-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMerge.peak.py
executable file
·167 lines (143 loc) · 8.16 KB
/
Merge.peak.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
#!/usr/bin/env python3
# -*- encoding: utf-8 -*-
'''
***********************************************************
* Author : Zhou Wei *
* Date : 2020/09/07 17:23:28 *
* E-mail : [email protected] *
* Version : -- *
* You are using the program scripted by Zhou Wei. *
* If you find some bugs, please *
* Please let me know and acknowledge in your publication. *
* Thank you! *
* Best wishes! *
***********************************************************
'''
import os
import errno
import argparse
############################################
############################################
## PARSE ARGUMENTS
############################################
############################################
Description = 'Add sample boolean files and aggregate columns from merged MACS narrow or broad peak file.'
Epilog = """Example usage: python macs2_merged_expand.py <MERGED_INTERVAL_FILE> <SAMPLE_NAME_LIST> <OUTFILE> --is_narrow_peak --min_replicates 1"""
argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
## REQUIRED PARAMETERS
argParser.add_argument('MERGED_INTERVAL_FILE', help="Merged MACS2 interval file created using linux sort and mergeBed.")
argParser.add_argument('SAMPLE_NAME_LIST', help="Comma-separated list of sample names as named in individual MACS2 broadPeak/narrowPeak output file e.g. SAMPLE_R1 for SAMPLE_R1_peak_1.")
argParser.add_argument('OUTFILE', help="Full path to output directory.")
## OPTIONAL PARAMETERS
argParser.add_argument('-in', '--is_narrow_peak', dest="IS_NARROW_PEAK", help="Whether merged interval file was generated from narrow or broad peak files (default: False).",action='store_true')
argParser.add_argument('-mr', '--min_replicates', type=int, dest="MIN_REPLICATES", default=1, help="Minumum number of replicates per sample required to contribute to merged peak (default: 1).")
args = argParser.parse_args()
############################################
############################################
## MAIN FUNCTION
############################################
############################################
## MergedIntervalTxtFile is file created using commands below:
## 1) broadPeak
## sort -k1,1 -k2,2n <MACS_BROADPEAK_FILES_LIST> | mergeBed -c 2,3,4,5,6,7,8,9 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > merged_peaks.txt
## 2) narrowPeak
## sort -k1,1 -k2,2n <MACS_NARROWPEAK_FILE_LIST> | mergeBed -c 2,3,4,5,6,7,8,9,10 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > merged_peaks.txt
def macs2_merged_expand(MergedIntervalTxtFile,SampleNameList,OutFile,isNarrow=False,minReplicates=1):
#makedir(os.path.dirname(OutFile))
os.makedirs( os.path.dirname(OutFile) , exist_ok=True)
combFreqDict = {}
totalOutIntervals = 0
SampleNameList = sorted(SampleNameList)
fin = open(MergedIntervalTxtFile,'r')
fout = open(OutFile,'w')
oFields = ['chr','start','end','interval_id','num_peaks','num_samples'] + [x+'.bool' for x in SampleNameList] + [x+'.fc' for x in SampleNameList] + [x+'.qval' for x in SampleNameList] + [x+'.pval' for x in SampleNameList] + [x+'.start' for x in SampleNameList] + [x+'.end' for x in SampleNameList]
if isNarrow:
oFields += [x+'.summit' for x in SampleNameList]
fout.write('\t'.join(oFields) + '\n')
while True:
line = fin.readline()
if line:
lspl = line.strip().split('\t')
chromID = lspl[0]; mstart = int(lspl[1]); mend = int(lspl[2]);
starts = [int(x) for x in lspl[3].split(',')]; ends = [int(x) for x in lspl[4].split(',')]
names = lspl[5].split(','); fcs = [float(x) for x in lspl[8].split(',')]
pvals = [float(x) for x in lspl[9].split(',')]; qvals = [float(x) for x in lspl[10].split(',')]
summits = []
if isNarrow:
summits = [int(x) for x in lspl[11].split(',')]
## GROUP SAMPLES BY REMOVING TRAILING *_R*
groupDict = {}
for sID in ['_'.join(x.split('_')[:-2]) for x in names]:
gID = '_'.join(sID.split('_')[:-1])
if gID not in groupDict:
groupDict[gID] = []
if sID not in groupDict[gID]:
groupDict[gID].append(sID)
## GET SAMPLES THAT PASS REPLICATE THRESHOLD
passRepThreshList = []
for gID,sIDs in groupDict.items():
if len(sIDs) >= minReplicates:
passRepThreshList += sIDs
## GET VALUES FROM INDIVIDUAL PEAK SETS
fcDict = {}; qvalDict = {}; pvalDict = {}; startDict = {}; endDict = {}; summitDict = {}
for idx in range(len(names)):
sample = '_'.join(names[idx].split('_')[:-2])
if sample in passRepThreshList:
if sample not in fcDict:
fcDict[sample] = []
fcDict[sample].append(str(fcs[idx]))
if sample not in qvalDict:
qvalDict[sample] = []
qvalDict[sample].append(str(qvals[idx]))
if sample not in pvalDict:
pvalDict[sample] = []
pvalDict[sample].append(str(pvals[idx]))
if sample not in startDict:
startDict[sample] = []
startDict[sample].append(str(starts[idx]))
if sample not in endDict:
endDict[sample] = []
endDict[sample].append(str(ends[idx]))
if isNarrow:
if sample not in summitDict:
summitDict[sample] = []
summitDict[sample].append(str(summits[idx]))
samples = sorted(fcDict.keys())
if samples != []:
numSamples = len(samples)
boolList = ['TRUE' if x in samples else 'FALSE' for x in SampleNameList]
fcList = [';'.join(fcDict[x]) if x in samples else 'NA' for x in SampleNameList]
qvalList = [';'.join(qvalDict[x]) if x in samples else 'NA' for x in SampleNameList]
pvalList = [';'.join(pvalDict[x]) if x in samples else 'NA' for x in SampleNameList]
startList = [';'.join(startDict[x]) if x in samples else 'NA' for x in SampleNameList]
endList = [';'.join(endDict[x]) if x in samples else 'NA' for x in SampleNameList]
oList = [str(x) for x in [chromID,mstart,mend,'Interval_'+str(totalOutIntervals+1),len(names),numSamples]+boolList+fcList+qvalList+pvalList+startList+endList]
if isNarrow:
oList += [';'.join(summitDict[x]) if x in samples else 'NA' for x in SampleNameList]
fout.write('\t'.join(oList) + '\n')
tsamples = tuple(sorted(samples))
if tsamples not in combFreqDict:
combFreqDict[tsamples] = 0
combFreqDict[tsamples] += 1
totalOutIntervals += 1
else:
fin.close()
fout.close()
break
## WRITE FILE FOR INTERVAL INTERSECT ACROSS SAMPLES.
## COMPATIBLE WITH UPSETR PACKAGE.
fout = open(OutFile[:-4]+'.intersect.txt','w')
combFreqItems = sorted([(combFreqDict[x],x) for x in combFreqDict.keys()],reverse=True)
for k,v in combFreqItems:
fout.write('%s\t%s\n' % ('&'.join(v),k))
fout.close()
############################################
############################################
## RUN FUNCTION
############################################
############################################
macs2_merged_expand(MergedIntervalTxtFile=args.MERGED_INTERVAL_FILE,SampleNameList=args.SAMPLE_NAME_LIST.split(','),OutFile=args.OUTFILE,isNarrow=args.IS_NARROW_PEAK,minReplicates=args.MIN_REPLICATES)
############################################
############################################
############################################
############################################