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
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
|
# Time-stamp: <2020-11-24 16:48:57 Tao Liu>
"""Description: obsolete function
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# python modules
# ------------------------------------
import os
import sys
from time import strftime
# ------------------------------------
# own python modules
# ------------------------------------
# from MACS3.IO import cBedGraphIO
# from MACS3.IO.cDiffScore import DiffScoreTrackI
# from MACS3.IO.cPeakIO import PeakIO
# from MACS3.OptValidator import opt_validate_diffpeak
# from MACS3.Prob import binomial_cdf_inv
# from MACS3.PeakModel import PeakModel,NotEnoughPairsException
# from MACS3.PeakDetect import PeakDetect
# from MACS3.Constants import *
# ------------------------------------
# constants
# ------------------------------------
# ------------------------------------
# Misc functions
# ------------------------------------
import logging
import MACS3.Utilities.Logger
logger = logging.getLogger(__name__)
debug = logger.debug
info = logger.info
# ------------------------------------
# Main function
# ------------------------------------
def run( args ):
"""The Differential function/pipeline for MACS.
"""
return
# # Parse options...
# options = opt_validate_diffpeak( args )
# #0 output arguments
# # info("\n"+options.argtxt)
# ofile_prefix = options.name
# # check if tag files exist
# with open(options.t1bdg) as f: pass
# with open(options.c1bdg) as f: pass
# with open(options.t2bdg) as f: pass
# with open(options.c2bdg) as f: pass
# if not options.peaks1 == '':
# info("Read peaks for condition 1...")
# p1io = PeakIO()
# with open(options.peaks1, 'rU') as f:
# p1io.read_from_xls(f)
# if not options.peaks2 == '':
# info("Read peaks for condition 2...")
# p2io = PeakIO()
# with open(options.peaks2, 'rU') as f:
# p2io.read_from_xls(f)
# #1 Read tag files
# info("Read and build treatment 1 bedGraph...")
# t1bio = cBedGraphIO.bedGraphIO(options.t1bdg)
# t1btrack = t1bio.build_bdgtrack()
# info("Read and build control 1 bedGraph...")
# c1bio = cBedGraphIO.bedGraphIO(options.c1bdg)
# c1btrack = c1bio.build_bdgtrack()
# if len(options.depth) >=2:
# depth1 = options.depth[0]
# depth2 = options.depth[1]
# else:
# depth1 = options.depth[0]
# depth2 = depth1
# info("Read and build treatment 2 bedGraph...")
# t2bio = cBedGraphIO.bedGraphIO(options.t2bdg)
# t2btrack = t2bio.build_bdgtrack()
# info("Read and build control 2 bedGraph...")
# c2bio = cBedGraphIO.bedGraphIO(options.c2bdg)
# c2btrack = c2bio.build_bdgtrack()
# #3 Call Peaks
# diffscore = DiffScoreTrackI( t1btrack,
# c1btrack,
# t2btrack,
# c2btrack,
# depth1, depth2 )
# diffscore.finalize()
# if options.call_peaks:
# diffscore.set_track_score_method(options.track_score_method)
# info("Calling peaks")
# if options.track_score_method == 'p':
# diffscore.call_peaks(cutoff = options.peaks_log_pvalue,
# min_length = options.pminlen)
# elif options.track_score_method == 'q':
# diffscore.call_peaks(cutoff = options.peaks_log_qvalue,
# min_length = options.pminlen)
# else:
# raise NotImplementedError
# else:
# info("Using existing peaks")
# diffscore.store_peaks(p1io, p2io)
# info("Rebuilding chromosomes")
# diffscore.rebuild_chromosomes()
# diffscore.annotate_peaks()
# info("Calling differentially occupied peaks")
# if options.score_method == 'p':
# diffscore.call_diff_peaks(cutoff = options.log_pvalue,
# min_length = options.dminlen,
# score_method = options.score_method)
# if options.score_method == 'q':
# diffscore.call_diff_peaks(cutoff = options.log_qvalue,
# min_length = options.dminlen,
# score_method = options.score_method)
# # diffscore.print_some_peaks()
# # diffscore.print_diff_peaks()
# info("Write output xls and BED files...")
# ofhd_xls = open( os.path.join( options.outdir, options.peakxls), "w" )
# ofhd_xls.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
# ofhd_xls.write( options.argtxt+"\n" )
# ofhd_bed = open( os.path.join( options.outdir, options.peakbed), "w" )
# # pass write method so we can print too, and include name
# diffscore.write_peaks(xls=ofhd_xls, bed=ofhd_bed,
# name = options.name, name_prefix="%s_peak_",
# description="Peaks for %s (Made with MACS v2, " + strftime("%x") + ")",
# trackline=options.trackline)
# ofhd_xls.close()
# ofhd_bed.close()
# if diffscore.has_peakio():
# info("Write annotated peak xls files...")
# ofhd_xls1 = open( os.path.join( options.outdir, options.peak1xls), "w" )
# ofhd_xls1.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
# ofhd_xls1.write(options.argtxt+"\n")
# ofhd_xls2 = open( os.path.join( options.outdir, options.peak2xls), "w" )
# ofhd_xls2.write("# This file is generated by MACS version, using the diffpeak module %s\n" % (MACS_VERSION))
# ofhd_xls2.write(options.argtxt+"\n")
# diffscore.write_peaks_by_summit(ofhd_xls1, ofhd_xls2,
# name = options.name, name_prefix="%s_peak_")
# ofhd_xls1.close()
# ofhd_xls2.close()
# if options.store_bdg:
# info("#4 Write output bedgraph files...")
# ofhd_logLR = open( os.path.join( options.outdir, options.bdglogLR), "w" )
# ofhd_pvalue = open( os.path.join( options.outdir, options.bdgpvalue), "w" )
# ofhd_logFC = open( os.path.join( options.outdir, options.bdglogFC), "w" )
# diffscore.write_bedgraphs(logLR=ofhd_logLR, pvalue=ofhd_pvalue,
# logFC=ofhd_logFC, name = options.name,
# description=" for %s (Made with MACS v2, " + strftime("%x") + ")",
# trackline=options.trackline)
# ofhd_logLR.close()
# ofhd_pvalue.close()
# ofhd_logFC.close()
# def cal_max_dup_tags ( genome_size, tags_number, p=1e-5 ):
# """Calculate the maximum duplicated tag number based on genome
# size, total tag number and a p-value based on binomial
# distribution. Brute force algorithm to calculate reverse CDF no
# more than MAX_LAMBDA(100000).
# """
# return binomial_cdf_inv(1-p,tags_number,1.0/genome_size)
# def load_frag_files_options ( options ):
# """From the options, load treatment fragments and control fragments (if available).
# """
# options.info("#1 read treatment fragments...")
# tp = options.parser(options.tfile[0])
# treat = tp.build_petrack()
# treat.sort()
# if len(options.tfile) > 1:
# # multiple input
# for tfile in options.tfile[1:]:
# tp = options.parser(tfile)
# treat = tp.append_petrack( treat )
# treat.sort()
# options.tsize = tp.d
# if options.cfile:
# options.info("#1.2 read input fragments...")
# cp = options.parser(options.cfile[0])
# control = cp.build_petrack()
# control_d = cp.d
# control.sort()
# if len(options.cfile) > 1:
# # multiple input
# for cfile in options.cfile[1:]:
# cp = options.parser(cfile)
# control = cp.append_petrack( control )
# control.sort()
# else:
# control = None
# options.info("#1 mean fragment size is determined as %d bp from treatment" % options.tsize)
# if control is not None:
# options.info("#1 note: mean fragment size in control is %d bp -- value ignored" % control_d)
# return (treat, control)
# def load_tag_files_options ( options ):
# """From the options, load treatment tags and control tags (if available).
# """
# options.info("#1 read treatment tags...")
# tp = options.parser(options.tfile[0])
# if not options.tsize: # override tsize if user specified --tsize
# ttsize = tp.tsize()
# options.tsize = ttsize
# treat = tp.build_fwtrack()
# treat.sort()
# if len(options.tfile) > 1:
# # multiple input
# for tfile in options.tfile[1:]:
# tp = options.parser(tfile)
# treat = tp.append_fwtrack( treat )
# treat.sort()
# if options.cfile:
# options.info("#1.2 read input tags...")
# control = options.parser(options.cfile[0]).build_fwtrack()
# control.sort()
# if len(options.cfile) > 1:
# # multiple input
# for cfile in options.cfile[1:]:
# cp = options.parser(cfile)
# control = cp.append_fwtrack( control )
# control.sort()
# else:
# control = None
# options.info("#1 tag size is determined as %d bps" % options.tsize)
# return (treat, control)
|
