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