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comparison bin/bsf-call @ 0:06f8460885ff

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author yutaka-saito
date Sun, 19 Apr 2015 20:51:13 +0900
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-1:000000000000 0:06f8460885ff
1 #!/usr/bin/env python
2 """
3 Bisulfighter::bsf-call
4
5 Bisulfighter (http://epigenome.cbrc.jp/bisulfighter)
6 by National Institute of Advanced Industrial Science and Technology (AIST)
7 is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
8 http://creativecommons.org/licenses/by-nc-sa/3.0/
9 """
10
11 __version__= "1.3"
12
13 from optparse import OptionParser
14 import os
15 import sys
16 import re
17
18 prog = 'bsf-call'
19 usage = """%prog [options] refgenome read1 read2 ...
20 example: %prog -o experiment.txt hg38.fa paired-sample1-1.fastq,paired-sample1-2.fastq"""
21 description = "A mapping of the read bisulfite treated by LAST, to detect methylated cytosine (mC) of the results, and outputs the detection result to the file."
22
23 op = OptionParser(prog=prog, usage=usage, description=description, version="%s-%s" % (prog, __version__))
24
25 op.add_option("-c", "--coverage", type="int", default=5, metavar="C",
26 help="threshold of read coverate (default: %default)")
27
28 # op.add_option("-d", "--pe-direction", type="string", default="ff",
29 # help="direction of paired-end probes: ff, fr, rf, rr (default: %default)")
30 #
31 op.add_option("-l", "--lower-bound", type="float", default=0.05, metavar="L",
32 help="threshold of mC ratio (default: %default)")
33
34 op.add_option("-p", "--multi-thread", type="int", default=1, metavar="P",
35 help="number of threads (default: %default)")
36
37 op.add_option("-s", "", type="int", default=150, metavar="S",
38 help="threshold of the alignment score at filtering (default: %default)")
39
40 op.add_option("-m", "", type="float", default=1e-9, metavar="M",
41 help="threshold of the mismap probability at filtering (default: %default)")
42
43 # op.add_option("", "--last", type="string", default="", metavar="OPT1,OPT2,...",
44 # help="options for LAST (lastal command)")
45 #
46 op.add_option("-o", "", type="string", default="bsf-call.out", metavar="FILE",
47 help="output file (default: bsf-call.out)")
48
49 op.add_option("-W", "", type="string", default="./bsfwork", metavar="WORKDIR",
50 help="work directory (default: ./bsfwork)")
51
52 op.add_option("", "--work-auto", action="store_true", dest="auto_create_work_dir", default=False,
53 help="create work directory automatically")
54
55 # op.add_option("-n", "", action="store_true", dest="use_cluster", default=False,
56 # help="run bsf-call on pc cluster")
57 #
58 # op.add_option("-q", "", type="string", default="", metavar="QUEUE_LIST",
59 # help="queue list")
60 #
61 op.add_option("-M", "", type="string", metavar="MAPPING_DIR",
62 help="mapping result directory")
63
64 op.add_option("-T", "", type="string", metavar="LOCAL_DIR",
65 help="local directory")
66
67 # op.add_option("-r", "", type="string", default="100M", metavar="SPLIT_READ_SIZE",
68 # help="split read size")
69 #
70 # op.add_option("", "--bam", action="store_true", dest="read_bam", default=False,
71 # help="read BAM file for mC detection")
72 #
73 # op.add_option("", "--sam", action="store_true", dest="read_sam", default=False,
74 # help="read SAM file for mC detection")
75 #
76 # op.add_option("-z", "--compress-prog", type="string", dest="z", metavar="COMPRESS_PROG", default="bzip2",
77 # help="compression program")
78
79 options, args = op.parse_args()
80
81 errors = []
82
83 work_dir = None
84 if options.W:
85 work_dir = options.W
86 else:
87 if not options.auto_create_work_dir:
88 work_dir = "bsfwork"
89
90 if options.M:
91 if len(args) < 1:
92 op.error("\n Reference genome is not specified.")
93
94 for result_dir in options.M.split(","):
95 if not os.path.exists(result_dir):
96 errors.append("Mapping result directory: '%s' does not exist." % options.M)
97
98 # if options.read_bam and options.read_sam:
99 # errors.append("--bam and --sam cannot be placed simultaneously.")
100
101 ref_genome = args[0]
102 reads = None
103 else:
104 if len(args) < 2:
105 op.error("\n Reference genome and read sequence is not specified.")
106
107 # if options.read_bam:
108 # errors.append("--bam option is specified but -M option is not specified.")
109
110 # if options.read_sam:
111 # errors.append("--sam option is specified but -M option is not specified.")
112
113 ref_genome = args[0]
114 reads = args[1:]
115
116 for read_files in reads:
117 for read_file in read_files.split(','):
118 if not os.path.exists(read_file):
119 errors.append("Read file: '%s' does not exists." % read_file)
120
121 if work_dir and os.path.exists(work_dir):
122 errors.append("Working directory: '%s' already exists." % work_dir)
123
124 if not os.path.exists(ref_genome):
125 errors.append("Reference genome: '%s' does not exists." % ref_genome)
126
127 # if options.read_bam or options.read_sam:
128 # try:
129 # import pysam
130 # except:
131 # errors.append("--bam or --sam is specified but pysam is not installed.")
132
133 if len(errors) > 0:
134 op.error("\n " + "\n ".join(errors))
135
136 cmd_opts = {}
137 cmd_opts["coverage"] = options.coverage
138 # cmd_opts["pe_direction"] = options.pe_direction
139 cmd_opts["num_threads"] = options.multi_thread
140 cmd_opts["lower_bound"] = options.lower_bound
141 cmd_opts["aln_score_thres"] = options.s
142 cmd_opts["aln_mismap_prob_thres"] = options.m
143 cmd_opts["output"] = options.o
144 # cmd_opts["last_opts"] = options.last
145 cmd_opts["work_dir"] = work_dir
146 # cmd_opts["use_cluster"] = options.use_cluster
147 # cmd_opts["queue_list"] = options.q
148 cmd_opts["mapping_dir"] = options.M
149 cmd_opts["local_dir"] = options.T
150 # cmd_opts["split_read_size"] = options.r
151 # cmd_opts["read_bam"] = options.read_bam
152 # cmd_opts["read_sam"] = options.read_sam
153 # cmd_opts["compress_prog"] = options.z
154
155 try:
156 sys.path.append('.');
157 import bsfcall
158 except ImportError:
159 errors.append("\"import bsfcall\" failed. Please be sure you have bsfcall.py in your python library path.");
160
161 import subprocess
162
163 # if not checkRunnable('last-map-probs'):
164 # sys.exit(1)
165 # if not checkRunnable('last-pair-probs'):
166 # sys.exit(1)
167 # if not checkRunnable(options.z):
168 # sys.exit(1)
169
170 if len(errors) > 0:
171 op.error("\n " + "\n ".join(errors))
172
173 # if cmd_opts["use_cluster"]:
174 # cmd_opts["num_threads"] = 1
175 # bsf_call = bsfcall.BsfCallCluster(ref_genome, reads, cmd_opts)
176 # else:
177 # bsf_call = bsfcall.BsfCall(ref_genome, reads, cmd_opts)
178 bsf_call = bsfcall.BsfCall(ref_genome, reads, cmd_opts)
179
180 bsf_call.execute()
181
182 sys.exit(0)
183
184 def checkRunnable(cmd):
185 for outline, errline in runProcess(cmd.split()):
186 if (re.match(r'error: subProcess:', errline) is not None):
187 print >>sys.stderr, '\"%s\" is not found.' % cmd
188 return False
189 return True
190
191 def runProcess(exe):
192 try:
193 p = subprocess.Popen(exe, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
194 except:
195 yield (None, 'error: runProcess: \'%s\' failed.' % ' '.join(exe))
196 return
197 while (True):
198 retcode = p.poll()
199 if (retcode is not None):
200 break
201 outline = p.stdout.readline()
202 errline = p.stderr.readline()
203 yield (outline, errline)
204