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47
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1 import argparse
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2 import logging
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3 import sys
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4 import os
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5 import re
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6
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0
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7 from collections import defaultdict
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47
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8
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9 def main():
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument("--input", help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation")
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12 parser.add_argument("--genes", help="The genes available in the 'best_match' column")
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13 parser.add_argument("--empty_region_filter", help="Where does the sequence start?", choices=['leader', 'FR1', 'CDR1', 'FR2'])
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14 parser.add_argument("--output", help="Output file")
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0
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15
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47
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16 args = parser.parse_args()
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17
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18 infile = args.input
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19 genes = str(args.genes).split(",")
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20 empty_region_filter = args.empty_region_filter
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21 outfile = args.output
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0
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22
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23 genedic = dict()
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0
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24
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25 mutationdic = dict()
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62
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26 mutationMatcher = re.compile("^(.)(\d+).(.),?[ ]?(.)?(\d+)?.?(.)?(.?.?.?.?.?)?")
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27 mutationMatcher = re.compile("^([actg])(\d+).([actg]),?[ ]?([A-Z])?(\d+)?.?([A-Z])?(.*)?")
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28 mutationMatcher = re.compile("^([actg])(\d+).([actg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
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29 mutationMatcher = re.compile("^([nactg])(\d+).([nactg]),?[ ]?([A-Z])?(\d+)?[>]?([A-Z;])?(.*)?")
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30 NAMatchResult = (None, None, None, None, None, None, '')
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31 geneMatchers = {gene: re.compile("^" + gene + ".*") for gene in genes}
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32 linecount = 0
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0
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33
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47
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34 IDIndex = 0
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35 best_matchIndex = 0
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36 fr1Index = 0
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37 cdr1Index = 0
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38 fr2Index = 0
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39 cdr2Index = 0
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40 fr3Index = 0
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41 first = True
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42 IDlist = []
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43 mutationList = []
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44 mutationListByID = {}
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45 cdr1LengthDic = {}
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46 cdr2LengthDic = {}
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47
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48 fr1LengthDict = {}
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49 fr2LengthDict = {}
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50 fr3LengthDict = {}
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51
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52 cdr1LengthIndex = 0
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53 cdr2LengthIndex = 0
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0
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54
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47
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55 fr1SeqIndex = 0
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56 fr2SeqIndex = 0
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57 fr3SeqIndex = 0
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58
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59 tandem_sum_by_class = defaultdict(int)
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60 expected_tandem_sum_by_class = defaultdict(float)
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0
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61
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47
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62 with open(infile, 'ru') as i:
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63 for line in i:
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64 if first:
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65 linesplt = line.split("\t")
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66 IDIndex = linesplt.index("Sequence.ID")
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67 best_matchIndex = linesplt.index("best_match")
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68 fr1Index = linesplt.index("FR1.IMGT")
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69 cdr1Index = linesplt.index("CDR1.IMGT")
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70 fr2Index = linesplt.index("FR2.IMGT")
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71 cdr2Index = linesplt.index("CDR2.IMGT")
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72 fr3Index = linesplt.index("FR3.IMGT")
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73 cdr1LengthIndex = linesplt.index("CDR1.IMGT.seq")
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74 cdr2LengthIndex = linesplt.index("CDR2.IMGT.seq")
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75 fr1SeqIndex = linesplt.index("FR1.IMGT.seq")
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76 fr2SeqIndex = linesplt.index("FR2.IMGT.seq")
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77 fr3SeqIndex = linesplt.index("FR3.IMGT.seq")
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78 first = False
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79 continue
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80 linecount += 1
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0
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81 linesplt = line.split("\t")
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82 ID = linesplt[IDIndex]
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83 genedic[ID] = linesplt[best_matchIndex]
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62
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84
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85 mutationdic[ID + "_FR1"] = []
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86 if len(linesplt[fr1Index]) > 5 and empty_region_filter == "leader":
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87 mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if x]
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88
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89 mutationdic[ID + "_CDR1"] = []
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90 if len(linesplt[cdr1Index]) > 5 and empty_region_filter in ["leader", "FR1"]:
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91 mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x]
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92
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93 mutationdic[ID + "_FR2"] = []
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94 if len(linesplt[fr2Index]) > 5 and empty_region_filter in ["leader", "FR1", "CDR1"]:
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95 mutationdic[ID + "_FR2"] = [mutationMatcher.match(x).groups() for x in linesplt[fr2Index].split("|") if x]
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96
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97 mutationdic[ID + "_CDR2"] = []
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98 if len(linesplt[cdr2Index]) > 5:
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99 mutationdic[ID + "_CDR2"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr2Index].split("|") if x]
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100
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101 mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"]
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102
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103 mutationdic[ID + "_FR3"] = []
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104 if len(linesplt[fr3Index]) > 5:
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105 mutationdic[ID + "_FR3"] = [mutationMatcher.match(x).groups() for x in linesplt[fr3Index].split("|") if x]
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106
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107 try:
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108 pass
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109 except Exception as e:
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110 print "Something went wrong while processing this line:"
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62
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111 print "line:", linecount
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112 print "fr1 len:", len(linesplt[fr1Index]), "value:", linesplt[fr1Index]
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113 print "cdr1 len:", len(linesplt[cdr1Index]), "value:", linesplt[cdr1Index]
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114 print "fr2 len:", len(linesplt[fr2Index]), "value:", linesplt[fr2Index]
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115 print "cdr2 len:", len(linesplt[cdr2Index]), "value:", linesplt[cdr2Index]
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116 print "fr3 len:", len(linesplt[fr3Index]), "value:", linesplt[fr3Index]
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117 print ID + "_FR1 in mutationdic", ID + "_FR1" in mutationdic
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118 print ID + "_CDR1 in mutationdic", ID + "_CDR1" in mutationdic
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119 print ID + "_FR2 in mutationdic", ID + "_FR2" in mutationdic
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120 print ID + "_CDR2 in mutationdic", ID + "_CDR2" in mutationdic
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121 print ID + "_FR3 in mutationdic", ID + "_FR3" in mutationdic
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47
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122 print linesplt
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123 print e
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124 mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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125 mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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126
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127 cdr1Length = len(linesplt[cdr1LengthIndex])
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128 cdr2Length = len(linesplt[cdr2LengthIndex])
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129
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130 #print linesplt[fr2SeqIndex]
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131 fr1Length = len(linesplt[fr1SeqIndex]) if empty_region_filter == "leader" else 0
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132 fr2Length = len(linesplt[fr2SeqIndex]) if empty_region_filter in ["leader", "FR1", "CDR1"] else 0
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133 fr3Length = len(linesplt[fr3SeqIndex])
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134
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135 cdr1LengthDic[ID] = cdr1Length
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136 cdr2LengthDic[ID] = cdr2Length
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137
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138 fr1LengthDict[ID] = fr1Length
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139 fr2LengthDict[ID] = fr2Length
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140 fr3LengthDict[ID] = fr3Length
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141
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142 IDlist += [ID]
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62
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143 print "len(mutationdic) =", len(mutationdic)
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47
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144
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62
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145 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "mutationdict.txt"), 'w') as out_handle:
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146 for ID, lst in mutationdic.iteritems():
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147 for mut in lst:
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148 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in mut])))
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149
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150 #tandem mutation stuff
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151 tandem_frequency = defaultdict(int)
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152 mutation_frequency = defaultdict(int)
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48
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153
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154 mutations_by_id_dic = {}
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155 first = True
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156 mutation_by_id_file = os.path.join(os.path.dirname(outfile), "mutation_by_id.txt")
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157 with open(mutation_by_id_file, 'r') as mutation_by_id:
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158 for l in mutation_by_id:
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159 if first:
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160 first = False
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161 continue
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162 splt = l.split("\t")
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163 mutations_by_id_dic[splt[0]] = int(splt[1])
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164
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165 tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt")
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166 with open(tandem_file, 'w') as o:
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167 highest_tandem_length = 0
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168
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169 o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n")
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170 for ID in IDlist:
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171 mutations = mutationListByID[ID]
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172 if len(mutations) == 0:
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173 continue
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174 last_mut = max(mutations, key=lambda x: int(x[1]))
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175
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176 last_mut_pos = int(last_mut[1])
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177
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178 mut_positions = [False] * (last_mut_pos + 1)
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179
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180 for mutation in mutations:
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181 frm, where, to, frmAA, whereAA, toAA, thing = mutation
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182 where = int(where)
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183 mut_positions[where] = True
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184
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185 tandem_muts = []
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186 tandem_start = -1
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187 tandem_length = 0
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188 for i in range(len(mut_positions)):
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189 if mut_positions[i]:
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190 if tandem_start == -1:
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191 tandem_start = i
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192 tandem_length += 1
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193 #print "".join(["1" if x else "0" for x in mut_positions[:i+1]])
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194 else:
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195 if tandem_length > 1:
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196 tandem_muts.append((tandem_start, tandem_length))
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197 #print "{0}{1} {2}:{3}".format(" " * (i - tandem_length), "^" * tandem_length, tandem_start, tandem_length)
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198 tandem_start = -1
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199 tandem_length = 0
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200 if tandem_length > 1: # if the sequence ends with a tandem mutation
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201 tandem_muts.append((tandem_start, tandem_length))
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202
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203 if len(tandem_muts) > 0:
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204 if highest_tandem_length < len(tandem_muts):
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205 highest_tandem_length = len(tandem_muts)
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0
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206
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47
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207 region_length = fr1LengthDict[ID] + cdr1LengthDic[ID] + fr2LengthDict[ID] + cdr2LengthDic[ID] + fr3LengthDict[ID]
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208 longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0)
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48
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209 num_mutations = mutations_by_id_dic[ID] # len(mutations)
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47
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210 f_num_mutations = float(num_mutations)
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211 num_tandem_muts = len(tandem_muts)
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212 expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length)
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213 o.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(ID,
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214 str(num_mutations),
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215 str(num_tandem_muts),
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216 str(region_length),
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217 str(round(expected_tandem_muts, 2)),
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218 str(longest_tandem[1]),
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219 str(tandem_muts)))
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220 gene = genedic[ID]
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221 if gene.find("unmatched") == -1:
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222 tandem_sum_by_class[gene] += num_tandem_muts
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223 expected_tandem_sum_by_class[gene] += expected_tandem_muts
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0
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224
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47
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225 tandem_sum_by_class["all"] += num_tandem_muts
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226 expected_tandem_sum_by_class["all"] += expected_tandem_muts
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0
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227
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47
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228 gene = gene[:3]
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229 if gene in ["IGA", "IGG"]:
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230 tandem_sum_by_class[gene] += num_tandem_muts
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231 expected_tandem_sum_by_class[gene] += expected_tandem_muts
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232 else:
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233 tandem_sum_by_class["unmatched"] += num_tandem_muts
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234 expected_tandem_sum_by_class["unmatched"] += expected_tandem_muts
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235
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40
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236
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47
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237 for tandem_mut in tandem_muts:
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238 tandem_frequency[str(tandem_mut[1])] += 1
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239 #print "\t".join([ID, str(len(tandem_muts)), str(longest_tandem[1]) , str(tandem_muts)])
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240
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241 tandem_freq_file = os.path.join(os.path.dirname(outfile), "tandem_frequency.txt")
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242 with open(tandem_freq_file, 'w') as o:
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243 for frq in sorted([int(x) for x in tandem_frequency.keys()]):
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244 o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)]))
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0
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245
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47
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246 tandem_row = []
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247 genes_extra = list(genes)
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248 genes_extra.append("all")
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249 for x, y, in zip([tandem_sum_by_class[x] for x in genes_extra], [expected_tandem_sum_by_class[x] for x in genes_extra]):
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250 if y != 0:
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251 tandem_row += [x, round(y, 2), round(x / y, 2)]
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252 else:
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253 tandem_row += [x, round(y, 2), 0]
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0
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254
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47
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255 tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt")
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256 with open(tandem_freq_file, 'w') as o:
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257 o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row])))
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258
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259 #print mutationList, linecount
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260
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62
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261 AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] and i[5] != ";" else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent
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47
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262 if AALength < 60:
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263 AALength = 64
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264
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265 AA_mutation = [0] * AALength
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266 AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "IGE": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]}
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267 AA_mutation_empty = AA_mutation[:]
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268
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269 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
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270 with open(aa_mutations_by_id_file, 'w') as o:
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271 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
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272 for ID in mutationListByID.keys():
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273 AA_mutation_for_ID = AA_mutation_empty[:]
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274 for mutation in mutationListByID[ID]:
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275 if mutation[4]:
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276 AA_mutation_position = int(mutation[4])
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277 AA_mutation[AA_mutation_position] += 1
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278 AA_mutation_for_ID[AA_mutation_position] += 1
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279 clss = genedic[ID][:3]
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280 AA_mutation_dic[clss][AA_mutation_position] += 1
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281 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
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0
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282
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283
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284
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47
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285 #absent AA stuff
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286 absentAACDR1Dic = defaultdict(list)
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287 absentAACDR1Dic[5] = range(29,36)
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288 absentAACDR1Dic[6] = range(29,35)
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289 absentAACDR1Dic[7] = range(30,35)
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290 absentAACDR1Dic[8] = range(30,34)
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291 absentAACDR1Dic[9] = range(31,34)
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292 absentAACDR1Dic[10] = range(31,33)
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293 absentAACDR1Dic[11] = [32]
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0
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294
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47
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295 absentAACDR2Dic = defaultdict(list)
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296 absentAACDR2Dic[0] = range(55,65)
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297 absentAACDR2Dic[1] = range(56,65)
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298 absentAACDR2Dic[2] = range(56,64)
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299 absentAACDR2Dic[3] = range(57,64)
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300 absentAACDR2Dic[4] = range(57,63)
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301 absentAACDR2Dic[5] = range(58,63)
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302 absentAACDR2Dic[6] = range(58,62)
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303 absentAACDR2Dic[7] = range(59,62)
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304 absentAACDR2Dic[8] = range(59,61)
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305 absentAACDR2Dic[9] = [60]
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0
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306
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47
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307 absentAA = [len(IDlist)] * (AALength-1)
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308 for k, cdr1Length in cdr1LengthDic.iteritems():
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309 for c in absentAACDR1Dic[cdr1Length]:
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310 absentAA[c] -= 1
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0
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311
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47
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312 for k, cdr2Length in cdr2LengthDic.iteritems():
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313 for c in absentAACDR2Dic[cdr2Length]:
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314 absentAA[c] -= 1
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0
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315
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316
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47
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317 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
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318 with open(aa_mutations_by_id_file, 'w') as o:
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319 o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
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320 for ID in IDlist:
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321 absentAAbyID = [1] * (AALength-1)
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322 cdr1Length = cdr1LengthDic[ID]
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323 for c in absentAACDR1Dic[cdr1Length]:
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324 absentAAbyID[c] -= 1
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0
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325
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47
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326 cdr2Length = cdr2LengthDic[ID]
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327 for c in absentAACDR2Dic[cdr2Length]:
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328 absentAAbyID[c] -= 1
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329 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
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0
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330
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47
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331 if linecount == 0:
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332 print "No data, exiting"
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333 with open(outfile, 'w') as o:
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334 o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
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335 o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))
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336 o.write("WA (%)," + ("0,0,0\n" * len(genes)))
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337 o.write("TW (%)," + ("0,0,0\n" * len(genes)))
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338 import sys
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0
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339
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47
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340 sys.exit()
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0
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341
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47
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342 hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
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343 RGYWCount = {}
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344 WRCYCount = {}
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345 WACount = {}
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346 TWCount = {}
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0
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347
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47
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348 #IDIndex = 0
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349 ataIndex = 0
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350 tatIndex = 0
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351 aggctatIndex = 0
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352 atagcctIndex = 0
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353 first = True
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354 with open(infile, 'ru') as i:
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355 for line in i:
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356 if first:
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357 linesplt = line.split("\t")
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358 ataIndex = linesplt.index("X.a.t.a")
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359 tatIndex = linesplt.index("t.a.t.")
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360 aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.")
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361 atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.")
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362 first = False
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|
|
363 continue
|
|
0
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364 linesplt = line.split("\t")
|
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47
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365 gene = linesplt[best_matchIndex]
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366 ID = linesplt[IDIndex]
|
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367 RGYW = [(int(x), int(y), z) for (x, y, z) in
|
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368 [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]
|
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369 WRCY = [(int(x), int(y), z) for (x, y, z) in
|
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370 [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]
|
|
|
371 WA = [(int(x), int(y), z) for (x, y, z) in
|
|
|
372 [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]
|
|
|
373 TW = [(int(x), int(y), z) for (x, y, z) in
|
|
|
374 [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]
|
|
|
375 RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0
|
|
0
|
376
|
|
62
|
377 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "RGYW.txt"), 'a') as out_handle:
|
|
|
378 for hotspot in RGYW:
|
|
|
379 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in hotspot])))
|
|
|
380
|
|
47
|
381 mutationList = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
|
|
|
382 for mutation in mutationList:
|
|
|
383 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
|
|
62
|
384 mutation_in_RGYW = any(((start <= int(where) <= end) for (start, end, region) in RGYW))
|
|
|
385 mutation_in_WRCY = any(((start <= int(where) <= end) for (start, end, region) in WRCY))
|
|
|
386 mutation_in_WA = any(((start <= int(where) <= end) for (start, end, region) in WA))
|
|
|
387 mutation_in_TW = any(((start <= int(where) <= end) for (start, end, region) in TW))
|
|
0
|
388
|
|
47
|
389 in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW])
|
|
0
|
390
|
|
47
|
391 if in_how_many_motifs > 0:
|
|
|
392 RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs
|
|
|
393 WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs
|
|
|
394 WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs
|
|
|
395 TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs
|
|
0
|
396
|
|
|
397
|
|
47
|
398 def mean(lst):
|
|
|
399 return (float(sum(lst)) / len(lst)) if len(lst) > 0 else 0.0
|
|
0
|
400
|
|
|
401
|
|
47
|
402 def median(lst):
|
|
|
403 lst = sorted(lst)
|
|
|
404 l = len(lst)
|
|
|
405 if l == 0:
|
|
|
406 return 0
|
|
|
407 if l == 1:
|
|
|
408 return lst[0]
|
|
|
409
|
|
|
410 l = int(l / 2)
|
|
0
|
411
|
|
47
|
412 if len(lst) % 2 == 0:
|
|
|
413 return float(lst[l] + lst[(l - 1)]) / 2.0
|
|
|
414 else:
|
|
|
415 return lst[l]
|
|
0
|
416
|
|
47
|
417 funcs = {"mean": mean, "median": median, "sum": sum}
|
|
0
|
418
|
|
47
|
419 directory = outfile[:outfile.rfind("/") + 1]
|
|
|
420 value = 0
|
|
|
421 valuedic = dict()
|
|
0
|
422
|
|
47
|
423 for fname in funcs.keys():
|
|
|
424 for gene in genes:
|
|
|
425 with open(directory + gene + "_" + fname + "_value.txt", 'r') as v:
|
|
|
426 valuedic[gene + "_" + fname] = float(v.readlines()[0].rstrip())
|
|
|
427 with open(directory + "all_" + fname + "_value.txt", 'r') as v:
|
|
|
428 valuedic["total_" + fname] = float(v.readlines()[0].rstrip())
|
|
|
429
|
|
0
|
430
|
|
47
|
431 def get_xyz(lst, gene, f, fname):
|
|
|
432 x = round(round(f(lst), 1))
|
|
|
433 y = valuedic[gene + "_" + fname]
|
|
|
434 z = str(round(x / float(y) * 100, 1)) if y != 0 else "0"
|
|
|
435 return (str(x), str(y), z)
|
|
0
|
436
|
|
47
|
437 dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount}
|
|
|
438 arr = ["RGYW", "WRCY", "WA", "TW"]
|
|
0
|
439
|
|
47
|
440 for fname in funcs.keys():
|
|
|
441 func = funcs[fname]
|
|
|
442 foutfile = outfile[:outfile.rindex("/")] + "/hotspot_analysis_" + fname + ".txt"
|
|
|
443 with open(foutfile, 'w') as o:
|
|
|
444 for typ in arr:
|
|
|
445 o.write(typ + " (%)")
|
|
|
446 curr = dic[typ]
|
|
|
447 for gene in genes:
|
|
|
448 geneMatcher = geneMatchers[gene]
|
|
|
449 if valuedic[gene + "_" + fname] is 0:
|
|
|
450 o.write(",0,0,0")
|
|
|
451 else:
|
|
|
452 x, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]], gene, func, fname)
|
|
|
453 o.write("," + x + "," + y + "," + z)
|
|
|
454 x, y, z = get_xyz([y for x, y in curr.iteritems() if not genedic[x].startswith("unmatched")], "total", func, fname)
|
|
|
455 #x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname)
|
|
|
456 o.write("," + x + "," + y + "," + z + "\n")
|
|
0
|
457
|
|
|
458
|
|
47
|
459 # for testing
|
|
|
460 seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
|
|
|
461 with open(seq_motif_file, 'w') as o:
|
|
|
462 o.write("ID\tRGYW\tWRCY\tWA\tTW\n")
|
|
|
463 for ID in IDlist:
|
|
|
464 #o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str(round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n")
|
|
|
465 o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")
|
|
|
466
|
|
|
467 if __name__ == "__main__":
|
|
|
468 main()
|
