Mercurial > repos > mvdbeek > mismatch_frequencies

annotate mismatch_frequencies.py @ 28:bb3d962e8cb1 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mismatch_frequencies commit 10a7e3877c2568d9c23de53fc97dc1c902ff0524-dirty
author mvdbeek
date Sat, 22 Dec 2018 04:14:53 -0500
parents 6590be3f8e3f
children
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1 import re
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2 import string
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3 import pysam
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4 import matplotlib
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5 import pandas as pd
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6 from collections import defaultdict
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7 from collections import OrderedDict
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8 import argparse
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9 import itertools
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10
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11 matplotlib.use('pdf')
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12 import matplotlib.pyplot as plt # noqa: E402
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14
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15 class MismatchFrequencies:
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16 '''Iterate over a SAM/BAM alignment file, collecting reads with mismatches. One
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17 class instance per alignment file. The result_dict attribute will contain a
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18 nested dictionary with name, readlength and mismatch count.'''
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19 def __init__(self, result_dict={}, alignment_file=None, name="name", minimal_readlength=21,
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20 maximal_readlength=21,
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21 number_of_allowed_mismatches=1,
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22 ignore_5p_nucleotides=0,
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23 ignore_3p_nucleotides=0,
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24 possible_mismatches=[
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25 'AC', 'AG', 'AT',
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26 'CA', 'CG', 'CT',
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27 'GA', 'GC', 'GT',
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28 'TA', 'TC', 'TG'
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29 ]):
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30
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31 self.result_dict = result_dict
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32 self.name = name
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33 self.minimal_readlength = minimal_readlength
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34 self.maximal_readlength = maximal_readlength
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35 self.number_of_allowed_mismatches = number_of_allowed_mismatches
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36 self.ignore_5p_nucleotides = ignore_5p_nucleotides
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37 self.ignore_3p_nucleotides = ignore_3p_nucleotides
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38 self.possible_mismatches = possible_mismatches
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39
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40 if alignment_file:
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41 self.pysam_alignment = pysam.Samfile(alignment_file)
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42 self.references = self.pysam_alignment.references # names of fasta reference sequences
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43 result_dict[name] = self.get_mismatches(
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44 self.pysam_alignment,
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45 minimal_readlength,
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46 maximal_readlength,
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47 possible_mismatches
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48 )
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50 def get_mismatches(self, pysam_alignment, minimal_readlength,
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51 maximal_readlength, possible_mismatches):
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52 rec_dd = lambda: defaultdict(rec_dd)
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53 len_dict = rec_dd()
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54 for alignedread in pysam_alignment:
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55 if self.read_is_valid(alignedread, minimal_readlength, maximal_readlength):
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56 chromosome = pysam_alignment.getrname(alignedread.rname)
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57 try:
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58 len_dict[int(alignedread.rlen)][chromosome]['total valid reads'] += 1
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59 except TypeError:
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60 len_dict[int(alignedread.rlen)][chromosome]['total valid reads'] = 1
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61 MD = alignedread.opt('MD')
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62 if self.read_has_mismatch(alignedread, self.number_of_allowed_mismatches):
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63 (ref_base, mismatch_base) = self.read_to_reference_mismatch(MD, alignedread.seq, alignedread.is_reverse)
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64 if not ref_base:
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65 continue
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66 else:
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67 for i, base in enumerate(ref_base):
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68 if not ref_base[i]+mismatch_base[i] in possible_mismatches:
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69 continue
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70 try:
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71 len_dict[int(alignedread.rlen)][chromosome][ref_base[i]+mismatch_base[i]] += 1
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72 except TypeError:
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73 len_dict[int(alignedread.rlen)][chromosome][ref_base[i]+mismatch_base[i]] = 1
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74 return len_dict
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75
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76 def read_is_valid(self, read, min_readlength, max_readlength):
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77 '''Filter out reads that are unmatched, too short or
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78 too long or that contian insertions'''
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79 if read.is_unmapped:
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80 return False
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81 if read.rlen < min_readlength:
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82 return False
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83 if read.rlen > max_readlength:
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84 return False
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85 else:
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86 return True
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87
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88 def read_has_mismatch(self, read, number_of_allowed_mismatches=1):
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89 '''keep only reads with one mismatch. Could be simplified'''
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90 NM = read.opt('NM')
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91 if NM < 1: # filter out reads with no mismatch
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92 return False
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93 if NM > number_of_allowed_mismatches: # filter out reads with more than 1 mismtach
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94 return False
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95 else:
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96 return True
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97
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98 def mismatch_in_allowed_region(self, readseq, mismatch_position):
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99 '''
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100 >>> M = MismatchFrequencies()
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101 >>> readseq = 'AAAAAA'
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102 >>> mismatch_position = 2
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103 >>> M.mismatch_in_allowed_region(readseq, mismatch_position)
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104 True
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105 >>> M = MismatchFrequencies(ignore_3p_nucleotides=2, ignore_5p_nucleotides=2)
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106 >>> readseq = 'AAAAAA'
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107 >>> mismatch_position = 1
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108 >>> M.mismatch_in_allowed_region(readseq, mismatch_position)
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109 False
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110 >>> readseq = 'AAAAAA'
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111 >>> mismatch_position = 4
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112 >>> M.mismatch_in_allowed_region(readseq, mismatch_position)
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113 False
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114 '''
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115 mismatch_position += 1 # To compensate for starting the count at 0
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116 five_p = self.ignore_5p_nucleotides
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117 three_p = self.ignore_3p_nucleotides
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118 if any([five_p > 0, three_p > 0]):
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119 if any([mismatch_position <= five_p,
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120 mismatch_position >= (len(readseq) + 1 - three_p)]): # Again compensate for starting the count at 0
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121 return False
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122 else:
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123 return True
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124 else:
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125 return True
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126
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127 def read_to_reference_mismatch(self, MD, readseq, is_reverse):
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128 '''
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129 This is where the magic happens. The MD tag contains SNP and indel information,
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130 without looking to the genome sequence. This is a typical MD tag: 3C0G2A6.
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131 3 bases of the read align to the reference, followed by a mismatch, where the
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132 reference base is C, followed by 10 bases aligned to the reference.
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133 suppose a reference 'CTTCGATAATCCTT'
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134 ||| || ||||||
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135 and a read 'CTTATATTATCCTT'.
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136 This situation is represented by the above MD tag.
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137 Given MD tag and read sequence this function returns the reference base C, G and A,
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138 and the mismatched base A, T, T.
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139 >>> M = MismatchFrequencies()
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140 >>> MD='3C0G2A7'
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141 >>> seq='CTTATATTATCCTT'
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142 >>> result=M.read_to_reference_mismatch(MD, seq, is_reverse=False)
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143 >>> result[0]=="CGA"
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144 True
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145 >>> result[1]=="ATT"
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146 True
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147 >>>
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148 '''
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149 search = re.finditer('[ATGC]', MD)
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150 if '^' in MD:
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151 print 'WARNING insertion detected, mismatch calling skipped for this read!!!'
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152 return (None, None)
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153 start_index = 0 # refers to the leading integer of the MD string before an edited base
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154 current_position = 0 # position of the mismatched nucleotide in the MD tag string
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155 mismatch_position = 0 # position of edited base in current read
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156 reference_base = ""
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157 mismatched_base = ""
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158 for result in search:
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159 current_position = result.start()
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160 mismatch_position = mismatch_position + 1 + int(MD[start_index:current_position]) # converts the leading characters before an edited base into integers
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161 start_index = result.end()
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162 reference_base += MD[result.end() - 1]
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163 mismatched_base += readseq[mismatch_position - 1]
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164 if is_reverse:
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165 reference_base = reverseComplement(reference_base)
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166 mismatched_base = reverseComplement(mismatched_base)
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167 mismatch_position = len(readseq)-mismatch_position-1
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168 if mismatched_base == 'N':
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169 return (None, None)
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170 if self.mismatch_in_allowed_region(readseq, mismatch_position):
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171 return (reference_base, mismatched_base)
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172 else:
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173 return (None, None)
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174
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175
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176 def reverseComplement(sequence):
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177 '''do a reverse complement of DNA base.
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178 >>> reverseComplement('ATGC')=='GCAT'
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179 True
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180 >>>
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181 '''
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182 sequence = sequence.upper()
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183 complement = string.maketrans('ATCGN', 'TAGCN')
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184 return sequence.upper().translate(complement)[::-1]
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185
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186
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187 def barplot(df, library, axes):
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188 df.plot(kind='bar', ax=axes, subplots=False,
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189 stacked=False, legend='test',
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190 title='Mismatch frequencies for {0}'.format(library))
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191
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192
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193 def df_to_tab(df, output):
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194 df.to_csv(output, sep='\t')
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195
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196
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197 def reduce_result(df, possible_mismatches):
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198 '''takes a pandas dataframe with full mismatch details and
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199 summarises the results for plotting.'''
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200 alignments = df['Alignment_file'].unique()
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201 readlengths = df['Readlength'].unique()
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202 combinations = itertools.product(*[alignments, readlengths]) # generate all possible combinations of readlength and alignment files
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203 reduced_dict = {}
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204 last_column = 3 + len(possible_mismatches)
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205 for combination in combinations:
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206 library_subset = df[df['Alignment_file'] == combination[0]]
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207 library_readlength_subset = library_subset[library_subset['Readlength'] == combination[1]]
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208 sum_of_library_and_readlength = library_readlength_subset.iloc[:, 3:last_column+1].sum()
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209 if combination[0] not in reduced_dict:
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210 reduced_dict[combination[0]] = {}
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211 reduced_dict[combination[0]][combination[1]] = sum_of_library_and_readlength.to_dict()
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212 return reduced_dict
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213
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214
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215 def plot_result(reduced_dict, args):
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216 names = reduced_dict.keys()
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217 nrows = len(names) / 2 + 1
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218 fig = plt.figure(figsize=(16, 32))
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219 for i, library in enumerate(names):
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220 axes = fig.add_subplot(nrows, 2, i+1)
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221 library_dict = reduced_dict[library]
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222 df = pd.DataFrame(library_dict)
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223 df.drop(['total aligned reads'], inplace=True)
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224 barplot(df, library, axes),
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225 axes.set_ylabel('Mismatch count / all valid reads * readlength')
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226 fig.savefig(args.output_pdf, format='pdf')
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227
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228
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229 def format_result_dict(result_dict, chromosomes, possible_mismatches):
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230 '''Turn nested dictionary into preformatted tab seperated lines'''
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231 header = "Reference sequence\tAlignment_file\tReadlength\t" + "\t".join(
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232 possible_mismatches) + "\ttotal aligned reads"
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233 libraries = result_dict.keys()
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234 readlengths = result_dict[libraries[0]].keys()
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235 result = []
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236 for chromosome in chromosomes:
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237 for library in libraries:
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238 for readlength in readlengths:
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239 line = []
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240 line.extend([chromosome, library, readlength])
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241 try:
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242 line.extend([result_dict[library][readlength][chromosome].get(mismatch, 0) for mismatch in possible_mismatches])
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243 line.extend([result_dict[library][readlength][chromosome].get(u'total valid reads', 0)])
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244 except KeyError:
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245 line.extend([0 for mismatch in possible_mismatches])
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246 line.extend([0])
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247 result.append(line)
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248 df = pd.DataFrame(result, columns=header.split('\t'))
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249 last_column = 3 + len(possible_mismatches)
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250 df['mismatches/per aligned nucleotides'] = df.iloc[:, 3:last_column].sum(1)/(df.iloc[:, last_column] * df['Readlength'])
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251 return df
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252
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253
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254 def setup_MismatchFrequencies(args):
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255 resultDict = OrderedDict()
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256 kw_list = [{'result_dict': resultDict,
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257 'alignment_file': alignment_file,
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258 'name': name,
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259 'minimal_readlength': args.min,
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260 'maximal_readlength': args.max,
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261 'number_of_allowed_mismatches': args.n_mm,
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262 'ignore_5p_nucleotides': args.five_p,
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263 'ignore_3p_nucleotides': args.three_p,
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264 'possible_mismatches': args.possible_mismatches}
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265 for alignment_file, name in zip(args.input, args.name)]
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266 return (kw_list, resultDict)
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267
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268
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269 def nested_dict_to_df(dictionary):
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270 dictionary = {(outerKey, innerKey): values for outerKey, innerDict in dictionary.iteritems() for innerKey, values in innerDict.iteritems()}
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271 df = pd.DataFrame.from_dict(dictionary).transpose()
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272 df.index.names = ['Library', 'Readlength']
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273 return df
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274
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275
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276 def run_MismatchFrequencies(args):
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277 kw_list, resultDict = setup_MismatchFrequencies(args)
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278 references = [MismatchFrequencies(**kw_dict).references for kw_dict in kw_list]
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279 return (resultDict, references[0])
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280
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281
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282 def main():
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283 result_dict, references = run_MismatchFrequencies(args)
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284 df = format_result_dict(result_dict, references, args.possible_mismatches)
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285 reduced_dict = reduce_result(df, args.possible_mismatches)
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286 plot_result(reduced_dict, args)
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287 reduced_df = nested_dict_to_df(reduced_dict)
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288 df_to_tab(reduced_df, args.output_tab)
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289 if args.expanded_output_tab:
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290 df_to_tab(df, args.expanded_output_tab)
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291 return reduced_dict
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292
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293 if __name__ == "__main__":
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294
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295 parser = argparse.ArgumentParser(description='Produce mismatch statistics for BAM/SAM alignment files.')
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296 parser.add_argument('--input', nargs='*', help='Input files in SAM/BAM format')
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297 parser.add_argument('--name', nargs='*', help='Name for input file to display in output file. Should have same length as the number of inputs')
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298 parser.add_argument('--output_pdf', help='Output filename for graph')
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299 parser.add_argument('--output_tab', help='Output filename for table')
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300 parser.add_argument('--expanded_output_tab', default=None, help='Output filename for table')
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301 parser.add_argument('--possible_mismatches', default=[
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302 'AC', 'AG', 'AT', 'CA', 'CG', 'CT', 'GA', 'GC', 'GT', 'TA', 'TC', 'TG'
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303 ], nargs='+', help='specify mismatches that should be counted for the mismatch frequency. The format is Reference base -> observed base, eg AG for A to G mismatches.')
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304 parser.add_argument('--min', '--minimal_readlength', type=int, help='minimum readlength')
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305 parser.add_argument('--max', '--maximal_readlength', type=int, help='maximum readlength')
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306 parser.add_argument('--n_mm', '--number_allowed_mismatches', type=int, default=1, help='discard reads with more than n mismatches')
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307 parser.add_argument('--five_p', '--ignore_5p_nucleotides', type=int, default=0, help='when calculating nucleotide mismatch frequencies ignore the first N nucleotides of the read')
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308 parser.add_argument('--three_p', '--ignore_3p_nucleotides', type=int, default=1, help='when calculating nucleotide mismatch frequencies ignore the last N nucleotides of the read')
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309 # args = parser.parse_args(['--input', '3mismatches_ago2ip_s2.bam', '3mismatches_ago2ip_ovary.bam','--possible_mismatches','AC','AG', 'CG', 'TG', 'CT','--name', 'Siomi1', 'Siomi2' , '--five_p', '3','--three_p','3','--output_pdf', 'out.pdf', '--output_tab', 'out.tab', '--expanded_output_tab', 'expanded.tab', '--min', '20', '--max', '22'])
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310 args = parser.parse_args()
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311 reduced_dict = main()