annotate shm_csr.py @ 82:a103134ee6e0 draft

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author davidvanzessen
date Thu, 25 Feb 2021 10:32:32 +0000
parents b6f9a640e098
children 729738462297
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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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7 from collections import defaultdict
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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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15
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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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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 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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33
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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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54
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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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61
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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.length")
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74 cdr2LengthIndex = linesplt.index("CDR2.IMGT.length")
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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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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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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 mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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108 mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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109
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110 try:
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111 cdr1Length = int(linesplt[cdr1LengthIndex])
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112 except:
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113 cdr1Length = 0
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114
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115 try:
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116 cdr2Length = int(linesplt[cdr2LengthIndex])
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117 except:
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118 cdr2Length = 0
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119
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120 #print linesplt[fr2SeqIndex]
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121 fr1Length = len(linesplt[fr1SeqIndex]) if empty_region_filter == "leader" else 0
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122 fr2Length = len(linesplt[fr2SeqIndex]) if empty_region_filter in ["leader", "FR1", "CDR1"] else 0
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123 fr3Length = len(linesplt[fr3SeqIndex])
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124
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125 cdr1LengthDic[ID] = cdr1Length
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126 cdr2LengthDic[ID] = cdr2Length
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127
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128 fr1LengthDict[ID] = fr1Length
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129 fr2LengthDict[ID] = fr2Length
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130 fr3LengthDict[ID] = fr3Length
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131
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132 IDlist += [ID]
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133 print "len(mutationdic) =", len(mutationdic)
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134
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135 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "mutationdict.txt"), 'w') as out_handle:
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136 for ID, lst in mutationdic.iteritems():
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137 for mut in lst:
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138 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in mut])))
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139
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140 #tandem mutation stuff
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141 tandem_frequency = defaultdict(int)
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142 mutation_frequency = defaultdict(int)
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143
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144 mutations_by_id_dic = {}
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145 first = True
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146 mutation_by_id_file = os.path.join(os.path.dirname(outfile), "mutation_by_id.txt")
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147 with open(mutation_by_id_file, 'r') as mutation_by_id:
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148 for l in mutation_by_id:
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149 if first:
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150 first = False
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151 continue
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152 splt = l.split("\t")
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153 mutations_by_id_dic[splt[0]] = int(splt[1])
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154
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155 tandem_file = os.path.join(os.path.dirname(outfile), "tandems_by_id.txt")
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156 with open(tandem_file, 'w') as o:
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157 highest_tandem_length = 0
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158
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159 o.write("Sequence.ID\tnumber_of_mutations\tnumber_of_tandems\tregion_length\texpected_tandems\tlongest_tandem\ttandems\n")
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160 for ID in IDlist:
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161 mutations = mutationListByID[ID]
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162 if len(mutations) == 0:
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163 continue
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164 last_mut = max(mutations, key=lambda x: int(x[1]))
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165
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166 last_mut_pos = int(last_mut[1])
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167
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168 mut_positions = [False] * (last_mut_pos + 1)
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169
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170 for mutation in mutations:
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171 frm, where, to, frmAA, whereAA, toAA, thing = mutation
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172 where = int(where)
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173 mut_positions[where] = True
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174
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175 tandem_muts = []
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176 tandem_start = -1
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177 tandem_length = 0
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178 for i in range(len(mut_positions)):
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179 if mut_positions[i]:
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180 if tandem_start == -1:
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181 tandem_start = i
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182 tandem_length += 1
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183 #print "".join(["1" if x else "0" for x in mut_positions[:i+1]])
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184 else:
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185 if tandem_length > 1:
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parents:
diff changeset
186 tandem_muts.append((tandem_start, tandem_length))
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davidvanzessen
parents:
diff changeset
187 #print "{0}{1} {2}:{3}".format(" " * (i - tandem_length), "^" * tandem_length, tandem_start, tandem_length)
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davidvanzessen
parents:
diff changeset
188 tandem_start = -1
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davidvanzessen
parents:
diff changeset
189 tandem_length = 0
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davidvanzessen
parents:
diff changeset
190 if tandem_length > 1: # if the sequence ends with a tandem mutation
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davidvanzessen
parents:
diff changeset
191 tandem_muts.append((tandem_start, tandem_length))
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davidvanzessen
parents:
diff changeset
192
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davidvanzessen
parents:
diff changeset
193 if len(tandem_muts) > 0:
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davidvanzessen
parents:
diff changeset
194 if highest_tandem_length < len(tandem_muts):
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davidvanzessen
parents:
diff changeset
195 highest_tandem_length = len(tandem_muts)
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davidvanzessen
parents:
diff changeset
196
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davidvanzessen
parents:
diff changeset
197 region_length = fr1LengthDict[ID] + cdr1LengthDic[ID] + fr2LengthDict[ID] + cdr2LengthDic[ID] + fr3LengthDict[ID]
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davidvanzessen
parents:
diff changeset
198 longest_tandem = max(tandem_muts, key=lambda x: x[1]) if len(tandem_muts) else (0, 0)
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davidvanzessen
parents:
diff changeset
199 num_mutations = mutations_by_id_dic[ID] # len(mutations)
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davidvanzessen
parents:
diff changeset
200 f_num_mutations = float(num_mutations)
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davidvanzessen
parents:
diff changeset
201 num_tandem_muts = len(tandem_muts)
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davidvanzessen
parents:
diff changeset
202 expected_tandem_muts = f_num_mutations * (f_num_mutations - 1.0) / float(region_length)
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davidvanzessen
parents:
diff changeset
203 o.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(ID,
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davidvanzessen
parents:
diff changeset
204 str(num_mutations),
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davidvanzessen
parents:
diff changeset
205 str(num_tandem_muts),
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davidvanzessen
parents:
diff changeset
206 str(region_length),
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davidvanzessen
parents:
diff changeset
207 str(round(expected_tandem_muts, 2)),
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davidvanzessen
parents:
diff changeset
208 str(longest_tandem[1]),
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davidvanzessen
parents:
diff changeset
209 str(tandem_muts)))
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davidvanzessen
parents:
diff changeset
210 gene = genedic[ID]
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davidvanzessen
parents:
diff changeset
211 if gene.find("unmatched") == -1:
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davidvanzessen
parents:
diff changeset
212 tandem_sum_by_class[gene] += num_tandem_muts
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davidvanzessen
parents:
diff changeset
213 expected_tandem_sum_by_class[gene] += expected_tandem_muts
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davidvanzessen
parents:
diff changeset
214
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davidvanzessen
parents:
diff changeset
215 tandem_sum_by_class["all"] += num_tandem_muts
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davidvanzessen
parents:
diff changeset
216 expected_tandem_sum_by_class["all"] += expected_tandem_muts
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davidvanzessen
parents:
diff changeset
217
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davidvanzessen
parents:
diff changeset
218 gene = gene[:3]
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davidvanzessen
parents:
diff changeset
219 if gene in ["IGA", "IGG"]:
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davidvanzessen
parents:
diff changeset
220 tandem_sum_by_class[gene] += num_tandem_muts
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davidvanzessen
parents:
diff changeset
221 expected_tandem_sum_by_class[gene] += expected_tandem_muts
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davidvanzessen
parents:
diff changeset
222 else:
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davidvanzessen
parents:
diff changeset
223 tandem_sum_by_class["unmatched"] += num_tandem_muts
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davidvanzessen
parents:
diff changeset
224 expected_tandem_sum_by_class["unmatched"] += expected_tandem_muts
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davidvanzessen
parents:
diff changeset
225
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davidvanzessen
parents:
diff changeset
226
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davidvanzessen
parents:
diff changeset
227 for tandem_mut in tandem_muts:
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davidvanzessen
parents:
diff changeset
228 tandem_frequency[str(tandem_mut[1])] += 1
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davidvanzessen
parents:
diff changeset
229 #print "\t".join([ID, str(len(tandem_muts)), str(longest_tandem[1]) , str(tandem_muts)])
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davidvanzessen
parents:
diff changeset
230
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davidvanzessen
parents:
diff changeset
231 tandem_freq_file = os.path.join(os.path.dirname(outfile), "tandem_frequency.txt")
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davidvanzessen
parents:
diff changeset
232 with open(tandem_freq_file, 'w') as o:
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davidvanzessen
parents:
diff changeset
233 for frq in sorted([int(x) for x in tandem_frequency.keys()]):
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davidvanzessen
parents:
diff changeset
234 o.write("{0}\t{1}\n".format(frq, tandem_frequency[str(frq)]))
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davidvanzessen
parents:
diff changeset
235
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davidvanzessen
parents:
diff changeset
236 tandem_row = []
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davidvanzessen
parents:
diff changeset
237 genes_extra = list(genes)
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davidvanzessen
parents:
diff changeset
238 genes_extra.append("all")
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davidvanzessen
parents:
diff changeset
239 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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davidvanzessen
parents:
diff changeset
240 if y != 0:
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davidvanzessen
parents:
diff changeset
241 tandem_row += [x, round(y, 2), round(x / y, 2)]
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davidvanzessen
parents:
diff changeset
242 else:
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davidvanzessen
parents:
diff changeset
243 tandem_row += [x, round(y, 2), 0]
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davidvanzessen
parents:
diff changeset
244
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davidvanzessen
parents:
diff changeset
245 tandem_freq_file = os.path.join(os.path.dirname(outfile), "shm_overview_tandem_row.txt")
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davidvanzessen
parents:
diff changeset
246 with open(tandem_freq_file, 'w') as o:
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davidvanzessen
parents:
diff changeset
247 o.write("Tandems/Expected (ratio),{0}\n".format(",".join([str(x) for x in tandem_row])))
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davidvanzessen
parents:
diff changeset
248
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davidvanzessen
parents:
diff changeset
249 #print mutationList, linecount
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davidvanzessen
parents:
diff changeset
250
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davidvanzessen
parents:
diff changeset
251 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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davidvanzessen
parents:
diff changeset
252 if AALength < 60:
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davidvanzessen
parents:
diff changeset
253 AALength = 64
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davidvanzessen
parents:
diff changeset
254
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davidvanzessen
parents:
diff changeset
255 AA_mutation = [0] * AALength
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davidvanzessen
parents:
diff changeset
256 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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davidvanzessen
parents:
diff changeset
257 AA_mutation_empty = AA_mutation[:]
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davidvanzessen
parents:
diff changeset
258
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davidvanzessen
parents:
diff changeset
259 print "AALength:", AALength
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davidvanzessen
parents:
diff changeset
260 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt"
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davidvanzessen
parents:
diff changeset
261 with open(aa_mutations_by_id_file, 'w') as o:
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davidvanzessen
parents:
diff changeset
262 o.write("ID\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
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davidvanzessen
parents:
diff changeset
263 for ID in mutationListByID.keys():
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davidvanzessen
parents:
diff changeset
264 AA_mutation_for_ID = AA_mutation_empty[:]
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davidvanzessen
parents:
diff changeset
265 for mutation in mutationListByID[ID]:
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davidvanzessen
parents:
diff changeset
266 if mutation[4] and mutation[5] != ";":
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davidvanzessen
parents:
diff changeset
267 AA_mutation_position = int(mutation[4])
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davidvanzessen
parents:
diff changeset
268 try:
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davidvanzessen
parents:
diff changeset
269 AA_mutation[AA_mutation_position] += 1
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davidvanzessen
parents:
diff changeset
270 AA_mutation_for_ID[AA_mutation_position] += 1
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davidvanzessen
parents:
diff changeset
271 except Exception as e:
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davidvanzessen
parents:
diff changeset
272 print e
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davidvanzessen
parents:
diff changeset
273 print mutation
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davidvanzessen
parents:
diff changeset
274 sys.exit()
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davidvanzessen
parents:
diff changeset
275 clss = genedic[ID][:3]
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davidvanzessen
parents:
diff changeset
276 AA_mutation_dic[clss][AA_mutation_position] += 1
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davidvanzessen
parents:
diff changeset
277 o.write(ID + "\t" + genedic[ID] + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n")
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davidvanzessen
parents:
diff changeset
278
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davidvanzessen
parents:
diff changeset
279
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davidvanzessen
parents:
diff changeset
280
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davidvanzessen
parents:
diff changeset
281 #absent AA stuff
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davidvanzessen
parents:
diff changeset
282 absentAACDR1Dic = defaultdict(list)
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davidvanzessen
parents:
diff changeset
283 absentAACDR1Dic[5] = range(29,36)
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davidvanzessen
parents:
diff changeset
284 absentAACDR1Dic[6] = range(29,35)
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davidvanzessen
parents:
diff changeset
285 absentAACDR1Dic[7] = range(30,35)
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davidvanzessen
parents:
diff changeset
286 absentAACDR1Dic[8] = range(30,34)
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davidvanzessen
parents:
diff changeset
287 absentAACDR1Dic[9] = range(31,34)
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davidvanzessen
parents:
diff changeset
288 absentAACDR1Dic[10] = range(31,33)
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davidvanzessen
parents:
diff changeset
289 absentAACDR1Dic[11] = [32]
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davidvanzessen
parents:
diff changeset
290
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davidvanzessen
parents:
diff changeset
291 absentAACDR2Dic = defaultdict(list)
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davidvanzessen
parents:
diff changeset
292 absentAACDR2Dic[0] = range(55,65)
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davidvanzessen
parents:
diff changeset
293 absentAACDR2Dic[1] = range(56,65)
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davidvanzessen
parents:
diff changeset
294 absentAACDR2Dic[2] = range(56,64)
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davidvanzessen
parents:
diff changeset
295 absentAACDR2Dic[3] = range(57,64)
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davidvanzessen
parents:
diff changeset
296 absentAACDR2Dic[4] = range(57,63)
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davidvanzessen
parents:
diff changeset
297 absentAACDR2Dic[5] = range(58,63)
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davidvanzessen
parents:
diff changeset
298 absentAACDR2Dic[6] = range(58,62)
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davidvanzessen
parents:
diff changeset
299 absentAACDR2Dic[7] = range(59,62)
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davidvanzessen
parents:
diff changeset
300 absentAACDR2Dic[8] = range(59,61)
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davidvanzessen
parents:
diff changeset
301 absentAACDR2Dic[9] = [60]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
302
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davidvanzessen
parents:
diff changeset
303 absentAA = [len(IDlist)] * (AALength-1)
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davidvanzessen
parents:
diff changeset
304 for k, cdr1Length in cdr1LengthDic.iteritems():
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davidvanzessen
parents:
diff changeset
305 for c in absentAACDR1Dic[cdr1Length]:
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davidvanzessen
parents:
diff changeset
306 absentAA[c] -= 1
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davidvanzessen
parents:
diff changeset
307
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davidvanzessen
parents:
diff changeset
308 for k, cdr2Length in cdr2LengthDic.iteritems():
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davidvanzessen
parents:
diff changeset
309 for c in absentAACDR2Dic[cdr2Length]:
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davidvanzessen
parents:
diff changeset
310 absentAA[c] -= 1
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davidvanzessen
parents:
diff changeset
311
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davidvanzessen
parents:
diff changeset
312
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davidvanzessen
parents:
diff changeset
313 aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt"
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davidvanzessen
parents:
diff changeset
314 with open(aa_mutations_by_id_file, 'w') as o:
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davidvanzessen
parents:
diff changeset
315 o.write("ID\tcdr1length\tcdr2length\tbest_match\t" + "\t".join([str(x) for x in range(1,AALength)]) + "\n")
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davidvanzessen
parents:
diff changeset
316 for ID in IDlist:
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davidvanzessen
parents:
diff changeset
317 absentAAbyID = [1] * (AALength-1)
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davidvanzessen
parents:
diff changeset
318 cdr1Length = cdr1LengthDic[ID]
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davidvanzessen
parents:
diff changeset
319 for c in absentAACDR1Dic[cdr1Length]:
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davidvanzessen
parents:
diff changeset
320 absentAAbyID[c] -= 1
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davidvanzessen
parents:
diff changeset
321
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davidvanzessen
parents:
diff changeset
322 cdr2Length = cdr2LengthDic[ID]
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davidvanzessen
parents:
diff changeset
323 for c in absentAACDR2Dic[cdr2Length]:
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davidvanzessen
parents:
diff changeset
324 absentAAbyID[c] -= 1
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davidvanzessen
parents:
diff changeset
325 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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davidvanzessen
parents:
diff changeset
326
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davidvanzessen
parents:
diff changeset
327 if linecount == 0:
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davidvanzessen
parents:
diff changeset
328 print "No data, exiting"
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davidvanzessen
parents:
diff changeset
329 with open(outfile, 'w') as o:
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davidvanzessen
parents:
diff changeset
330 o.write("RGYW (%)," + ("0,0,0\n" * len(genes)))
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davidvanzessen
parents:
diff changeset
331 o.write("WRCY (%)," + ("0,0,0\n" * len(genes)))
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davidvanzessen
parents:
diff changeset
332 o.write("WA (%)," + ("0,0,0\n" * len(genes)))
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davidvanzessen
parents:
diff changeset
333 o.write("TW (%)," + ("0,0,0\n" * len(genes)))
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davidvanzessen
parents:
diff changeset
334 import sys
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
335
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davidvanzessen
parents:
diff changeset
336 sys.exit()
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davidvanzessen
parents:
diff changeset
337
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davidvanzessen
parents:
diff changeset
338 hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
339 RGYWCount = {}
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davidvanzessen
parents:
diff changeset
340 WRCYCount = {}
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davidvanzessen
parents:
diff changeset
341 WACount = {}
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davidvanzessen
parents:
diff changeset
342 TWCount = {}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
343
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davidvanzessen
parents:
diff changeset
344 #IDIndex = 0
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davidvanzessen
parents:
diff changeset
345 ataIndex = 0
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davidvanzessen
parents:
diff changeset
346 tatIndex = 0
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davidvanzessen
parents:
diff changeset
347 aggctatIndex = 0
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
348 atagcctIndex = 0
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davidvanzessen
parents:
diff changeset
349 first = True
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davidvanzessen
parents:
diff changeset
350 with open(infile, 'ru') as i:
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davidvanzessen
parents:
diff changeset
351 for line in i:
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davidvanzessen
parents:
diff changeset
352 if first:
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davidvanzessen
parents:
diff changeset
353 linesplt = line.split("\t")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
354 ataIndex = linesplt.index("X.a.t.a")
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davidvanzessen
parents:
diff changeset
355 tatIndex = linesplt.index("t.a.t.")
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davidvanzessen
parents:
diff changeset
356 aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.")
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davidvanzessen
parents:
diff changeset
357 atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.")
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davidvanzessen
parents:
diff changeset
358 first = False
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
359 continue
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davidvanzessen
parents:
diff changeset
360 linesplt = line.split("\t")
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davidvanzessen
parents:
diff changeset
361 gene = linesplt[best_matchIndex]
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davidvanzessen
parents:
diff changeset
362 ID = linesplt[IDIndex]
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davidvanzessen
parents:
diff changeset
363 RGYW = [(int(x), int(y), z) for (x, y, z) in
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
364 [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]]
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davidvanzessen
parents:
diff changeset
365 WRCY = [(int(x), int(y), z) for (x, y, z) in
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davidvanzessen
parents:
diff changeset
366 [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]]
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davidvanzessen
parents:
diff changeset
367 WA = [(int(x), int(y), z) for (x, y, z) in
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davidvanzessen
parents:
diff changeset
368 [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]]
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davidvanzessen
parents:
diff changeset
369 TW = [(int(x), int(y), z) for (x, y, z) in
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davidvanzessen
parents:
diff changeset
370 [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]]
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davidvanzessen
parents:
diff changeset
371 RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0
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davidvanzessen
parents:
diff changeset
372
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davidvanzessen
parents:
diff changeset
373 with open(os.path.join(os.path.dirname(os.path.abspath(infile)), "RGYW.txt"), 'a') as out_handle:
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davidvanzessen
parents:
diff changeset
374 for hotspot in RGYW:
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davidvanzessen
parents:
diff changeset
375 out_handle.write("{0}\t{1}\n".format(ID, "\t".join([str(x) for x in hotspot])))
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davidvanzessen
parents:
diff changeset
376
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davidvanzessen
parents:
diff changeset
377 mutationList = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"]
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davidvanzessen
parents:
diff changeset
378 for mutation in mutationList:
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davidvanzessen
parents:
diff changeset
379 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
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davidvanzessen
parents:
diff changeset
380 mutation_in_RGYW = any(((start <= int(where) <= end) for (start, end, region) in RGYW))
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davidvanzessen
parents:
diff changeset
381 mutation_in_WRCY = any(((start <= int(where) <= end) for (start, end, region) in WRCY))
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davidvanzessen
parents:
diff changeset
382 mutation_in_WA = any(((start <= int(where) <= end) for (start, end, region) in WA))
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davidvanzessen
parents:
diff changeset
383 mutation_in_TW = any(((start <= int(where) <= end) for (start, end, region) in TW))
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davidvanzessen
parents:
diff changeset
384
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davidvanzessen
parents:
diff changeset
385 in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW])
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davidvanzessen
parents:
diff changeset
386
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davidvanzessen
parents:
diff changeset
387 if in_how_many_motifs > 0:
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davidvanzessen
parents:
diff changeset
388 RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs
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davidvanzessen
parents:
diff changeset
389 WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs
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davidvanzessen
parents:
diff changeset
390 WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs
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davidvanzessen
parents:
diff changeset
391 TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs
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davidvanzessen
parents:
diff changeset
392
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davidvanzessen
parents:
diff changeset
393 mutations_in_motifs_file = os.path.join(os.path.dirname(os.path.abspath(infile)), "mutation_in_motifs.txt")
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davidvanzessen
parents:
diff changeset
394 if not os.path.exists(mutation_by_id_file):
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davidvanzessen
parents:
diff changeset
395 with open(mutations_in_motifs_file, 'w') as out_handle:
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davidvanzessen
parents:
diff changeset
396 out_handle.write("{0}\n".format("\t".join([
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davidvanzessen
parents:
diff changeset
397 "Sequence.ID",
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davidvanzessen
parents:
diff changeset
398 "mutation_position",
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davidvanzessen
parents:
diff changeset
399 "region",
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davidvanzessen
parents:
diff changeset
400 "from_nt",
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davidvanzessen
parents:
diff changeset
401 "to_nt",
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davidvanzessen
parents:
diff changeset
402 "mutation_position_AA",
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davidvanzessen
parents:
diff changeset
403 "from_AA",
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davidvanzessen
parents:
diff changeset
404 "to_AA",
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davidvanzessen
parents:
diff changeset
405 "motif",
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davidvanzessen
parents:
diff changeset
406 "motif_start_nt",
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davidvanzessen
parents:
diff changeset
407 "motif_end_nt",
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davidvanzessen
parents:
diff changeset
408 "rest"
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davidvanzessen
parents:
diff changeset
409 ])))
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davidvanzessen
parents:
diff changeset
410
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davidvanzessen
parents:
diff changeset
411 with open(mutations_in_motifs_file, 'a') as out_handle:
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davidvanzessen
parents:
diff changeset
412 motif_dic = {"RGYW": RGYW, "WRCY": WRCY, "WA": WA, "TW": TW}
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davidvanzessen
parents:
diff changeset
413 for mutation in mutationList:
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davidvanzessen
parents:
diff changeset
414 frm, where, to, AAfrm, AAwhere, AAto, junk = mutation
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davidvanzessen
parents:
diff changeset
415 for motif in motif_dic.keys():
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davidvanzessen
parents:
diff changeset
416
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davidvanzessen
parents:
diff changeset
417 for start, end, region in motif_dic[motif]:
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davidvanzessen
parents:
diff changeset
418 if start <= int(where) <= end:
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davidvanzessen
parents:
diff changeset
419 out_handle.write("{0}\n".format(
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davidvanzessen
parents:
diff changeset
420 "\t".join([
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davidvanzessen
parents:
diff changeset
421 ID,
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davidvanzessen
parents:
diff changeset
422 where,
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davidvanzessen
parents:
diff changeset
423 region,
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davidvanzessen
parents:
diff changeset
424 frm,
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davidvanzessen
parents:
diff changeset
425 to,
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davidvanzessen
parents:
diff changeset
426 str(AAwhere),
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davidvanzessen
parents:
diff changeset
427 str(AAfrm),
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davidvanzessen
parents:
diff changeset
428 str(AAto),
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davidvanzessen
parents:
diff changeset
429 motif,
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davidvanzessen
parents:
diff changeset
430 str(start),
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davidvanzessen
parents:
diff changeset
431 str(end),
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davidvanzessen
parents:
diff changeset
432 str(junk)
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davidvanzessen
parents:
diff changeset
433 ])
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davidvanzessen
parents:
diff changeset
434 ))
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davidvanzessen
parents:
diff changeset
435
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davidvanzessen
parents:
diff changeset
436
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davidvanzessen
parents:
diff changeset
437
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davidvanzessen
parents:
diff changeset
438 def mean(lst):
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davidvanzessen
parents:
diff changeset
439 return (float(sum(lst)) / len(lst)) if len(lst) > 0 else 0.0
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davidvanzessen
parents:
diff changeset
440
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davidvanzessen
parents:
diff changeset
441
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davidvanzessen
parents:
diff changeset
442 def median(lst):
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davidvanzessen
parents:
diff changeset
443 lst = sorted(lst)
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davidvanzessen
parents:
diff changeset
444 l = len(lst)
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davidvanzessen
parents:
diff changeset
445 if l == 0:
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davidvanzessen
parents:
diff changeset
446 return 0
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davidvanzessen
parents:
diff changeset
447 if l == 1:
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davidvanzessen
parents:
diff changeset
448 return lst[0]
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davidvanzessen
parents:
diff changeset
449
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davidvanzessen
parents:
diff changeset
450 l = int(l / 2)
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davidvanzessen
parents:
diff changeset
451
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davidvanzessen
parents:
diff changeset
452 if len(lst) % 2 == 0:
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davidvanzessen
parents:
diff changeset
453 return float(lst[l] + lst[(l - 1)]) / 2.0
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davidvanzessen
parents:
diff changeset
454 else:
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davidvanzessen
parents:
diff changeset
455 return lst[l]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
456
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davidvanzessen
parents:
diff changeset
457 funcs = {"mean": mean, "median": median, "sum": sum}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
458
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davidvanzessen
parents:
diff changeset
459 directory = outfile[:outfile.rfind("/") + 1]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
460 value = 0
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
461 valuedic = dict()
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
462
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davidvanzessen
parents:
diff changeset
463 for fname in funcs.keys():
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
464 for gene in genes:
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davidvanzessen
parents:
diff changeset
465 with open(directory + gene + "_" + fname + "_value.txt", 'r') as v:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
466 valuedic[gene + "_" + fname] = float(v.readlines()[0].rstrip())
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
467 with open(directory + "all_" + fname + "_value.txt", 'r') as v:
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davidvanzessen
parents:
diff changeset
468 valuedic["total_" + fname] = float(v.readlines()[0].rstrip())
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
469
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
470
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
471 def get_xyz(lst, gene, f, fname):
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
472 x = round(round(f(lst), 1))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
473 y = valuedic[gene + "_" + fname]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
474 z = str(round(x / float(y) * 100, 1)) if y != 0 else "0"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
475 return (str(x), str(y), z)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
476
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
477 dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount}
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
478 arr = ["RGYW", "WRCY", "WA", "TW"]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
479
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
480 for fname in funcs.keys():
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
481 func = funcs[fname]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
482 foutfile = outfile[:outfile.rindex("/")] + "/hotspot_analysis_" + fname + ".txt"
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
483 with open(foutfile, 'w') as o:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
484 for typ in arr:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
485 o.write(typ + " (%)")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
486 curr = dic[typ]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
487 for gene in genes:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
488 geneMatcher = geneMatchers[gene]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
489 if valuedic[gene + "_" + fname] is 0:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
490 o.write(",0,0,0")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
491 else:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
492 x, y, z = get_xyz([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]], gene, func, fname)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
493 o.write("," + x + "," + y + "," + z)
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davidvanzessen
parents:
diff changeset
494 x, y, z = get_xyz([y for x, y in curr.iteritems() if not genedic[x].startswith("unmatched")], "total", func, fname)
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davidvanzessen
parents:
diff changeset
495 #x, y, z = get_xyz([y for x, y in curr.iteritems()], "total", func, fname)
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davidvanzessen
parents:
diff changeset
496 o.write("," + x + "," + y + "," + z + "\n")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
497
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
498
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
499 # for testing
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davidvanzessen
parents:
diff changeset
500 seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt"
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davidvanzessen
parents:
diff changeset
501 with open(seq_motif_file, 'w') as o:
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
502 o.write("ID\tRGYW\tWRCY\tWA\tTW\n")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
503 for ID in IDlist:
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davidvanzessen
parents:
diff changeset
504 #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")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
505 o.write(ID + "\t" + str(RGYWCount[ID]) + "\t" + str(WRCYCount[ID]) + "\t" + str(WACount[ID]) + "\t" + str(TWCount[ID]) + "\n")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
506
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
507 if __name__ == "__main__":
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
508 main()