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ashanderashander
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Use line_profiler
To re-run ```sh pip install line_profiler kernprof -v -l tests/test_arg_recorder_with_wf.py > devel/prof.txt kernprof -v -l tests/test_recomb_collector.py > devel/prof_rc.txt ```
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‎devel/prof.txt‎

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Wrote profile results to test_arg_recorder_with_wf.py.lprof
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Timer unit: 1e-06 s
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Total time: 0.565759 s
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File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
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Function: add_individual at line 26
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Line # Hits Time Per Hit % Time Line Contents
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==============================================================
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26 @profile
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27 def add_individual(self, name, time, population=msprime.NULL_POPULATION,
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28 is_sample=False):
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29 '''Add a new individual.
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30 We need to add individuals when they are *born*,
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31 rather than the first time they reproduce, to ensure
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32 that records are output in order by birth time of the parent.
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33 '''
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34 101240 72447 0.7 12.8 if name not in self:
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35 101240 58303 0.6 10.3 self[name] = (msprime.Node(time=time, population=population,
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36 101240 297613 2.9 52.6 name=name, is_sample=is_sample), [])
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37 101240 137396 1.4 24.3 self.num_nodes = max(self.num_nodes, 1+int(name))
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Total time: 7.5774 s
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File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
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Function: add_record at line 39
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Line # Hits Time Per Hit % Time Line Contents
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==============================================================
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39 @profile
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40 def add_record(self, left, right, parent, children):
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41 '''
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42 Add records corresponding to a reproduction event in which children (a
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43 tuple of IDs) inherit from parent (a single ID) on the interval
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44 [left,right).
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45 '''
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46 # unneeded but helpful for debugging
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47 150314 120881 0.8 1.6 if parent not in self.keys():
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48 raise ValueError("Parent " + str(parent) +
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49 "'s birth time has not been recorded with " +
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50 ".add_individual().")
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51 # time = self[parent][0]
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52 150314 79151 0.5 1.0 new_rec = msprime.Edgeset(
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53 150314 71103 0.5 0.9 parent=parent,
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54 150314 66660 0.4 0.9 children=children,
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55 150314 65861 0.4 0.9 left=left,
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56 150314 325604 2.2 4.3 right=right)
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57 150314 6848145 45.6 90.4 merge_records(new_rec, self[parent][1])
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Total time: 4.08047 s
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File: /home/jaime/lib/ftprime/ftprime/argrecorder.py
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Function: merge_records at line 142
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Line # Hits Time Per Hit % Time Line Contents
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==============================================================
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142 @profile
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143 def merge_records(new, existing):
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144 '''
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145 Incorporate a new record (l,r,x,c,t[x])
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146 into a list of existing ones (a,b,x,C,t[x]) sorted on left endpoint.
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147 Keeping them in sorted order simplifies the procedure
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148 (makes it so we don't have to split the new record).
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149 '''
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150 150314 101369 0.7 2.5 k = 0
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151 150314 87001 0.6 2.1 cur_left = new.left
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152 # print("MR: -----")
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153 # print("adding", new)
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154 # print(" to", existing)
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155 308472 241009 0.8 5.9 while (k < len(existing)) and (cur_left < new.right):
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156 158158 124833 0.8 3.1 left = existing[k].left
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157 158158 93386 0.6 2.3 right = existing[k].right
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158 158158 90150 0.6 2.2 parent = existing[k].parent
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159 158158 96347 0.6 2.4 children = existing[k].children
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160 # print("k:",k)
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161 # print("existing:",existing[k])
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162 # print("cur_left:",cur_left)
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163 158158 92653 0.6 2.3 if new.parent != parent:
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164 raise ValueError("Trying to merge records with different parents.")
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165 158158 85414 0.5 2.1 if right <= cur_left:
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166 # no overlap
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167 # print("no overlap")
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168 15534 8903 0.6 0.2 k += 1
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169 15534 7404 0.5 0.2 continue
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170 142624 77301 0.5 1.9 if cur_left < left:
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171 # print("dangling left")
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172 15409 10416 0.7 0.3 existing.insert(k, msprime.Edgeset(
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173 15409 7887 0.5 0.2 left=cur_left,
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174 15409 16021 1.0 0.4 right=min(new.right, left),
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175 15409 7897 0.5 0.2 parent=parent,
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176 15409 43180 2.8 1.1 children=new.children))
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177 15409 15864 1.0 0.4 cur_left = min(new.right, left)
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178 15409 9449 0.6 0.2 k += 1
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179 15409 7490 0.5 0.2 continue
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180 127215 393801 3.1 9.7 combined_children = tuple(sorted(children+new.children))
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181 127215 87066 0.7 2.1 combined_rec = msprime.Edgeset(
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182 127215 67410 0.5 1.7 left=cur_left,
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183 127215 234108 1.8 5.7 right=min(new.right, right),
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184 127215 73773 0.6 1.8 parent=new.parent,
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185 127215 312244 2.5 7.7 children=combined_children)
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186 127215 78337 0.6 1.9 if cur_left == left:
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187 # print("equal left")
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188 105571 67860 0.6 1.7 if new.right < right:
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189 # print("overlap right")
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190 21590 13336 0.6 0.3 mod_rec = msprime.Edgeset(
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191 21590 12284 0.6 0.3 left=new.right,
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192 21590 11592 0.5 0.3 right=right,
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193 21590 11575 0.5 0.3 parent=parent,
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194 21590 149418 6.9 3.7 children=children)
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195 21590 19858 0.9 0.5 existing[k] = combined_rec
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196 21590 13557 0.6 0.3 k += 1
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197 21590 20224 0.9 0.5 existing.insert(k, mod_rec)
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198 21590 13962 0.6 0.3 k += 1
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199 else:
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200 # print("dangling right")
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201 83981 71541 0.9 1.8 existing[k] = combined_rec
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202 83981 55980 0.7 1.4 k += 1
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203 else:
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204 # here we know that left < cur_left < right
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205 # print("overlap left")
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206 21644 13649 0.6 0.3 mod_rec = msprime.Edgeset(
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207 21644 11864 0.5 0.3 left=left,
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208 21644 11487 0.5 0.3 right=cur_left,
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209 21644 11471 0.5 0.3 parent=parent,
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210 21644 93849 4.3 2.3 children=children)
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211 21644 20146 0.9 0.5 existing[k] = mod_rec
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212 21644 13783 0.6 0.3 k += 1
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213 21644 20156 0.9 0.5 existing.insert(k, combined_rec)
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214 21644 13301 0.6 0.3 k += 1
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215 21644 14807 0.7 0.4 if new.right < right:
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216 # print("overlap right")
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217 existing.insert(k, msprime.Edgeset(
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218 left=new.right,
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219 right=right,
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220 parent=parent,
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221 children=children))
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222 k += 1
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223 127215 110940 0.9 2.7 cur_left = min(new.right, right)
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224 # add whatever's left at the end
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225 150314 101572 0.7 2.5 if cur_left < new.right:
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226 82579 60579 0.7 1.5 existing.insert(k, msprime.Edgeset(
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227 82579 47194 0.6 1.2 left=cur_left,
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228 82579 50544 0.6 1.2 right=new.right,
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229 82579 47932 0.6 1.2 parent=new.parent,
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230 82579 428151 5.2 10.5 children=new.children))
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231 # print("getting")
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232 # for x in existing:
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233 # print(" ", x)
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234 150314 77143 0.5 1.9 return None
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