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1 #!/usr/bin/env python
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2 """
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3 Extract genome annotation from a GFF3 (a tab delimited format
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4 for storing sequence features and annotations:
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5 http://www.sequenceontology.org/gff3.shtml) file.
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6
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7 Usage: ParseGFF.py in.gff3 out.mat
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8
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9 Requirements:
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10 Scipy :- http://scipy.org/
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11 Numpy :- http://numpy.org/
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12
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13 Copyright (C) 2010-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany
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14 """
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15 import re, sys, os
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16 import scipy.io as sio
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17 import numpy as np
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18
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19 def createExon(strand_p, five_p_utr, cds_cod, three_p_utr):
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20 """Create exon cordinates from UTR's and CDS region
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21 """
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22 exon_pos = []
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23 if strand_p == '+':
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24 utr5_start, utr5_end = 0, 0
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25 if five_p_utr != []:
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26 utr5_start, utr5_end = five_p_utr[-1][0], five_p_utr[-1][1]
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27 cds_5start, cds_5end = cds_cod[0][0], cds_cod[0][1]
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28 jun_exon = []
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29 if cds_5start-utr5_end == 0 or cds_5start-utr5_end == 1:
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30 jun_exon = [utr5_start, cds_5end]
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31 if len(cds_cod) == 1:
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32 five_prime_flag = 0
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33 if jun_exon != []:
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34 five_p_utr = five_p_utr[:-1]
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35 five_prime_flag = 1
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36 for utr5 in five_p_utr:
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37 exon_pos.append(utr5)
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38 jun_exon = []
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39 utr3_start, utr3_end = 0, 0
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40 if three_p_utr != []:
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41 utr3_start = three_p_utr[0][0]
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42 utr3_end = three_p_utr[0][1]
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43 if utr3_start-cds_5end == 0 or utr3_start-cds_5end == 1:
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44 jun_exon = [cds_5start, utr3_end]
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45 three_prime_flag = 0
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46 if jun_exon != []:
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47 cds_cod = cds_cod[:-1]
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48 three_p_utr = three_p_utr[1:]
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49 three_prime_flag = 1
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50 if five_prime_flag == 1 and three_prime_flag == 1:
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51 exon_pos.append([utr5_start, utr3_end])
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52 if five_prime_flag == 1 and three_prime_flag == 0:
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53 exon_pos.append([utr5_start, cds_5end])
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54 cds_cod = cds_cod[:-1]
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55 if five_prime_flag == 0 and three_prime_flag == 1:
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56 exon_pos.append([cds_5start, utr3_end])
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57 for cds in cds_cod:
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58 exon_pos.append(cds)
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59 for utr3 in three_p_utr:
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60 exon_pos.append(utr3)
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61 else:
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62 if jun_exon != []:
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63 five_p_utr = five_p_utr[:-1]
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64 cds_cod = cds_cod[1:]
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65 for utr5 in five_p_utr:
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66 exon_pos.append(utr5)
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67 exon_pos.append(jun_exon) if jun_exon != [] else ''
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68 jun_exon = []
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69 utr3_start, utr3_end = 0, 0
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70 if three_p_utr != []:
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71 utr3_start = three_p_utr[0][0]
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72 utr3_end = three_p_utr[0][1]
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73 cds_3start = cds_cod[-1][0]
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74 cds_3end = cds_cod[-1][1]
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75 if utr3_start-cds_3end == 0 or utr3_start-cds_3end == 1:
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76 jun_exon = [cds_3start, utr3_end]
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77 if jun_exon != []:
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78 cds_cod = cds_cod[:-1]
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79 three_p_utr = three_p_utr[1:]
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80 for cds in cds_cod:
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81 exon_pos.append(cds)
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82 exon_pos.append(jun_exon) if jun_exon != [] else ''
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83 for utr3 in three_p_utr:
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84 exon_pos.append(utr3)
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85 elif strand_p == '-':
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86 utr3_start, utr3_end = 0, 0
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87 if three_p_utr != []:
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88 utr3_start = three_p_utr[-1][0]
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89 utr3_end = three_p_utr[-1][1]
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90 cds_3start = cds_cod[0][0]
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91 cds_3end = cds_cod[0][1]
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92 jun_exon = []
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93 if cds_3start-utr3_end == 0 or cds_3start-utr3_end == 1:
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94 jun_exon = [utr3_start, cds_3end]
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95 if len(cds_cod) == 1:
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96 three_prime_flag = 0
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97 if jun_exon != []:
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98 three_p_utr = three_p_utr[:-1]
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99 three_prime_flag = 1
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100 for utr3 in three_p_utr:
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101 exon_pos.append(utr3)
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102 jun_exon = []
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103 (utr5_start, utr5_end) = (0, 0)
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104 if five_p_utr != []:
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105 utr5_start = five_p_utr[0][0]
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106 utr5_end = five_p_utr[0][1]
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107 if utr5_start-cds_3end == 0 or utr5_start-cds_3end == 1:
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108 jun_exon = [cds_3start, utr5_end]
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109 five_prime_flag = 0
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110 if jun_exon != []:
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111 cds_cod = cds_cod[:-1]
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112 five_p_utr = five_p_utr[1:]
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113 five_prime_flag = 1
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114 if three_prime_flag == 1 and five_prime_flag == 1:
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115 exon_pos.append([utr3_start, utr5_end])
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116 if three_prime_flag == 1 and five_prime_flag == 0:
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117 exon_pos.append([utr3_start, cds_3end])
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118 cds_cod = cds_cod[:-1]
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119 if three_prime_flag == 0 and five_prime_flag == 1:
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120 exon_pos.append([cds_3start, utr5_end])
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121 for cds in cds_cod:
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122 exon_pos.append(cds)
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123 for utr5 in five_p_utr:
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124 exon_pos.append(utr5)
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125 else:
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126 if jun_exon != []:
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127 three_p_utr = three_p_utr[:-1]
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128 cds_cod = cds_cod[1:]
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129 for utr3 in three_p_utr:
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130 exon_pos.append(utr3)
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131 if jun_exon != []:
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132 exon_pos.append(jun_exon)
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133 jun_exon = []
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134 (utr5_start, utr5_end) = (0, 0)
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135 if five_p_utr != []:
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136 utr5_start = five_p_utr[0][0]
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137 utr5_end = five_p_utr[0][1]
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138 cds_5start = cds_cod[-1][0]
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139 cds_5end = cds_cod[-1][1]
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140 if utr5_start-cds_5end == 0 or utr5_start-cds_5end == 1:
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141 jun_exon = [cds_5start, utr5_end]
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142 if jun_exon != []:
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143 cds_cod = cds_cod[:-1]
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144 five_p_utr = five_p_utr[1:]
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145 for cds in cds_cod:
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146 exon_pos.append(cds)
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147 if jun_exon != []:
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148 exon_pos.append(jun_exon)
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149 for utr5 in five_p_utr:
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150 exon_pos.append(utr5)
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151 return exon_pos
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152
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153 def init_gene():
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154 """Initializing the gene structure
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155 """
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156 gene_details=dict(chr='',
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157 exons=[],
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158 gene_info={},
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159 id='',
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160 is_alt_spliced=0,
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161 name='',
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162 source='',
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163 start='',
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164 stop='',
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165 strand='',
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166 transcripts=[])
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167 return gene_details
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168
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169 def FeatureValueFormat(singlegene):
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170 """Make feature value compactable to write in a .mat format
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171 """
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172 comp_exon = np.zeros((len(singlegene['exons']),), dtype=np.object)
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173 for i in range(len(singlegene['exons'])):
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174 comp_exon[i]= np.array(singlegene['exons'][i])
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175 singlegene['exons'] = comp_exon
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176 comp_transcripts = np.zeros((len(singlegene['transcripts']),), dtype=np.object)
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177 for i in range(len(singlegene['transcripts'])):
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178 comp_transcripts[i] = np.array(singlegene['transcripts'][i])
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179 singlegene['transcripts'] = comp_transcripts
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180 return singlegene
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181
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182 def CreateGeneModels(genes_cmpt, transcripts_cmpt, exons_cmpt, utr3_cmpt, utr5_cmpt, cds_cmpt):
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183 """Creating Coding/Non-coding gene models from parsed GFF objects.
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184 """
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185 gene_counter, gene_models=1, []
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186 for gene_entry in genes_cmpt: ## Figure out the genes and transcripts associated feature
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187 if gene_entry in transcripts_cmpt:
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188 gene=init_gene()
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189 gene['id']=gene_counter
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190 gene['name']=gene_entry[1]
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191 gene['chr']=genes_cmpt[gene_entry]['chr']
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192 gene['source']=genes_cmpt[gene_entry]['source']
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193 gene['start']=genes_cmpt[gene_entry]['start']
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194 gene['stop']=genes_cmpt[gene_entry]['stop']
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195 gene['strand']=genes_cmpt[gene_entry]['strand']
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196 if not gene['strand'] in ['+', '-']:
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197 gene['strand']='.' # Strand info not known replaced with a dot symbol instead of None, ?, . etc.
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198 gene['gene_info']=dict(ID=gene_entry[1])
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199 if len(transcripts_cmpt[gene_entry])>1:
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200 gene['is_alt_spliced'] = 1
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201 for tids in transcripts_cmpt[gene_entry]: ## transcript section related tags
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202 gene['transcripts'].append(tids['ID'])
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203 if len(exons_cmpt) != 0:
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204 if (gene['chr'], tids['ID']) in exons_cmpt:
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205 exon_cod=[[feat_exon['start'], feat_exon['stop']] for feat_exon in exons_cmpt[(gene['chr'], tids['ID'])]]
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206 else: ## build exon coordinates from UTR3, UTR5 and CDS
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207 utr5_pos, cds_pos, utr3_pos = [], [], []
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208 if (gene['chr'], tids['ID']) in utr5_cmpt:
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209 utr5_pos=[[feat_utr5['start'], feat_utr5['stop']] for feat_utr5 in utr5_cmpt[(gene['chr'], tids['ID'])]]
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210 if (gene['chr'], tids['ID']) in cds_cmpt:
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211 cds_pos=[[feat_cds['start'], feat_cds['stop']] for feat_cds in cds_cmpt[(gene['chr'], tids['ID'])]]
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212 if (gene['chr'], tids['ID']) in utr3_cmpt:
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213 utr3_pos=[[feat_utr3['start'], feat_utr3['stop']] for feat_utr3 in utr3_cmpt[(gene['chr'], tids['ID'])]]
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214 exon_cod=createExon(gene['strand'], utr5_pos, cds_pos, utr3_pos)
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215 if gene['strand']=='-':
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216 if len(exon_cod) >1:
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217 if exon_cod[0][0] > exon_cod[-1][0]:
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218 exon_cod.reverse()
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219 if exon_cod:
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220 gene['exons'].append(exon_cod)
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221 gene=FeatureValueFormat(gene) # get prepare for MAT writing
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222 gene_counter+=1
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223 gene_models.append(gene)
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224 return gene_models
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225
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226 def GFFParse(gff_file):
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227 """Parsing GFF file based on feature relationship.
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228 """
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229 genes, utr5, exons=dict(), dict(), dict()
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230 transcripts, utr3, cds=dict(), dict(), dict()
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231 # TODO Include growing key words of different non-coding/coding transcripts
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232 features=['mRNA', 'transcript', 'ncRNA', 'miRNA', 'pseudogenic_transcript', 'rRNA', 'snoRNA', 'snRNA', 'tRNA', 'scRNA']
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233 gff_handle=open(gff_file, "rU")
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234 for gff_line in gff_handle:
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235 gff_line=gff_line.strip('\n\r').split('\t')
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236 if re.match(r'#|>', gff_line[0]): # skip commented line and fasta identifier line
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237 continue
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238 if len(gff_line)==1: # skip fasta sequence/empty line if present
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239 continue
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240 assert len(gff_line)==9, '\t'.join(gff_line) # not found 9 tab-delimited fields in this line
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241 if '' in gff_line: # skip this line if there any field with an empty value
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242 print 'Skipping..', '\t'.join(gff_line)
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243 continue
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244 if gff_line[-1][-1]==';': # trim the last ';' character
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245 gff_line[-1]=gff_line[-1].strip(';')
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246 if gff_line[2] in ['gene', 'pseudogene']:
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247 gid, gene_info=None, dict()
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248 gene_info['start']=int(gff_line[3])
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249 gene_info['stop']=int(gff_line[4])
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250 gene_info['chr']=gff_line[0]
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251 gene_info['source']=gff_line[1]
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252 gene_info['strand']=gff_line[6]
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253 for attb in gff_line[-1].split(';'):
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254 attb=attb.split('=') # gff attributes are separated by key=value pair
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255 if attb[0]=='ID':
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256 gid=attb[1]
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257 break
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258 genes[(gff_line[0], gid)]=gene_info # store gene information based on the chromosome and gene symbol.
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259 elif gff_line[2] in features:
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260 gid, mrna_info=None, dict()
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261 mrna_info['start']=int(gff_line[3])
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262 mrna_info['stop']=int(gff_line[4])
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263 mrna_info['chr']=gff_line[0]
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264 mrna_info['strand']=gff_line[6]
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265 for attb in gff_line[-1].split(';'):
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266 attb=attb.split('=')
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267 if attb[0]=='Parent':
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268 gid=attb[1]
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269 elif attb[0]=='ID':
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270 mrna_info[attb[0]]=attb[1]
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271 for fid in gid.split(','): # child may be mapped to multiple parents ex: Parent=AT01,AT01-1-Protein
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272 if (gff_line[0], fid) in transcripts:
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273 transcripts[(gff_line[0], fid)].append(mrna_info)
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274 else:
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275 transcripts[(gff_line[0], fid)]=[mrna_info]
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276 elif gff_line[2] in ['exon']:
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277 tids, exon_info=None, dict()
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278 exon_info['start']=int(gff_line[3])
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279 exon_info['stop']=int(gff_line[4])
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280 exon_info['chr']=gff_line[0]
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281 exon_info['strand']=gff_line[6]
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282 for attb in gff_line[-1].split(';'):
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283 attb=attb.split('=')
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284 if attb[0]=='Parent':
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285 tids=attb[1]
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286 break
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287 for tid in tids.split(','):
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288 if (gff_line[0], tid) in exons:
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289 exons[(gff_line[0], tid)].append(exon_info)
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290 else:
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291 exons[(gff_line[0], tid)]=[exon_info]
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292 elif gff_line[2] in ['five_prime_UTR']:
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293 utr5_info, tids=dict(), None
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294 utr5_info['start']=int(gff_line[3])
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295 utr5_info['stop']=int(gff_line[4])
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296 utr5_info['chr']=gff_line[0]
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297 utr5_info['strand']=gff_line[6]
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298 for attb in gff_line[-1].split(';'):
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299 attb=attb.split('=')
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300 if attb[0]=='Parent':
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301 tids=attb[1]
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302 break
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303 for tid in tids.split(','):
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304 if (gff_line[0], tid) in utr5:
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305 utr5[(gff_line[0], tid)].append(utr5_info)
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306 else:
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307 utr5[(gff_line[0], tid)]=[utr5_info]
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308 elif gff_line[2] in ['CDS']:
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309 cds_info, tids=dict(), None
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310 cds_info['start']=int(gff_line[3])
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311 cds_info['stop']=int(gff_line[4])
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312 cds_info['chr']=gff_line[0]
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313 cds_info['strand']=gff_line[6]
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314 for attb in gff_line[-1].split(';'):
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315 attb=attb.split('=')
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316 if attb[0]=='Parent':
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317 tids=attb[1]
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318 break
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319 for tid in tids.split(','):
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320 if (gff_line[0], tid) in cds:
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321 cds[(gff_line[0], tid)].append(cds_info)
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322 else:
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323 cds[(gff_line[0], tid)]=[cds_info]
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324 elif gff_line[2] in ['three_prime_UTR']:
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325 utr3_info, tids=dict(), None
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326 utr3_info['start']=int(gff_line[3])
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327 utr3_info['stop']=int(gff_line[4])
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328 utr3_info['chr']=gff_line[0]
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329 utr3_info['strand']=gff_line[6]
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330 for attb in gff_line[-1].split(';'):
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331 attb=attb.split('=')
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332 if attb[0]=='Parent':
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333 tids=attb[1]
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334 break
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335 for tid in tids.split(','):
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336 if (gff_line[0], tid) in utr3:
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337 utr3[(gff_line[0], tid)].append(utr3_info)
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338 else:
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339 utr3[(gff_line[0], tid)]=[utr3_info]
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340 gff_handle.close()
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341 return genes, transcripts, exons, utr3, utr5, cds
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342
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343 def __main__():
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344 """This function provides a best way to extract genome feature
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345 information from a GFF3 file for the rQuant downstream processing.
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346 """
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347 try:
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348 gff_file = sys.argv[1]
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349 mat_file = sys.argv[2]
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350 except:
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351 print __doc__
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352 sys.exit(-1)
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353 genes, transcripts, exons, utr3, utr5, cds=GFFParse(gff_file)
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354 gene_models=CreateGeneModels(genes, transcripts, exons, utr3, utr5, cds)
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355 # TODO Write to matlab/octave struct instead of cell arrays.
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356 sio.savemat(mat_file,
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357 mdict=dict(genes=gene_models),
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358 format='5',
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359 oned_as='row')
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360
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361 if __name__=='__main__':
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362 __main__()
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