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aging-research
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species

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dvc.yaml 4.0 KB
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  1. stages:
    2. 

  2.   select_samples:
    3. 

  3.     cmd: papermill -f parameters/select_samples.yaml  --progress-bar --report-mode
    4. 

  4.       notebooks/select_samples.ipynb data/output/notebooks/select_samples.ipynb
    5. 

  5.     deps:
    6. 

  6.       - parameters/select_samples.yaml
    7. 

  7.       - data/input/genes/by_animal_class
    8. 

  8.       - data/input/species.tsv
    9. 

  9.       - data/input/samples.tsv
    10. 

  10.       - data/input/total_mtDNA_base_composition.csv
    11. 

  11.       - notebooks/select_samples.ipynb
    12. 

  12.     outs:
    13. 

  13.       - data/interim/selected/gestation_days
    14. 

  14.       - data/interim/selected/lifespan
    15. 

  15.       - data/interim/selected/mass_kg
    16. 

  16.       - data/interim/selected/metabolic_rate
    17. 

  17.       - data/interim/selected/mtGC
    18. 

  18.       - data/interim/selected/temperature
    19. 

  19.       - data/output/counts/species_sample_count.tsv
    20. 

  20.       - data/output/counts/tissue_sample_count.tsv
    21. 

  21.       - data/output/counts/species_tissue_sample_count.tsv
    22. 

  22.       - data/output/notebooks/select_samples.ipynb
    23. 

  23.   stage_one:
    24. 

  24.     cmd: papermill -f parameters/stage_one_shap_selection.yaml  --progress-bar --report-mode
    25. 

  25.       notebooks/stage_one_shap_selection.ipynb data/output/notebooks/stage_one_shap_selection.ipynb
    26. 

  26.     deps:
    27. 

  27.       - parameters/stage_one_shap_selection.yaml
    28. 

  28.       - data/interim/optimization/gestation_days.sqlite
    29. 

  29.       - data/interim/optimization/lifespan.sqlite
    30. 

  30.       - data/interim/optimization/mass_kg.sqlite
    31. 

  31.       - data/interim/optimization/metabolic_rate.sqlite
    32. 

  32.       - data/interim/optimization/mtGC.sqlite
    33. 

  33.       - data/interim/optimization/temperature.sqlite
    34. 

  34.     outs:
    35. 

  35.       #- data/output/notebooks/stage_one_shap_selection.ipynb
    36. 

  36.       - data/interim/stage_1/results_concatenated.tsv
    37. 

  37.       - data/interim/stage_1/partitions
    38. 

  38.       - data/interim/stage_2/input
    39. 

  39.       - data/output/plots/stage_one_summary_lifespan.svg
    40. 

  40.       - data/output/plots/stage_two_untuned_summary_lifespan.svg
    41. 

  41.       - data/output/stage_1/gestation_days_selected.tsv
    42. 

  42.       - data/output/stage_1/mass_kg_selected.tsv
    43. 

  43.       - data/output/stage_1/mtGC_selected.tsv
    44. 

  44.       - data/output/stage_1/lifespan_selected.tsv
    45. 

  45.       - data/output/stage_1/metabolic_rate_selected.tsv
    46. 

  46.       - data/output/stage_1/temperature_selected.tsv
    47. 

  47.   stage_two:
    48. 

  48.     cmd: papermill -f parameters/stage_two_shap_selection.yaml  --progress-bar --report-mode
    49. 

  49.       notebooks/stage_two_shap_selection.ipynb data/output/notebooks/stage_two_shap_selection.ipynb
    50. 

  50.     deps:
    51. 

  51.       - data/interim/stage_1/results_concatenated.tsv
    52. 

  52.       - data/interim/optimization/lifespan.sqlite
    53. 

  53.       - data/interim/stage_2/input
    54. 

  54.     outs:
    55. 

  55.       - data/interim/stage_2/partitions
    56. 

  56.       - data/output/stage_2/lifespan.tsv
    57. 

  57.       - data/output/plots/stage_two_summary_lifespan.svg
    58. 

  58.       - data/output/plots/stage_two_decision_lifespan.svg
    59. 

  59.       #  - data/output/notebooks/stage_two_shap_selection.ipynb
    60. 

  60.   tune:
    61. 

  61.     cmd: python tune.py
    62. 

  62.     params:
    63. 

  63.       - parameters/tune.yaml:
    64. 

  64.           - trait
    65. 

  65.           - metrics
    66. 

  66.           - trials
    67. 

  67.           - folds
    68. 

  68.           - hold_outs
    69. 

  69.           - repeats
    70. 

  70.           - not_validated_species
    71. 

  71.           - threads
    72. 

  72.           - debug_local
    73. 

  73.     deps:
    74. 

  74.       - data/interim/selected/gestation_days
    75. 

  75.       - data/interim/selected/lifespan
    76. 

  76.       - data/interim/selected/mass_kg
    77. 

  77.       - data/interim/selected/metabolic_rate
    78. 

  78.       - data/interim/selected/mtGC
    79. 

  79.       - data/interim/selected/temperature
    80. 

  80.   results_intersections:
    81. 

  81.     cmd: papermill -f parameters/results_intersections.yaml  --progress-bar --report-mode
    82. 

  82.       notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
    83. 

  83.     deps:
    84. 

  84.       - parameters/results_intersections.yaml
    85. 

  85.       - data/output/external/causality
    86. 

  86.       - data/output/external/linear
    87. 

  87.       - data/output/external/shap
    88. 

  88.       - data/output/external/causality/causal_relations_5_tissues_anton_species_5_bootstraps.csv
    89. 

  89.     outs:
    90. 

  90.       - data/output/notebooks/results_intersections.ipynb
    91. 

  91.       - data/output/intersections/genage_human_intersections.tsv
    92. 

  92.       - data/output/intersections/genage_model_intersections.tsv
    93. 

  93.       - data/output/intersections/intersections_5_and_7.tsv
    94. 

  94.       - data/output/intersections/intersections.tsv
    95. 

  95.       - data/output/intersections/new_old_comparison.tsv
    96.
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Access key (If needed)

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species is now integrated with Azure Cloud Storage!

Delete Storage Key

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