annotate BSseeker2/bs_seeker2-call_methylation.py @ 1:8b26adf64adc draft default tip

V2.0.5
author weilong-guo
date Tue, 05 Nov 2013 01:55:39 -0500
parents e6df770c0e58
children
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1 #!/usr/bin/env python
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2
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3 from optparse import OptionParser, OptionGroup
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4 from bs_utils.utils import *
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5
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6 try :
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7 import pysam
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8 except ImportError :
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9 print "[Error] Cannot import \"pysam\" package. Have you installed it?"
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10 exit(-1)
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11
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12 import gzip
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13
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14 def context_calling(seq, position):
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15
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16 word=seq[position]
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17 word=word.upper()
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18
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19 context="--"
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20 context_CH="--"
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21 if position + 2 < len(seq) and position - 2 >= 0:
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22
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23 if word == "C":
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24 word2 = seq[position+1]
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25 context_CH = word + word2
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26 if word2 == "G":
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27 context = "CG"
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28 elif word2 in ['A','C','T']:
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29 word3 = seq[position+2]
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30 if word3 == "G":
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31 context = "CHG"
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32 elif word3 in ['A','C','T']:
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33 context="CHH"
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34
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35 elif word == "G":
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36 word2 = seq[position-1]
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37 context_CH = word + word2
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38 context_CH = context_CH.translate(string.maketrans("ATCG", "TAGC"))
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39 if word2 == "C":
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40 context = "CG"
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41 elif word2 in ['A','G','T']:
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42 word3 = seq[position-2]
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43 if word3 == "C":
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44 context = "CHG"
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45 elif word3 in ['A','G','T']:
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46 context = "CHH"
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47
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48 return word, context, context_CH
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49
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50
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51
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52 if __name__ == '__main__':
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53
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54 parser = OptionParser()
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55 parser.add_option("-i", "--input", type="string", dest="infilename",help="BAM output from bs_seeker2-align.py", metavar="INFILE")
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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)
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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")
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58
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59 parser.add_option("--wig", type="string", dest="wig_file",help="The output .wig file [INFILE.wig]", metavar="OUTFILE")
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60 parser.add_option("--CGmap", type="string", dest="CGmap_file",help="The output .CGmap file [INFILE.CGmap]", metavar="OUTFILE")
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61 parser.add_option("--ATCGmap", type="string", dest="ATCGmap_file",help="The output .ATCGmap file [INFILE.ATCGmap]", metavar="OUTFILE")
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62
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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)
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64 parser.add_option("--txt", action="store_true", dest="text",help="Show CGmap and ATCGmap in .gz [Default: %default]", default = False)
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65
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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)
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67 parser.add_option("-v", "--version", action="store_true", dest="version",help="show version of BS-Seeker2", metavar="version", default = False)
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68
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69 (options, args) = parser.parse_args()
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70
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71
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72 # if no options were given by the user, print help and exit
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73 if len(sys.argv) == 1:
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74 parser.print_help()
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75 exit(0)
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76
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77 if options.version :
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78 show_version()
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79 exit (-1)
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80 else :
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81 show_version()
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82
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83
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84 if options.infilename is None:
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85 error('-i option is required')
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86 if not os.path.isfile(options.infilename):
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87 error('Cannot find input file: %s' % options.infilename)
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88
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89 open_log(options.infilename+'.call_methylation_log')
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90 db_d = lambda fname: os.path.join( os.path.expanduser(options.dbpath), fname) # bug fixed, weilong
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91
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92 logm('sorting BS-Seeker alignments')
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93 sorted_input_filename = options.infilename+'_sorted'
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94 pysam.sort(options.infilename, sorted_input_filename)
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95 sorted_input_filename += '.bam'
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96 logm('indexing sorted alignments')
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97 pysam.index(sorted_input_filename)
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98
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99 logm('calculating methylation levels')
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100 if options.text :
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101 ATCGmap_fname = options.ATCGmap_file or ((options.output_prefix or options.infilename) + '.ATCGmap')
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102 ATCGmap = open(ATCGmap_fname, 'w')
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103
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104 CGmap_fname = options.CGmap_file or ((options.output_prefix or options.infilename) + '.CGmap')
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105 CGmap = open(CGmap_fname, 'w')
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106 else :
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107 ATCGmap_fname = options.ATCGmap_file or ((options.output_prefix or options.infilename) + '.ATCGmap.gz')
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108 ATCGmap = gzip.open(ATCGmap_fname, 'wb')
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109
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110 CGmap_fname = options.CGmap_file or ((options.output_prefix or options.infilename) + '.CGmap.gz')
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111 CGmap = gzip.open(CGmap_fname, 'wb')
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112
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113 wiggle_fname = options.wig_file or ((options.output_prefix or options.infilename) + '.wig')
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114 wiggle = open(wiggle_fname, 'w')
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115
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116 sorted_input = pysam.Samfile(sorted_input_filename, 'rb')
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117
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118 chrom = None
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119 nucs = ['A', 'T', 'C', 'G', 'N']
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120 ATCG_fwd = dict((n, 0) for n in nucs)
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121 ATCG_rev = dict((n, 0) for n in nucs)
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122 for col in sorted_input.pileup():
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123 col_chrom = sorted_input.getrname(col.tid)
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124 if chrom != col_chrom:
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125 chrom = col_chrom
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126 chrom_seq = deserialize(db_d(chrom))
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127 wiggle.write('variableStep chrom=%s\n' % chrom)
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128
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129 for n in nucs:
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130 ATCG_fwd[n] = 0
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131 ATCG_rev[n] = 0
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132
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133 nuc, context, subcontext = context_calling(chrom_seq, col.pos)
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134 total_reads = 0
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135
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136 for pr in col.pileups:
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137 # print pr
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138 if (not pr.indel) : # skip indels
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139 #if ( (options.RM_SX) and (pr.alignment.tags[1][1] == 1) ):
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140 ##=== Fixed error reported by Roberto
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141 #print options.RM_SX, dict(pr.alignment.tags)["XS"]
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142 #if ( (options.RM_SX) and (dict(pr.alignment.tags)["XS"] == 1) ):
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143
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144 if ( (options.RM_SX) and (dict(pr.alignment.tags).get("XS",0) == 1) ):
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145 # print "Debug: ", options.RM_SX, pr.alignment.tags[1]
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146 # when need to filter and read with tag (XS==1), then remove the reads
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147 continue
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148
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149 if pr.qpos >= len(pr.alignment.seq):
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150 print 'WARNING: read %s has an invalid alignment. Discarding.. ' % pr.alignment.qname
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151 continue
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152 read_nuc = pr.alignment.seq[pr.qpos]
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153 if pr.alignment.is_reverse:
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154 ATCG_rev[read_nuc] += 1
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155 else:
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156 ATCG_fwd[read_nuc] += 1
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157
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158 if read_nuc != 'N':
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159 total_reads += 1
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160
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161 cnts = lambda d: '\t'.join(str(d[n]) for n in nucs)
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162 fwd_counts = cnts(ATCG_fwd)
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163 rev_counts = cnts(ATCG_rev)
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164
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165 meth_level = None
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166 meth_cytosines = 0
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167 unmeth_cytosines = 0
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168
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169 if nuc == 'C':
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170 # plus strand: take the ratio of C's to T's from reads that come from the forward strand
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171 meth_cytosines = ATCG_fwd['C']
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172 unmeth_cytosines = ATCG_fwd['T']
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173
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174 elif nuc == 'G':
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175 # minus strand: take the ratio of G's to A's from reads that come from the reverse strand
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176 meth_cytosines = ATCG_rev['G']
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177 unmeth_cytosines = ATCG_rev['A']
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178
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179 if meth_cytosines + unmeth_cytosines > 0:
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180 meth_level = float(meth_cytosines)/(meth_cytosines + unmeth_cytosines)
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181
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182 pos = col.pos + 1
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183
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184 meth_level_string = str(meth_level) if meth_level is not None else 'na'
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185 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())
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186 #
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parents:
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187 all_cytosines = meth_cytosines + unmeth_cytosines
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188 if (meth_level is not None) and (all_cytosines >= options.read_no):
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189 # print all_cytosines
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190 if nuc == 'C':
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191 wiggle.write('%d\t%f\n' % (pos, meth_level))
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192 else :
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193 wiggle.write('%d\t-%f\n' % (pos, meth_level))
1
weilong-guo
parents: 0
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194
weilong-guo
parents: 0
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195 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())
0
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196 ATCGmap.close()
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parents:
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197 CGmap.close()
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198 wiggle.close()
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199
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200 logm('Wiggle: %s'% wiggle_fname)
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parents:
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201 logm('ATCGMap: %s' % ATCGmap_fname)
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parents:
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202 logm('CGmap: %s' % CGmap_fname)
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parents:
diff changeset
203