Mercurial > repos > weilong-guo > bs_seeker2

comparison BSseeker2/bs_seeker2-call_methylation.py @ 0:e6df770c0e58 draft

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Initial upload
author weilong-guo
date Fri, 12 Jul 2013 18:47:28 -0400
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children 8b26adf64adc
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-1:000000000000 0:e6df770c0e58
1 #!/usr/bin/python
2
3 from optparse import OptionParser, OptionGroup
4 from bs_utils.utils import *
5
6 try :
7 import pysam
8 except ImportError :
9 print "[Error] Cannot import \"pysam\" package. Have you installed it?"
10 exit(-1)
11
12 import gzip
13
14 def context_calling(seq, position):
15
16 word=seq[position]
17 word=word.upper()
18
19 context="--"
20 context_CH="--"
21 if position + 2 < len(seq) and position - 2 >= 0:
22
23 if word == "C":
24 word2 = seq[position+1]
25 context_CH = word + word2
26 if word2 == "G":
27 context = "CG"
28 elif word2 in ['A','C','T']:
29 word3 = seq[position+2]
30 if word3 == "G":
31 context = "CHG"
32 elif word3 in ['A','C','T']:
33 context="CHH"
34
35 elif word == "G":
36 word2 = seq[position-1]
37 context_CH = word + word2
38 context_CH = context_CH.translate(string.maketrans("ATCG", "TAGC"))
39 if word2 == "C":
40 context = "CG"
41 elif word2 in ['A','G','T']:
42 word3 = seq[position-2]
43 if word3 == "C":
44 context = "CHG"
45 elif word3 in ['A','G','T']:
46 context = "CHH"
47
48 return word, context, context_CH
49
50
51
52 if __name__ == '__main__':
53
54 parser = OptionParser()
55 parser.add_option("-i", "--input", type="string", dest="infilename",help="BAM output from bs_seeker2-align.py", metavar="INFILE")
56 parser.add_option("-d", "--db", type="string", dest="dbpath",help="Path to the reference genome library (generated in preprocessing genome) [Default: %default]" , metavar="DBPATH", default = reference_genome_path)
57 parser.add_option("-o", "--output-prefix", type="string", dest="output_prefix",help="The output prefix to create ATCGmap and wiggle files [INFILE]", metavar="OUTFILE")
58
59 parser.add_option("--wig", type="string", dest="wig_file",help="The output .wig file [INFILE.wig]", metavar="OUTFILE")
60 parser.add_option("--CGmap", type="string", dest="CGmap_file",help="The output .CGmap file [INFILE.CGmap]", metavar="OUTFILE")
61 parser.add_option("--ATCGmap", type="string", dest="ATCGmap_file",help="The output .ATCGmap file [INFILE.ATCGmap]", metavar="OUTFILE")
62
63 parser.add_option("-x", "--rm-SX", action="store_true", dest="RM_SX",help="Removed reads with tag \'XS:i:1\', which would be considered as not fully converted by bisulfite treatment [Default: %default]", default = False)
64 parser.add_option("--txt", action="store_true", dest="text",help="Show CGmap and ATCGmap in .gz [Default: %default]", default = False)
65
66 parser.add_option("-r", "--read-no",type = "int", dest="read_no",help="The least number of reads covering one site to be shown in wig file [Default: %default]", default = 1)
67 parser.add_option("-v", "--version", action="store_true", dest="version",help="show version of BS-Seeker2", metavar="version", default = False)
68
69 (options, args) = parser.parse_args()
70
71
72 # if no options were given by the user, print help and exit
73 if len(sys.argv) == 1:
74 print parser.print_help()
75 exit(0)
76
77 if options.version :
78 show_version()
79 exit (-1)
80 else :
81 show_version()
82
83
84 if options.infilename is None:
85 error('-i option is required')
86 if not os.path.isfile(options.infilename):
87 error('Cannot find input file: %s' % options.infilename)
88
89 open_log(options.infilename+'.call_methylation_log')
90 db_d = lambda fname: os.path.join( os.path.expanduser(options.dbpath), fname) # bug fixed, weilong
91
92 logm('sorting BS-Seeker alignments')
93 sorted_input_filename = options.infilename+'_sorted'
94 pysam.sort(options.infilename, sorted_input_filename)
95 sorted_input_filename += '.bam'
96 logm('indexing sorted alignments')
97 pysam.index(sorted_input_filename)
98
99 logm('calculating methylation levels')
100 if options.text :
101 ATCGmap_fname = options.ATCGmap_file or ((options.output_prefix or options.infilename) + '.ATCGmap')
102 ATCGmap = open(ATCGmap_fname, 'w')
103
104 CGmap_fname = options.CGmap_file or ((options.output_prefix or options.infilename) + '.CGmap')
105 CGmap = open(CGmap_fname, 'w')
106 else :
107 ATCGmap_fname = options.ATCGmap_file or ((options.output_prefix or options.infilename) + '.ATCGmap.gz')
108 ATCGmap = gzip.open(ATCGmap_fname, 'wb')
109
110 CGmap_fname = options.CGmap_file or ((options.output_prefix or options.infilename) + '.CGmap.gz')
111 CGmap = gzip.open(CGmap_fname, 'wb')
112
113 wiggle_fname = options.wig_file or ((options.output_prefix or options.infilename) + '.wig')
114 wiggle = open(wiggle_fname, 'w')
115
116 sorted_input = pysam.Samfile(sorted_input_filename, 'rb')
117
118 chrom = None
119 nucs = ['A', 'T', 'C', 'G', 'N']
120 ATCG_fwd = dict((n, 0) for n in nucs)
121 ATCG_rev = dict((n, 0) for n in nucs)
122 for col in sorted_input.pileup():
123 col_chrom = sorted_input.getrname(col.tid)
124 if chrom != col_chrom:
125 chrom = col_chrom
126 chrom_seq = deserialize(db_d(chrom))
127 wiggle.write('variableStep chrom=%s\n' % chrom)
128
129 for n in nucs:
130 ATCG_fwd[n] = 0
131 ATCG_rev[n] = 0
132
133 nuc, context, subcontext = context_calling(chrom_seq, col.pos)
134 total_reads = 0
135
136
137
138 for pr in col.pileups:
139 # print pr
140 if (not pr.indel) : # skip indels
141 #if ( (options.RM_SX) and (pr.alignment.tags[1][1] == 1) ):
142 ##=== Fixed error reported by Roberto
143 #print options.RM_SX, dict(pr.alignment.tags)["XS"]
144 #if ( (options.RM_SX) and (dict(pr.alignment.tags)["XS"] == 1) ):
145
146 if ( (options.RM_SX) and (dict(pr.alignment.tags).get("XS",0) == 1) ):
147 # print "Debug: ", options.RM_SX, pr.alignment.tags[1]
148 # when need to filter and read with tag (XS==1), then remove the reads
149 continue
150
151 if pr.qpos >= len(pr.alignment.seq):
152 print 'WARNING: read %s has an invalid alignment. Discarding.. ' % pr.alignment.qname
153 continue
154 read_nuc = pr.alignment.seq[pr.qpos]
155 # print "read_nuc=", read_nuc
156 if pr.alignment.is_reverse:
157 ATCG_rev[read_nuc] += 1
158 else:
159 ATCG_fwd[read_nuc] += 1
160
161 if read_nuc != 'N':
162 total_reads += 1
163
164 cnts = lambda d: '\t'.join(str(d[n]) for n in nucs)
165 fwd_counts = cnts(ATCG_fwd)
166 rev_counts = cnts(ATCG_rev)
167
168 meth_level = None
169 meth_cytosines = 0
170 unmeth_cytosines = 0
171
172 if nuc == 'C':
173 # plus strand: take the ratio of C's to T's from reads that come from the forward strand
174 meth_cytosines = ATCG_fwd['C']
175 unmeth_cytosines = ATCG_fwd['T']
176
177 elif nuc == 'G':
178 # minus strand: take the ratio of G's to A's from reads that come from the reverse strand
179 meth_cytosines = ATCG_rev['G']
180 unmeth_cytosines = ATCG_rev['A']
181
182 if meth_cytosines + unmeth_cytosines > 0:
183 meth_level = float(meth_cytosines)/(meth_cytosines + unmeth_cytosines)
184
185 pos = col.pos + 1
186
187 meth_level_string = str(meth_level) if meth_level is not None else 'na'
188 ATCGmap.write('%(chrom)s\t%(nuc)s\t%(pos)d\t%(context)s\t%(subcontext)s\t%(fwd_counts)s\t%(rev_counts)s\t%(meth_level_string)s\n' % locals())
189 #
190 all_cytosines = meth_cytosines + unmeth_cytosines
191 if (meth_level is not None) and (all_cytosines >= options.read_no):
192 # print all_cytosines
193 if nuc == 'C':
194 wiggle.write('%d\t%f\n' % (pos, meth_level))
195 else :
196 wiggle.write('%d\t-%f\n' % (pos, meth_level))
197 CGmap.write('%(chrom)s\t%(nuc)s\t%(pos)d\t%(context)s\t%(subcontext)s\t%(meth_level_string)s\t%(meth_cytosines)s\t%(all_cytosines)s\n' % locals())
198 ATCGmap.close()
199 CGmap.close()
200 wiggle.close()
201
202 logm('Wiggle: %s'% wiggle_fname)
203 logm('ATCGMap: %s' % ATCGmap_fname)
204 logm('CGmap: %s' % CGmap_fname)
205