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1 #!/usr/bin/env python
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2 """
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3 Common utility functions
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4 """
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5
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6 import os
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7 import re
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8 import sys
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9 import gzip
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10 import bz2
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11 import numpy
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12
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13 def init_gene():
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14 """
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15 Initializing the gene structure
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16 """
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17
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18 gene_det = [('id', 'f8'),
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19 ('anno_id', numpy.dtype),
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20 ('confgenes_id', numpy.dtype),
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21 ('name', 'S25'),
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22 ('source', 'S25'),
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23 ('gene_info', numpy.dtype),
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24 ('alias', 'S15'),
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25 ('name2', numpy.dtype),
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26 ('strand', 'S2'),
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27 ('score', 'S15'),
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28 ('chr', 'S15'),
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29 ('chr_num', numpy.dtype),
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30 ('paralogs', numpy.dtype),
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31 ('start', 'f8'),
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32 ('stop', 'f8'),
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33 ('transcripts', numpy.dtype),
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34 ('transcript_type', numpy.dtype),
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35 ('transcript_info', numpy.dtype),
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36 ('transcript_status', numpy.dtype),
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37 ('transcript_valid', numpy.dtype),
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38 ('exons', numpy.dtype),
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39 ('exons_confirmed', numpy.dtype),
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40 ('cds_exons', numpy.dtype),
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41 ('utr5_exons', numpy.dtype),
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42 ('utr3_exons', numpy.dtype),
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43 ('tis', numpy.dtype),
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44 ('tis_conf', numpy.dtype),
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45 ('tis_info', numpy.dtype),
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46 ('cdsStop', numpy.dtype),
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47 ('cdsStop_conf', numpy.dtype),
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48 ('cdsStop_info', numpy.dtype),
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49 ('tss', numpy.dtype),
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50 ('tss_info', numpy.dtype),
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51 ('tss_conf', numpy.dtype),
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52 ('cleave', numpy.dtype),
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53 ('cleave_info', numpy.dtype),
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54 ('cleave_conf', numpy.dtype),
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55 ('polya', numpy.dtype),
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56 ('polya_info', numpy.dtype),
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57 ('polya_conf', numpy.dtype),
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58 ('is_alt', 'f8'),
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59 ('is_alt_spliced', 'f8'),
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60 ('is_valid', numpy.dtype),
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61 ('transcript_complete', numpy.dtype),
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62 ('is_complete', numpy.dtype),
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63 ('is_correctly_gff3_referenced', 'S5'),
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64 ('splicegraph', numpy.dtype) ]
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65
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66 return gene_det
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67
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68 def open_file(fname):
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69 """
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70 Open the file (supports .gz .bz2) and returns the handler
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71
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72 @args fname: input file name for reading
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73 @type fname: str
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74 """
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75
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76 try:
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77 if os.path.splitext(fname)[1] == ".gz":
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78 FH = gzip.open(fname, 'rb')
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79 elif os.path.splitext(fname)[1] == ".bz2":
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80 FH = bz2.BZ2File(fname, 'rb')
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81 else:
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82 FH = open(fname, 'rU')
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83 except Exception as error:
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84 sys.exit(error)
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85
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86 return FH
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87
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88 def add_CDS_phase(strand, cds):
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89 """
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90 Calculate CDS phase and add to the CDS exons
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91
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92 @args strand: feature strand information
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93 @type strand: +/-
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94 @args cds: coding exon coordinates
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95 @type cds: numpy array [[int, int, int]]
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96 """
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97
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98 cds_region, cds_flag = [], 0
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99 if strand == '+':
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100 for cdspos in cds:
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101 if cds_flag == 0:
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102 cdspos = (cdspos[0], cdspos[1], 0)
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103 diff = (cdspos[1]-(cdspos[0]-1))%3
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104 else:
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105 xy = 0
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106 if diff == 0:
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107 cdspos = (cdspos[0], cdspos[1], 0)
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108 elif diff == 1:
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109 cdspos = (cdspos[0], cdspos[1], 2)
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110 xy = 2
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111 elif diff == 2:
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112 cdspos = (cdspos[0], cdspos[1], 1)
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113 xy = 1
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114 diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3
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115 cds_region.append(cdspos)
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116 cds_flag = 1
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117 elif strand == '-':
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118 cds.reverse()
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119 for cdspos in cds:
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120 if cds_flag == 0:
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121 cdspos = (cdspos[0], cdspos[1], 0)
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122 diff = (cdspos[1]-(cdspos[0]-1))%3
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123 else:
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124 xy = 0
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125 if diff == 0:
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126 cdspos = (cdspos[0], cdspos[1], 0)
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127 elif diff == 1:
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128 cdspos = (cdspos[0], cdspos[1], 2)
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129 xy = 2
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130 elif diff == 2:
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131 cdspos = (cdspos[0], cdspos[1], 1)
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132 xy = 1
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133 diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3
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134 cds_region.append(cdspos)
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135 cds_flag = 1
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136 cds_region.reverse()
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137 return cds_region
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138
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139 def buildUTR(cc, ec, strand):
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140 """
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141 Build UTR regions from a given set of CDS and exon coordiantes of a gene
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142
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143 @args cc: coding exon coordinates
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144 @type cc: numpy array [[int, int, int]]
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145 @args ec: exon coordinates
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146 @type ec: numpy array [[int, int]]
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147 @args strand: feature strand information
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148 @type strand: +/-
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149 """
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150
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151 utr5 = []
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152 utr3 = []
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153 if strand == '+':
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154 cds_s = cc[0][0]
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155 for ex in ec:
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156 if ex[0] <= cds_s and cds_s <= ex[1]:
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157 if ex[0] != cds_s:utr5.append((ex[0], cds_s-1))
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158 break
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159 else:
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160 utr5.append(ex)
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161 cds_e = cc[-1][1]
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162 for i in range(len(ec)):
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163 i += 1
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164 if ec[-i][0] <= cds_e and cds_e <= ec[-i][1]:
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165 if ec[-i][1] != cds_e:utr3.append((cds_e +1, ec[-i][1]))
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166 break
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167 else:
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168 utr3.append(ec[-i])
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169 utr3.reverse()
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170 elif strand == '-':
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171 cds_s = cc[-1][1]
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172 for i in range(len(ec)):
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173 i += 1
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174 if ec[-i][0] <= cds_s and cds_s <= ec[-i][1]:
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175 if ec[-i][1] != cds_s:utr5.append((cds_s+1, ec[-i][1]))
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176 break
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177 else:
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178 utr5.append(ec[-i])
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179 utr5.reverse()
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180 cds_e = cc[0][0]
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181 for ex in ec:
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182 if ex[0] <= cds_e and cds_e <= ex[1]:
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183 if ex[0] != cds_e:utr3.append((ex[0], cds_e-1))
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184 break
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185 else:
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186 utr3.append(ex)
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187 return utr5, utr3
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188
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189 def make_Exon_cod(strand_p, five_p_utr, cds_cod, three_p_utr):
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190 """
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191 Create exon cordinates from UTR's and CDS region
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192
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193 @args strand_p: feature strand information
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194 @type strand_p: +/-
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195 @args five_p_utr: five prime utr exon coordinates
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196 @type five_p_utr: numpy array [[int, int]]
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197 @args cds_cod: coding exon coordinates
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198 @type cds_cod: numpy array [[int, int, int]]
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199 @args three_p_utr: three prime utr exon coordinates
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200 @type three_p_utr: numpy array [[int, int]]
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201 """
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202
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203 exon_pos = []
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204 if strand_p == '+':
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205 utr5_start, utr5_end = 0, 0
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206 if five_p_utr != []:
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207 utr5_start, utr5_end = five_p_utr[-1][0], five_p_utr[-1][1]
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208 cds_5start, cds_5end = cds_cod[0][0], cds_cod[0][1]
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209 jun_exon = []
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210 if cds_5start-utr5_end == 0 or cds_5start-utr5_end == 1:
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211 jun_exon = [utr5_start, cds_5end]
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212 if len(cds_cod) == 1:
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213 five_prime_flag = 0
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214 if jun_exon != []:
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215 five_p_utr = five_p_utr[:-1]
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216 five_prime_flag = 1
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217 for utr5 in five_p_utr:
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218 exon_pos.append(utr5)
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219 jun_exon = []
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220 utr3_start, utr3_end = 0, 0
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221 if three_p_utr != []:
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222 utr3_start = three_p_utr[0][0]
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223 utr3_end = three_p_utr[0][1]
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224 if utr3_start-cds_5end == 0 or utr3_start-cds_5end == 1:
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225 jun_exon = [cds_5start, utr3_end]
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226 three_prime_flag = 0
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227 if jun_exon != []:
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228 cds_cod = cds_cod[:-1]
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229 three_p_utr = three_p_utr[1:]
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230 three_prime_flag = 1
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231 if five_prime_flag == 1 and three_prime_flag == 1:
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232 exon_pos.append([utr5_start, utr3_end])
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233 if five_prime_flag == 1 and three_prime_flag == 0:
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234 exon_pos.append([utr5_start, cds_5end])
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235 cds_cod = cds_cod[:-1]
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236 if five_prime_flag == 0 and three_prime_flag == 1:
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237 exon_pos.append([cds_5start, utr3_end])
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238 for cds in cds_cod:
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239 exon_pos.append(cds)
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240 for utr3 in three_p_utr:
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241 exon_pos.append(utr3)
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242 else:
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243 if jun_exon != []:
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244 five_p_utr = five_p_utr[:-1]
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245 cds_cod = cds_cod[1:]
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246 for utr5 in five_p_utr:
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247 exon_pos.append(utr5)
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248 exon_pos.append(jun_exon) if jun_exon != [] else ''
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249 jun_exon = []
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250 utr3_start, utr3_end = 0, 0
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251 if three_p_utr != []:
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252 utr3_start = three_p_utr[0][0]
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253 utr3_end = three_p_utr[0][1]
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254 cds_3start = cds_cod[-1][0]
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255 cds_3end = cds_cod[-1][1]
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256 if utr3_start-cds_3end == 0 or utr3_start-cds_3end == 1:
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257 jun_exon = [cds_3start, utr3_end]
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258 if jun_exon != []:
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259 cds_cod = cds_cod[:-1]
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260 three_p_utr = three_p_utr[1:]
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261 for cds in cds_cod:
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262 exon_pos.append(cds)
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263 exon_pos.append(jun_exon) if jun_exon != [] else ''
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264 for utr3 in three_p_utr:
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265 exon_pos.append(utr3)
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266 elif strand_p == '-':
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267 utr3_start, utr3_end = 0, 0
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268 if three_p_utr != []:
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269 utr3_start = three_p_utr[-1][0]
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270 utr3_end = three_p_utr[-1][1]
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271 cds_3start = cds_cod[0][0]
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272 cds_3end = cds_cod[0][1]
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273 jun_exon = []
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274 if cds_3start-utr3_end == 0 or cds_3start-utr3_end == 1:
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275 jun_exon = [utr3_start, cds_3end]
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276 if len(cds_cod) == 1:
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277 three_prime_flag = 0
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278 if jun_exon != []:
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279 three_p_utr = three_p_utr[:-1]
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280 three_prime_flag = 1
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281 for utr3 in three_p_utr:
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282 exon_pos.append(utr3)
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283 jun_exon = []
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284 (utr5_start, utr5_end) = (0, 0)
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285 if five_p_utr != []:
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286 utr5_start = five_p_utr[0][0]
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287 utr5_end = five_p_utr[0][1]
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288 if utr5_start-cds_3end == 0 or utr5_start-cds_3end == 1:
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289 jun_exon = [cds_3start, utr5_end]
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290 five_prime_flag = 0
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291 if jun_exon != []:
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292 cds_cod = cds_cod[:-1]
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293 five_p_utr = five_p_utr[1:]
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294 five_prime_flag = 1
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295 if three_prime_flag == 1 and five_prime_flag == 1:
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296 exon_pos.append([utr3_start, utr5_end])
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297 if three_prime_flag == 1 and five_prime_flag == 0:
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298 exon_pos.append([utr3_start, cds_3end])
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299 cds_cod = cds_cod[:-1]
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300 if three_prime_flag == 0 and five_prime_flag == 1:
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301 exon_pos.append([cds_3start, utr5_end])
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302 for cds in cds_cod:
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303 exon_pos.append(cds)
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304 for utr5 in five_p_utr:
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305 exon_pos.append(utr5)
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306 else:
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307 if jun_exon != []:
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308 three_p_utr = three_p_utr[:-1]
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309 cds_cod = cds_cod[1:]
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310 for utr3 in three_p_utr:
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311 exon_pos.append(utr3)
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312 if jun_exon != []:
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313 exon_pos.append(jun_exon)
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314 jun_exon = []
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315 (utr5_start, utr5_end) = (0, 0)
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316 if five_p_utr != []:
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317 utr5_start = five_p_utr[0][0]
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318 utr5_end = five_p_utr[0][1]
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319 cds_5start = cds_cod[-1][0]
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320 cds_5end = cds_cod[-1][1]
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321 if utr5_start-cds_5end == 0 or utr5_start-cds_5end == 1:
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322 jun_exon = [cds_5start, utr5_end]
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323 if jun_exon != []:
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324 cds_cod = cds_cod[:-1]
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325 five_p_utr = five_p_utr[1:]
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326 for cds in cds_cod:
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327 exon_pos.append(cds)
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328 if jun_exon != []:
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329 exon_pos.append(jun_exon)
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330 for utr5 in five_p_utr:
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331 exon_pos.append(utr5)
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332 return exon_pos
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