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1 # ----------------------------------------------------------------------#
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2 # Copyright (c) 2011, Richard Lupat & Jason Li.
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3 #
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4 # > Source License <
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5 # This file is part of CONTRA.
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6 #
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7 # CONTRA is free software: you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation, either version 3 of the License, or
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10 # (at your option) any later version.
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11 #
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12 # CONTRA is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License
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18 # along with CONTRA. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 #
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21 #-----------------------------------------------------------------------#
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22 # Last Updated : 03 Oct 2011 11:00AM
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23
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24 import sys
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25
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26 def outputwrite(output, gene,chr,a,b,c,id,n,sOri, eOri):
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27 id = str(id)
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28 n = str(n)
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29 output.write(gene+"\t"+chr+"\t"+a+"\t"+b+"\t"+c+"\t"+id+"\t"+n+"\t"+sOri+"\t"+eOri+"\n")
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30
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31 def outputwrite2(output2, chr,c,sOri, eOri):
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32 output2.write(chr+"\t"+sOri+"\t"+eOri+"\t"+c+"\n")
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33
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34
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35 def convertGeneCoordinate(targetList, bufLocFolder):
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36 inputfile2 = bufLocFolder + "chr/"
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37 outputfile = bufLocFolder + "geneRefCoverage.txt"
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38 outputfile2= bufLocFolder + "geneRefCoverage2.txt"
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39
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40 output= open(outputfile,"w")
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41 output2 = open(outputfile2 , "w")
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42
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43 rn = 1
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44 prevchr = ""
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45 for target in targetList:
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46 chr = target.chr
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47 starts = target.oriStart.split(",")
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48 ends = target.oriEnd.split(",")
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49
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50 if ((len(chr) > 5) or (chr[len(chr)-1] == "M")):
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51 continue
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52
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53 if (prevchr != chr):
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54 print chr #progress checking
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55 prevchr = chr
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56 t = 0
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57 covFile = file.readlines(open(inputfile2+chr+".txt","r"))
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58
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59 for n in range(0,target.numberExon):
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60 if t >= len(covFile):
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61 break
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62 cov = covFile[t].split()
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63 while ((int(starts[n]) < int(cov[1])) or (int(starts[n]) >= int(cov[2]))):
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64 if (int(cov[1]) > int(starts[n])):
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65 t-=1
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66 else:
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67 t+=1
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68 cov = covFile[t].split()
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69
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70 while ((int(ends[n]) < int(cov[1])) or (int(ends[n]) > int(cov[2]))):
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71 # print output #
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72 if (rn == 1):
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73 prev = target.id
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74 nID = target.id
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75 if (nID != prev):
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76 rn = 1
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77 ref1 = str(rn)
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78 ref2 = str(int(cov[2]) - int(starts[n]) + rn)
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79 outputwrite(output, target.gene,chr,ref1,ref2,cov[3],target.id,n,starts[n],cov[2])
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80
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81 outputwrite2(output2, chr,cov[3],starts[n],cov[2])
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82
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83
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84 rn = int(ref2)
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85 prev = nID
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86 # -- #
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87
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88 # get to the next line of inputfile#
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89 t+= 1
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90 cov = covFile[t].split()
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91 starts[n] = cov[1]
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92
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93 #print output #
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94 if (t == 0) and (t >= len(covFile)):
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95 continue
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96
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97 if (rn == 1):
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98 prev = target.id
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99 nID = target.id
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100 if (nID != prev):
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101 rn = 1
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102 ref1 = str(rn)
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103 ref2 = str(int(ends[n]) - int(starts[n]) + rn)
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104 outputwrite(output, target.gene, chr, ref1, ref2, cov[3], target.id, n, starts[n], ends[n])
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105
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106 outputwrite2(output2, chr, cov[3], starts[n], ends[n])
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107
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108
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109 rn = int(ref2)
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110 prev = nID
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111 # -- #
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112 output.close()
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113 output2.close()
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114
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115
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116 def convertGeneCoordinate2(targetList, bufLocFolder):
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117 inputfile2 = bufLocFolder + "chr/"
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118 outputfile = bufLocFolder + "geneRefCoverage.txt"
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119 outputfile_avg = bufLocFolder + "geneRefCoverage_targetAverage.txt"
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120
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121 output= open(outputfile,"w")
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122 output_avg = open(outputfile_avg,"w")
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123
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124 rn = 1
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125 prevchr = ""
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126 for target in targetList:
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127 chr = target.chr
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128 starts = target.oriStart.split(",")
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129 ends = target.oriEnd.split(",")
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130 target_ttl_readdepth = 0
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131 starts_leftmost = starts[0]
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132
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133
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134 if ((len(chr) > 5) or (chr[len(chr)-1] == "M")):
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135 continue
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136
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137 if (prevchr != chr):
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138 print chr #progress checking
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139 prevchr = chr
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140 t = 0
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141 covFile = file.readlines(open(inputfile2+chr+".txt","r"))
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142
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143 for n in range(0,target.numberExon):
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144 if t >= len(covFile):
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145 break
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146 cov = covFile[t].split()
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147 while ((int(starts[n]) < int(cov[1])) or (int(starts[n]) >= int(cov[2]))):
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148 if (int(cov[1]) > int(starts[n])): t-=1
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149 else:
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150 t+=1
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151 cov = covFile[t].split()
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152
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153 while ((int(ends[n]) < int(cov[1])) or (int(ends[n]) > int(cov[2]))):
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154 # print output #
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155 if (rn == 1):
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156 prev = target.id
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157 nID = target.id
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158 if (nID != prev):
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159 rn = 1
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160 ref1 = str(rn)
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161 ref2 = str(int(cov[2]) - int(starts[n]) + rn)
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162 outputwrite2(output, chr,cov[3],starts[n],cov[2])
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163 tmprange=int(cov[2])-int(starts[n])+1
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164 target_ttl_readdepth+=int(cov[3])*tmprange
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165 #target_length+=tmprange
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166
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167 rn = int(ref2)
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168 prev = nID
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169 # -- #
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170
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171 # get to the next line of inputfile#
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172 t+= 1
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173 cov = covFile[t].split()
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174 starts[n] = cov[1]
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175
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176 #print output #
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177 if (t == 0) and (t >= len(covFile)):
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178 continue
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179
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180 if (rn == 1):
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181 prev = target.id
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182 nID = target.id
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183 if (nID != prev):
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184 rn = 1
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185 ref1 = str(rn)
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186 ref2 = str(int(ends[n]) - int(starts[n]) + rn)
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187 outputwrite2(output, chr, cov[3], starts[n], ends[n])
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188 tmprange=int(ends[n])-int(starts[n])+1
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189 target_ttl_readdepth+=int(cov[3])*tmprange
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190 #target_length+=tmprange
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191 target_length = int(ends[n])-int(starts_leftmost)+1
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192 output_avg.write("\t".join([chr,starts_leftmost,ends[n],str(target_ttl_readdepth/target_length),str(target_length)])+"\n")
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193
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194 rn = int(ref2)
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195 prev = nID
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196 # -- #
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197 output.close()
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198 output_avg.close()
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199
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