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  1. select_genes:
  2. cmd: papermill -f stages/1_select_genes_and_species.yaml --progress-bar --report-mode
  3. notebooks/1_select_genes_and_species.ipynb data/output/notebooks/1_select_genes_and_species_report.ipynb
  4. deps:
  5. - path: data/input/genes/by_animal_class
  6. md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
  7. - path: data/input/samples.tsv
  8. md5: 17e2bb8020c8ac1f8c3c7445fac901c3
  9. - path: data/input/species.tsv
  10. md5: cdf6379f1d78780afc6f650b10636494
  11. - path: notebooks/1_select_genes_and_species.ipynb
  12. md5: 201de29fbe33b8bf5b546fcf16ec15f6
  13. - path: stages/1_select_genes_and_species.yaml
  14. md5: 22f95cba7413c7c641fec0720b8338ee
  15. outs:
  16. - path: data/interim/selected_expressions.tsv
  17. md5: d872ec9f5ff9ac16d7dd6d877cc077b1
  18. - path: data/interim/selected_genes.tsv
  19. md5: dc2b3b921d9fb4ed358a085c53426307
  20. - path: data/interim/selected_samples.tsv
  21. md5: f3a11a4ad6550a7f356bf51e7a4e183b
  22. - path: data/interim/selected_species.tsv
  23. md5: 74a64f77b443ed7b6e9b44240953ec7a
  24. - path: data/output/counts/species_sample_count.tsv
  25. md5: eced40b842c0ec786a43d0e8c1da073d
  26. - path: data/output/counts/species_tissue_sample_count.tsv
  27. md5: 7e78391b84b265bdc0db65ef0f293056
  28. - path: data/output/counts/tissue_sample_count.tsv
  29. md5: 95d7d50886117aae30a8ee8c335f5076
  30. - path: data/output/notebooks/1_select_genes_and_species_report.ipynb
  31. md5: c170a67d0a586c49d1442695c78bdcbc
  32. select_samples:
  33. cmd: papermill -f parameters/select_samples.yaml --progress-bar --report-mode notebooks/select_samples.ipynb
  34. data/output/notebooks/select_samples.ipynb
  35. deps:
  36. - path: data/input/genes/by_animal_class
  37. md5: 5bb1b3db720c77cb0800fa40f0196f29.dir
  38. - path: data/input/samples.tsv
  39. md5: 17e2bb8020c8ac1f8c3c7445fac901c3
  40. - path: data/input/species.tsv
  41. md5: cdf6379f1d78780afc6f650b10636494
  42. - path: data/input/total_mtDNA_base_composition.csv
  43. md5: 3735cfc4beffb6c9356f908525345ee6
  44. - path: notebooks/select_samples.ipynb
  45. md5: 9db059d4bd6319903528a5f737f0f4f0
  46. - path: parameters/select_samples.yaml
  47. md5: ccd2ff9e431a861a3cabaf02eb5533ab
  48. outs:
  49. - path: data/interim/selected/gestation_days
  50. md5: 03f0461ba9a1ca26f052203b948cd78b.dir
  51. - path: data/interim/selected/lifespan
  52. md5: 4c5315e23281c98c3b5d748b84d32b3e.dir
  53. - path: data/interim/selected/mass_kg
  54. md5: f36dbab9692c98800c464052e8dc85af.dir
  55. - path: data/interim/selected/metabolic_rate
  56. md5: 470ea1aeccc3bafa4b93268181360e6d.dir
  57. - path: data/interim/selected/mtGC
  58. md5: fa17686c777e1fad034b626b1efad921.dir
  59. - path: data/interim/selected/temperature
  60. md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
  61. - path: data/output/counts/species_sample_count.tsv
  62. md5: 84c76b86cb61c5bf73c7f06c390dc064
  63. - path: data/output/counts/species_tissue_sample_count.tsv
  64. md5: e1b7a7f290203cad12f412d33e2a0bcb
  65. - path: data/output/counts/tissue_sample_count.tsv
  66. md5: 5a1441ea61f14d0242037f6a36c9d4a4
  67. - path: data/output/notebooks/select_samples.ipynb
  68. md5: 3e57c8aa755ebec3c8e2addf0f0c4e33
  69. results_intersections:
  70. cmd: papermill -f parameters/results_intersections.yaml --progress-bar --report-mode
  71. notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
  72. deps:
  73. - path: data/output/external/causality
  74. md5: c00e3428ab5aac19fdc6c5157b09fb33.dir
  75. - path: data/output/external/linear
  76. md5: 024046bb0390f0d3bd374580359ebff4.dir
  77. - path: parameters/results_intersections.yaml
  78. md5: 45a394673b593a63177a9853f01d24c4
  79. outs:
  80. - path: data/output/notebooks/results_intersections.ipynb
  81. md5: 42127d40730f345e12effb4dff4d55e2
  82. - path: data/output/results/shap_with_linear_genage.tsv
  83. md5: 6d3ebc5c50cc026941db3fc269a1746d
  84. - path: data/output/stage_2/shap_results.tsv
  85. md5: 9b052d5683d3e61e6845086801c5b709
  86. shap_selection:
  87. cmd: papermill -f parameters/shap_selection.yaml --progress-bar --report-mode notebooks/shap_selection.ipynb
  88. data/output/notebooks/shap_selection.ipynb
  89. deps:
  90. - path: data/interim/selected/gestation_days
  91. md5: 03f0461ba9a1ca26f052203b948cd78b.dir
  92. - path: data/interim/selected/lifespan
  93. md5: 65f40bf267437f9a07131d706e0fed3d.dir
  94. - path: data/interim/selected/mass_kg
  95. md5: f36dbab9692c98800c464052e8dc85af.dir
  96. - path: data/interim/selected/metabolic_rate
  97. md5: 470ea1aeccc3bafa4b93268181360e6d.dir
  98. - path: data/interim/selected/mtGC
  99. md5: fa17686c777e1fad034b626b1efad921.dir
  100. - path: data/interim/selected/temperature
  101. md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
  102. - path: parameters/shap_selection.yaml
  103. md5: 43734a0f6f4865a78d36e5ea7e773176
  104. outs:
  105. - path: data/interim/stage_1/results_concatenated.tsv
  106. md5: aed0d7ed5a721fb780f90a2dccbd70e5
  107. - path: data/interim/stage_2/input_data
  108. md5: 9f1ca3ea434625790c4cab969e07aab7.dir
  109. - path: data/output/notebooks/shap_selection.ipynb
  110. md5: c48cb96cd95b4936a3adb043018a6d8c
  111. - path: data/output/plots/stage_one_summary_lifespan.svg
  112. md5: dbe5c9bbbbf06e6a62bf2f447b78010f
  113. - path: data/output/plots/stage_two_untuned_summary_lifespan.svg
  114. md5: f10b432adda8d0ef644b972515cfba24
  115. tuning:
  116. cmd: echo "work in progress!"
  117. deps:
  118. - path: data/interim/selected/expressions.tsv
  119. md5: e8e8ea38f54eec4c9d51069d8cc2fde0
  120. - path: data/interim/selected/genes.tsv
  121. md5: 08f457c2517b3f601f5e58e3b1ec4ae0
  122. - path: data/interim/selected/genes_meta.tsv
  123. md5: 0387f21fcd4b287dc924432c8b90042d
  124. - path: data/interim/selected/samples.tsv
  125. md5: c370e925f56a0ed33b7dcb16553d4c39
  126. - path: data/interim/selected/species.tsv
  127. md5: 44e0c63a0d7749abcd43b3c1f92cc54b
  128. outs:
  129. - path: data/output/optimization/study.sqlite
  130. md5: ef8116b0684832e6e11749edcd4e5cbf
  131. tune:
  132. cmd: python tune.py
  133. deps:
  134. - path: data/interim/selected/gestation_days
  135. md5: 03f0461ba9a1ca26f052203b948cd78b.dir
  136. - path: data/interim/selected/lifespan
  137. md5: 4c5315e23281c98c3b5d748b84d32b3e.dir
  138. - path: data/interim/selected/mass_kg
  139. md5: f36dbab9692c98800c464052e8dc85af.dir
  140. - path: data/interim/selected/metabolic_rate
  141. md5: 470ea1aeccc3bafa4b93268181360e6d.dir
  142. - path: data/interim/selected/mtGC
  143. md5: fa17686c777e1fad034b626b1efad921.dir
  144. - path: data/interim/selected/temperature
  145. md5: 4f4453d99a2c54fd9422e5e85c7fa5be.dir
  146. params:
  147. parameters/tune.yaml:
  148. debug_local: true
  149. folds: 5
  150. hold_outs: 1
  151. metrics: r2_huber_kendall
  152. not_validated_species: true
  153. repeats: 10
  154. threads: 1
  155. trait: lifespan
  156. trials: 10
  157. stage_one:
  158. cmd: papermill -f parameters/stage_one_shap_selection.yaml --progress-bar --report-mode
  159. notebooks/stage_one_shap_selection.ipynb data/output/notebooks/stage_one_shap_selection.ipynb
  160. deps:
  161. - path: data/interim/optimization/gestation_days.sqlite
  162. md5: 8f2a409f95031e839202e4feb88e99e0
  163. - path: data/interim/optimization/lifespan.sqlite
  164. md5: 0f73d0f933f828dcc5e287e6c9cacd5b
  165. - path: data/interim/optimization/mass_kg.sqlite
  166. md5: 23ddb28f55e3146b58e646e6e329e6b7
  167. - path: data/interim/optimization/metabolic_rate.sqlite
  168. md5: 247702368a8eab9c8824cac26a7f66e3
  169. - path: data/interim/optimization/mtGC.sqlite
  170. md5: 08ebe078dd5041f18945a571d3415054
  171. - path: data/interim/optimization/temperature.sqlite
  172. md5: 6cbdb4405cd2a969fefc39cd95565e45
  173. - path: parameters/stage_one_shap_selection.yaml
  174. md5: 43734a0f6f4865a78d36e5ea7e773176
  175. outs:
  176. - path: data/interim/stage_1/partitions
  177. md5: c70cae310172de021ff95c4bebb96e21.dir
  178. - path: data/interim/stage_1/results_concatenated.tsv
  179. md5: 206bf0eb607029e3bd6ff9fdf22bf636
  180. - path: data/interim/stage_2/input
  181. md5: 0e23e5707e9e4cf0295e4b14e1d3cedd.dir
  182. - path: data/output/plots/stage_1/
  183. md5: bb4dbd82d36324094523b556c572345c.dir
  184. - path: data/output/stage_1/gestation_days_selected.tsv
  185. md5: 06a8f9d1da9583bd0d8926d094f7361a
  186. - path: data/output/stage_1/lifespan_selected.tsv
  187. md5: 31fcf98988b82e5027db92db47df6240
  188. - path: data/output/stage_1/mass_kg_selected.tsv
  189. md5: 35d066eb10b7c7f7d2cba20c2c72a25f
  190. - path: data/output/stage_1/metabolic_rate_selected.tsv
  191. md5: fb8c331c1713bcde1ef3850add59ae8d
  192. - path: data/output/stage_1/mtGC_selected.tsv
  193. md5: 589a0f09a8948829ba4dc465f81cd5ac
  194. - path: data/output/stage_1/temperature_selected.tsv
  195. md5: 645b89723a9fdaca13f21799fe842db7
  196. stage_two:
  197. cmd: papermill -f parameters/stage_two_shap_selection.yaml --progress-bar --report-mode
  198. notebooks/stage_two_shap_selection.ipynb data/output/notebooks/stage_two_shap_selection.ipynb
  199. deps:
  200. - path: data/interim/optimization/lifespan_2.sqlite
  201. md5: 4b479767827123b1a697440822d5b06e
  202. - path: data/interim/stage_1/results_concatenated.tsv
  203. md5: 206bf0eb607029e3bd6ff9fdf22bf636
  204. - path: data/interim/stage_2/input
  205. md5: 0e23e5707e9e4cf0295e4b14e1d3cedd.dir
  206. outs:
  207. - path: data/interim/stage_2/partitions
  208. md5: ec4b53d890a4a6a62edcca84d9fc58f2.dir
  209. - path: data/output/plots/interactions/
  210. md5: ad45d9e3067cffeadb60cc9331ebafe6.dir
  211. - path: data/output/plots/life_history_no_genes
  212. md5: 3b34200c00fa455938bcee249e8a0477.dir
  213. - path: data/output/plots/stage_2/decision_lifespan.svg
  214. md5: 227947f4eeb6b1deb7c50f54b682ec2b
  215. - path: data/output/plots/stage_2/heatmap_lifespan_unclustered.svg
  216. md5: 1e824d421b577011c784769085da926d
  217. - path: data/output/plots/stage_2/summary_lifespan.svg
  218. md5: 805c2eeb15f5b62195ba71de5398dc97
  219. - path: data/output/stage_2/lifespan.tsv
  220. md5: fd09fc97efb766069a635e0d2cb2035c
  221. - path: data/output/stage_2/lifespan_with_traits.tsv
  222. md5: 6a72662224500b1c2f3ff8d01121fd2f
  223. results:
  224. cmd: papermill -f parameters/results_intersections.yaml --progress-bar --report-mode
  225. notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
  226. deps:
  227. - path: data/output/external/causality
  228. md5: 49db2b61f6e05fef5d975c56f139322f.dir
  229. - path: data/output/external/causality/causal_selection.tsv
  230. md5: 055328523cd2cb3df99fe180e423d8f8
  231. - path: data/output/external/causality/signature_scores_ensembl_codes.csv
  232. md5: 4aad6c97755d71c87fe139c72c120c13
  233. - path: data/output/external/linear
  234. md5: 024046bb0390f0d3bd374580359ebff4.dir
  235. - path: notebooks/results_intersections.ipynb
  236. md5: 63982d25a471caa6d5c1285fb679bfa0
  237. - path: parameters/results_intersections.yaml
  238. md5: 45a394673b593a63177a9853f01d24c4
  239. outs:
  240. - path: data/output/notebooks/results_intersections.ipynb
  241. md5: 90e722d2cb5bd50a635dcd8cebb52d95
  242. - path: data/output/results/genage_intersection.tsv
  243. md5: b3cce68304b233b447a43ac771c9c647
  244. - path: data/output/results/shap_with_causal_linear.tsv
  245. md5: acf2db7ed9284c58dc30fc327dda0c6e
  246. - path: data/output/results/shap_with_linear.tsv
  247. md5: 28fc3e2bbebe7b7f9fc0bc7cd5e5dc97
  248. - path: data/output/stage_2/shap_results.tsv
  249. md5: 60a9cf8cd66d7011fe20b842801c34b4
  250. stage_three:
  251. cmd: papermill -f parameters/stage_three_shap_selection.yaml --progress-bar --report-mode
  252. notebooks/stage_three_shap_selection.ipynb data/output/notebooks/stage_three_shap_selection.ipynb
  253. deps:
  254. - path: data/interim/optimization/lifespan_3.sqlite
  255. md5: cc8844b2243a74b0368eebaecff4c9c4
  256. outs:
  257. - path: data/output/plots/stage_3/interactions/
  258. md5: 5c546f6f29787821989c7e649feb151f.dir
  259. - path: data/output/plots/stage_3/life_history/
  260. md5: 8b7645e7bd0bbc945c5791078e3a15f9.dir
  261. - path: data/output/plots/stage_3/stage_3_decision.svg
  262. md5: e81f2ae90173942b4f659cd52905958e
  263. - path: data/output/plots/stage_3/stage_3_heatmap_unclustered.svg
  264. md5: d0f1e476c35c248fdf84d49fd013f062
  265. - path: data/output/plots/stage_3/stage_3_interactions.png
  266. md5: 8db6f94afc5df7482e9eb24966048893
  267. - path: data/output/plots/stage_3/stage_3_summary.svg
  268. md5: 97b42fcb9529808b1735c36c82ea51dd
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