
plot_barplot(myvals, mytitle, mylabels,
ylabel='Fraction predicted binding regions',
mytext1="%i/%i" \
%(anchor_dic['binding'][0],
anchor_dic['total'][0]),
mytext2='%i/%i' %(anchor_dic['binding'][1],
anchor_dic['total'][1]),
mytext3="*Fisher's Exact Test\nP-value=%.2e" %pvalue,
ymin=0,
ymax=1,
width=0.5)
plt.show()
def main():
usage = 'usage: %prog anchor_results.txt anchor_results_null.txt\n'\
'Requires two input arguments:\n'\
'1) Interesting anchor results, output from run_anchor_batch.py\n'\
'2) Null anchor results, output from run_anchor_batch.py\n'
parser = OptionParser(usage=usage)
parser.add_option('-1', '--exon_label1', dest='exon_label1',
default='Exon label 1',
help='Exon label of anchor_results.txt.')
parser.add_option('-2', '--exon_label2', dest='exon_label2',
default='Exon label 2',
help='Exon label of anchor_results_null.txt')
parser.add_option('-t', '--title', dest='title',
default='Fraction of exons with predicted binding regions',
help='Title of plot.')
(options, args) = parser.parse_args()
if len(args) != 2:
print 'Two arguments need to be specified in command line.\n'
print usage
sys.exit()
anchor_results_path = args[0]
anchor_results_null_path = args[1]
exon_label1 = options.exon_label1
exon_label2 = options.exon_label2
mytitle = options.title
# init dic with keys and empty lists
anchor_dic = {}
for key in ['binding', 'non_binding', 'total']:
anchor_dic[key] = []
for results in [anchor_results_path, anchor_results_null_path]:
binding_count, total_count = count_anchor_results(results)
non_binding_count = total_count - binding_count
for key, val in zip(['binding', 'non_binding', 'total'],
[binding_count, non_binding_count, total_count]):
anchor_dic[key].append(val)
oddsratio, pvalue = \
fisher_exact([anchor_dic['binding'], anchor_dic['non_binding']])
print 'oddsratio: %s\npvalue: %s' %(oddsratio, pvalue)
# plot distributions (from plot_meme_motif_null_comparison.py)
mylabels = [exon_label1, exon_label2]
# Plot bargraphs
frac_binding = float(anchor_dic['binding'][0]) / anchor_dic['total'][0]
frac_binding_null = float(anchor_dic['binding'][1]) / anchor_dic['total'][1]
myvals = [frac_binding, frac_binding_null]
plot_barplot(myvals, mytitle, mylabels,
ylabel='Fraction predicted binding regions',
mytext1="%i/%i" \
%(anchor_dic['binding'][0],
anchor_dic['total'][0]),
mytext2='%i/%i' %(anchor_dic['binding'][1],
anchor_dic['total'][1]),
mytext3="*Fisher's Exact Test\nP-value=%.2e" %pvalue,
ymin=0,
ymax=1,
width=0.5)
plt.show()
