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1 from collections import defaultdict
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2 import re
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3 import argparse
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4
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5 parser = argparse.ArgumentParser()
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39
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6 parser.add_argument("--input",
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49
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7 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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8 parser.add_argument("--genes", help="The genes available in the 'best_match' column")
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31
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9 parser.add_argument("--includefr1", help="The genes available in the 'best_match' column")
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10 parser.add_argument("--output", help="Output file")
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11
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12 args = parser.parse_args()
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13
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4
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14 infile = args.input
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15 genes = str(args.genes).split(",")
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32
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16 print "includefr1 =", args.includefr1
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31
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17 include_fr1 = True if args.includefr1 == "yes" else False
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18 outfile = args.output
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4
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19
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20 genedic = dict()
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21
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22 mutationdic = dict()
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23 mutationMatcher = re.compile("^(.)(\d+).(.),?(.)?(\d+)?.?(.)?(.?.?.?.?.?)?")
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24 linecount = 0
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25
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4
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26 IDIndex = 0
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27 best_matchIndex = 0
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28 fr1Index = 0
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29 cdr1Index = 0
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30 fr2Index = 0
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31 cdr2Index = 0
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32 fr3Index = 0
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39
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33 first = True
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26
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34 IDlist = []
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35 mutationList = []
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43
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36 mutationListByID = {}
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37 cdr1LengthDic = {}
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38 cdr2LengthDic = {}
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26
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39
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4
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40 with open(infile, 'r') as i:
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43
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41 for line in i:
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42 if first:
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43 linesplt = line.split("\t")
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44 IDIndex = linesplt.index("Sequence.ID")
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45 best_matchIndex = linesplt.index("best_match")
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46 fr1Index = linesplt.index("FR1.IMGT")
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47 cdr1Index = linesplt.index("CDR1.IMGT")
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48 fr2Index = linesplt.index("FR2.IMGT")
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49 cdr2Index = linesplt.index("CDR2.IMGT")
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50 fr3Index = linesplt.index("FR3.IMGT")
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49
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51 cdr1LengthIndex = linesplt.index("CDR1.IMGT.Nb.of.nucleotides")
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52 cdr2LengthIndex = linesplt.index("CDR2.IMGT.Nb.of.nucleotides")
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43
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53 first = False
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54 continue
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55 linecount += 1
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56 linesplt = line.split("\t")
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57 ID = linesplt[IDIndex]
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58 genedic[ID] = linesplt[best_matchIndex]
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59 mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if
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60 x] if include_fr1 else []
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61 mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x]
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62 mutationdic[ID + "_FR2"] = [mutationMatcher.match(x).groups() for x in linesplt[fr2Index].split("|") if x]
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63 mutationdic[ID + "_CDR2"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr2Index].split("|") if x]
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64 mutationdic[ID + "_FR2-CDR2"] = mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"]
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65 mutationdic[ID + "_FR3"] = [mutationMatcher.match(x).groups() for x in linesplt[fr3Index].split("|") if x]
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66
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67 mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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68 mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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26
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69
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70 cdr1Length = linesplt[cdr1LengthIndex]
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71 cdr2Length = linesplt[cdr2LengthIndex]
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72
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73 cdr1LengthDic[ID] = int(cdr1Length) / 3
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74 cdr2LengthDic[ID] = int(cdr2Length) / 3
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75
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76 IDlist += [ID]
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77
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78 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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79
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80 AA_mutation = [0] * AALength
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81 AA_mutation_empty = AA_mutation[:]
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82
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83 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
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84 with open(aa_mutations_by_id_file, 'w') as o:
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85 for ID in mutationListByID.keys():
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86 AA_mutation_for_ID = AA_mutation_empty[:]
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87 for mutation in mutationListByID[ID]:
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88 if mutation[4]:
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89 AA_mutation[int(mutation[4])] += 1
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90 AA_mutation_for_ID[int(mutation[4])] += 1
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91 o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
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92
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93
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94
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95 #absent AA stuff
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96 absentAACDR1Dic = defaultdict(list)
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97 absentAACDR1Dic[5] = range(29,36)
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98 absentAACDR1Dic[6] = range(29,35)
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99 absentAACDR1Dic[7] = range(30,35)
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100 absentAACDR1Dic[8] = range(30,34)
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101 absentAACDR1Dic[9] = range(31,34)
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102 absentAACDR1Dic[10] = range(31,33)
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103 absentAACDR1Dic[11] = [32]
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104
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105 absentAACDR2Dic = defaultdict(list)
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106 absentAACDR2Dic[0] = range(55,65)
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107 absentAACDR2Dic[1] = range(56,65)
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108 absentAACDR2Dic[2] = range(56,64)
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109 absentAACDR2Dic[3] = range(57,64)
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110 absentAACDR2Dic[4] = range(57,63)
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111 absentAACDR2Dic[5] = range(58,63)
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112 absentAACDR2Dic[6] = range(58,62)
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113 absentAACDR2Dic[7] = range(59,62)
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114 absentAACDR2Dic[8] = range(59,61)
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115 absentAACDR2Dic[9] = [60]
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116
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117 absentAA = [len(IDlist)] * (AALength-1)
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118 for k, cdr1Length in cdr1LengthDic.iteritems():
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119 for c in absentAACDR1Dic[cdr1Length]:
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120 absentAA[c] -= 1
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121
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122 for k, cdr2Length in cdr2LengthDic.iteritems():
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123 for c in absentAACDR2Dic[cdr2Length]:
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124 absentAA[c] -= 1
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125
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126
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127 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
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128 with open(aa_mutations_by_id_file, 'w') as o:
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129 o.write("ID\tcdr1length\tcdr2length\t" + "\t".join([str(x) for x in range(1,AALength-1)]) + "\n")
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130 for ID in IDlist:
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131 absentAAbyID = [1] * (AALength-1)
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132 cdr1Length = cdr1LengthDic[ID]
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133 for c in absentAACDR1Dic[cdr1Length]:
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134 absentAAbyID[c] -= 1
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135
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136 cdr2Length = cdr2LengthDic[ID]
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137 for c in absentAACDR2Dic[cdr2Length]:
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138 absentAAbyID[c] -= 1
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139 o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n")
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140
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141
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26
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142
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143 aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt"
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144 with open(aa_mutations_file, 'w') as o:
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145 o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n")
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146 o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n")
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147 o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n")
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148
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0
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149 if linecount == 0:
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150 print "No data, exiting"
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151 with open(outfile, 'w') as o:
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152 o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
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153 o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))
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154 o.write("WA (%)," + ("0,0,0\n" * len(genes)))
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155 o.write("TW (%)," + ("0,0,0\n" * len(genes)))
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156 import sys
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157
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158 sys.exit()
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159
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160 hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
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161 RGYWCount = {g: 0 for g in genes}
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162 WRCYCount = {g: 0 for g in genes}
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163 WACount = {g: 0 for g in genes}
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164 TWCount = {g: 0 for g in genes}
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0
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165
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166 IDIndex = 0
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167 ataIndex = 0
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168 tatIndex = 0
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169 aggctatIndex = 0
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170 atagcctIndex = 0
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171 first = True
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172 with open(infile, 'r') as i:
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173 for line in i:
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174 if first:
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175 linesplt = line.split("\t")
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176 ataIndex = linesplt.index("X.a.t.a")
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177 tatIndex = linesplt.index("t.a.t.")
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178 aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.")
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179 atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.")
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180 first = False
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181 continue
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182 linesplt = line.split("\t")
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183 gene = linesplt[best_matchIndex]
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184 ID = linesplt[IDIndex]
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185 RGYW = [(int(x), int(y), z) for (x, y, z) in
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186 [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]
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187 WRCY = [(int(x), int(y), z) for (x, y, z) in
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188 [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]
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189 WA = [(int(x), int(y), z) for (x, y, z) in
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190 [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]
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191 TW = [(int(x), int(y), z) for (x, y, z) in
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192 [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]
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193 RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0
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194
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195 mutationList = (mutationdic[ID + "_FR1"] if include_fr1 else []) + mutationdic[ID + "_CDR1"] + mutationdic[
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196 ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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197 for mutation in mutationList:
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198 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
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199 mutation_in_RGYW = any([(start <= int(where) <= end) for (start, end, region) in RGYW])
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200 mutation_in_WRCY = any([(start <= int(where) <= end) for (start, end, region) in WRCY])
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201 mutation_in_WA = any([(start <= int(where) <= end) for (start, end, region) in WA])
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202 mutation_in_TW = any([(start <= int(where) <= end) for (start, end, region) in TW])
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203
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204 in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW])
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205
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206 if in_how_many_motifs > 0:
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207 RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs
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208 WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs
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209 WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs
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210 TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs
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0
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211
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212 directory = outfile[:outfile.rfind("/") + 1]
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22
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213 value = 0
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214 valuedic = dict()
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215 for gene in genes:
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216 with open(directory + gene + "_value.txt", 'r') as v:
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217 valuedic[gene] = int(v.readlines()[0].rstrip())
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218 with open(directory + "total_value.txt", 'r') as v:
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219 valuedic["total"] = int(v.readlines()[0].rstrip())
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220
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221 dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount}
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222 arr = ["RGYW", "WRCY", "WA", "TW"]
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223 with open(outfile, 'w') as o:
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224 for typ in arr:
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225 o.write(typ + " (%)")
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226 curr = dic[typ]
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227 for gene in genes:
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228 geneMatcher = re.compile(".*" + gene + ".*")
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229 if valuedic[gene] is 0:
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230 o.write(",0,0,0")
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231 else:
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232 x = int(round(sum([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]])))
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233 y = valuedic[gene]
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234 z = str(round(x / float(valuedic[gene]) * 100, 1))
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235 o.write("," + str(x) + "," + str(y) + "," + z)
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236 # for total
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237 x = int(round(sum([y for x, y in curr.iteritems()])))
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238 y = valuedic["total"]
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239 z = str(round(x / float(valuedic["total"]) * 100, 1))
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240 o.write("," + str(x) + "," + str(y) + "," + z + "\n")
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241
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242
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243 # for testing
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244 seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
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245 with open(seq_motif_file, 'w') as o:
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246 o.write("ID\tRGYWC\tWRCY\tWA\tTW\n")
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247 for ID in IDlist:
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248 o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str(
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249 round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n")
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