Mercurial > repos > cpt > cpt_intersect_adj
annotate intersect_and_adjacent.py @ 3:10000414e916 draft
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author | cpt |
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date | Mon, 12 Aug 2024 04:23:34 +0000 |
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1 #!/usr/bin/env python |
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2 import logging |
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3 import argparse |
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4 from intervaltree import IntervalTree, Interval |
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5 from CPT_GFFParser import gffParse, gffWrite |
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6 from Bio.SeqRecord import SeqRecord |
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7 from Bio.Seq import Seq |
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8 |
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9 logging.basicConfig(level=logging.INFO) |
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10 log = logging.getLogger(__name__) |
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11 |
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12 |
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13 def validFeat(rec): |
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14 for feat in rec.features: |
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15 if feat.type != "remark" and feat.type != "annotation": |
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16 return True |
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17 return False |
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18 |
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19 |
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20 def treeFeatures(features, window): |
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21 for feat in features: |
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22 # Interval(begin, end, data) |
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23 yield Interval( |
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24 int(feat.location.start) - int(window), |
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25 int(feat.location.end) + int(window), |
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26 feat.id, |
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27 ) |
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28 |
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29 |
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30 def treeFeatures_noRem(features, window): |
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31 for feat in features: |
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32 if feat.type == "remark" or feat.type == "annotation": |
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33 continue |
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34 # Interval(begin, end, data) |
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35 yield Interval( |
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36 int(feat.location.start) - int(window), |
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37 int(feat.location.end) + int(window), |
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38 feat.id, |
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39 ) |
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40 |
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41 |
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42 def intersect(a, b, window, stranding): |
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43 rec_a = list(gffParse(a)) |
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44 rec_b = list(gffParse(b)) |
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45 rec_a_out = [] |
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46 rec_b_out = [] |
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47 maxLen = min(len(rec_a), len(rec_b)) |
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48 iterate = 0 |
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49 |
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50 if maxLen > 0: |
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51 while iterate < maxLen: |
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52 rec_a_i = rec_a[iterate] |
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53 rec_b_i = rec_b[iterate] |
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54 |
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55 if (not validFeat(rec_a_i)) or (not validFeat(rec_b_i)): |
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56 rec_a_out.append( |
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57 SeqRecord( |
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58 rec_a[iterate].seq, |
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59 rec_a[iterate].id, |
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60 rec_a[iterate].name, |
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61 rec_a[iterate].description, |
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62 rec_a[iterate].dbxrefs, |
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63 [], |
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64 rec_a[iterate].annotations, |
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65 ) |
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66 ) |
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67 rec_b_out.append( |
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68 SeqRecord( |
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69 rec_b[iterate].seq, |
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70 rec_b[iterate].id, |
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71 rec_b[iterate].name, |
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72 rec_b[iterate].description, |
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73 rec_b[iterate].dbxrefs, |
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74 [], |
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75 rec_b[iterate].annotations, |
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76 ) |
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77 ) |
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78 iterate += 1 |
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79 continue |
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80 |
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81 a_neg = [] |
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82 a_pos = [] |
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83 b_neg = [] |
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84 b_pos = [] |
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85 tree_a = [] |
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86 tree_b = [] |
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87 if stranding == True: |
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88 for feat in rec_a_i.features: |
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89 if feat.type == "remark" or feat.type == "annotation": |
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90 continue |
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91 if feat.strand > 0: |
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92 a_pos.append( |
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93 Interval( |
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94 int(feat.location.start) - int(window), |
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95 int(feat.location.end) + int(window), |
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96 feat.id, |
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97 ) |
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98 ) |
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99 else: |
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100 a_neg.append( |
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101 Interval( |
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102 int(feat.location.start) - int(window), |
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103 int(feat.location.end) + int(window), |
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104 feat.id, |
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105 ) |
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106 ) |
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107 |
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108 for feat in rec_b_i.features: |
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109 if feat.type == "remark" or feat.type == "annotation": |
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110 continue |
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111 if feat.strand > 0: |
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112 b_pos.append( |
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113 Interval( |
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114 int(feat.location.start) - int(window), |
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115 int(feat.location.end) + int(window), |
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116 feat.id, |
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117 ) |
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118 ) |
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119 else: |
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120 b_neg.append( |
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121 Interval( |
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122 int(feat.location.start) - int(window), |
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123 int(feat.location.end) + int(window), |
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124 feat.id, |
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125 ) |
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126 ) |
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127 |
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128 else: |
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129 for feat in rec_a_i.features: |
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130 if feat.type == "remark" or feat.type == "annotation": |
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131 continue |
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132 tree_a.append( |
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133 Interval( |
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134 int(feat.location.start) - int(window), |
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135 int(feat.location.end) + int(window), |
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136 feat.id, |
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137 ) |
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138 ) |
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139 for feat in rec_b_i.features: |
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140 if feat.type == "remark" or feat.type == "annotation": |
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141 continue |
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142 tree_b.append( |
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143 Interval( |
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144 int(feat.location.start) - int(window), |
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145 int(feat.location.end) + int(window), |
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146 feat.id, |
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147 ) |
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148 ) |
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149 if stranding: |
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150 # builds interval tree from Interval objects of form (start, end, id) for each feature |
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151 # tree_a = IntervalTree(list(treeFeatures_noRem(rec_a_i.features, window))) |
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152 # tree_b = IntervalTree(list(treeFeatures_noRem(rec_b_i.features, window))) |
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153 # else: |
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154 tree_a_pos = IntervalTree(a_pos) |
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155 tree_a_neg = IntervalTree(a_neg) |
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156 tree_b_pos = IntervalTree(b_pos) |
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157 tree_b_neg = IntervalTree(b_neg) |
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158 else: |
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159 tree_a = IntervalTree(tree_a) |
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160 tree_b = IntervalTree(tree_b) |
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161 |
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162 # Used to map ids back to features later |
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163 rec_a_map = {f.id: f for f in rec_a_i.features} |
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164 rec_b_map = {f.id: f for f in rec_b_i.features} |
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165 |
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166 rec_a_hits_in_b = [] |
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167 rec_b_hits_in_a = [] |
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168 |
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169 for feature in rec_a_i.features: |
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170 # Save each feature in rec_a that overlaps a feature in rec_b |
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171 # hits = tree_b.find_range((int(feature.location.start), int(feature.location.end))) |
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172 |
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173 if feature.type == "remark" or feature.type == "annotation": |
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174 continue |
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175 |
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176 if stranding == False: |
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177 hits = tree_b[ |
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178 int(feature.location.start) : int(feature.location.end) |
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179 ] |
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180 |
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181 # feature id is saved in interval result.data, use map to get full feature |
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182 for hit in hits: |
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183 rec_a_hits_in_b.append(rec_b_map[hit.data]) |
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184 |
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185 else: |
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186 if feature.strand > 0: |
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187 hits_pos = tree_b_pos[ |
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188 int(feature.location.start) : int(feature.location.end) |
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189 ] |
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190 for hit in hits_pos: |
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191 rec_a_hits_in_b.append(rec_b_map[hit.data]) |
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192 else: |
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193 hits_neg = tree_b_neg[ |
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194 int(feature.location.start) : int(feature.location.end) |
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195 ] |
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196 for hit in hits_neg: |
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197 rec_a_hits_in_b.append(rec_b_map[hit.data]) |
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198 |
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199 for feature in rec_b_i.features: |
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200 if feature.type == "remark" or feature.type == "annotation": |
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201 continue |
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202 |
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203 if stranding == False: |
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204 hits = tree_a[ |
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205 int(feature.location.start) : int(feature.location.end) |
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206 ] |
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207 |
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208 # feature id is saved in interval result.data, use map to get full feature |
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209 for hit in hits: |
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210 rec_b_hits_in_a.append(rec_a_map[hit.data]) |
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211 |
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212 else: |
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213 if feature.strand > 0: |
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214 hits_pos = tree_a_pos[ |
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215 int(feature.location.start) : int(feature.location.end) |
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216 ] |
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217 for hit in hits_pos: |
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218 rec_b_hits_in_a.append(rec_a_map[hit.data]) |
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219 else: |
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220 hits_neg = tree_a_neg[ |
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221 int(feature.location.start) : int(feature.location.end) |
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222 ] |
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223 for hit in hits_neg: |
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224 rec_b_hits_in_a.append(rec_a_map[hit.data]) |
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225 |
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226 # Remove duplicate features using sets |
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227 rec_a_out.append( |
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228 SeqRecord( |
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229 rec_a[iterate].seq, |
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230 rec_a[iterate].id, |
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231 rec_a[iterate].name, |
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232 rec_a[iterate].description, |
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233 rec_a[iterate].dbxrefs, |
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234 sorted(set(rec_a_hits_in_b), key=lambda feat: feat.location.start), |
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235 rec_a[iterate].annotations, |
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236 ) |
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237 ) |
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238 rec_b_out.append( |
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239 SeqRecord( |
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240 rec_b[iterate].seq, |
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241 rec_b[iterate].id, |
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242 rec_b[iterate].name, |
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243 rec_b[iterate].description, |
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244 rec_b[iterate].dbxrefs, |
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245 sorted(set(rec_b_hits_in_a), key=lambda feat: feat.location.start), |
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246 rec_b[iterate].annotations, |
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247 ) |
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248 ) |
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249 iterate += 1 |
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250 |
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251 else: |
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252 # If one input is empty, output two empty result files. |
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253 rec_a_out = [SeqRecord(Seq(""), "none")] |
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254 rec_b_out = [SeqRecord(Seq(""), "none")] |
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255 return rec_a_out, rec_b_out |
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256 |
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257 |
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258 if __name__ == "__main__": |
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259 parser = argparse.ArgumentParser( |
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260 description="rebase gff3 features against parent locations", epilog="" |
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261 ) |
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262 parser.add_argument("a", type=argparse.FileType("r")) |
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263 parser.add_argument("b", type=argparse.FileType("r")) |
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264 parser.add_argument( |
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265 "window", |
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266 type=int, |
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267 default=50, |
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268 help="Allows features this far away to still be considered 'adjacent'", |
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269 ) |
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270 parser.add_argument( |
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271 "stranding", |
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272 nargs="?", |
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273 default="", |
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274 help="Only allow adjacency for same-strand features if set to '-stranding'", |
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275 ) |
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276 parser.add_argument("--oa", type=str, default="a_hits_near_b.gff") |
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277 parser.add_argument("--ob", type=str, default="b_hits_near_a.gff") |
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278 args = parser.parse_args() |
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279 |
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280 stranding = args.stranding == "-stranding" |
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281 b, a = intersect(args.a, args.b, args.window, args.stranding) |
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282 |
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283 with open(args.oa, "w") as handle: |
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284 for rec in a: |
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285 gffWrite([rec], handle) |
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286 |
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287 with open(args.ob, "w") as handle: |
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288 for rec in b: |
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289 gffWrite([rec], handle) |