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