kg_microbe.transform_utils.bactotraits package
Submodules
kg_microbe.transform_utils.bactotraits.bactotraits module
BactoTraits transform class.
- class kg_microbe.transform_utils.bactotraits.bactotraits.BactoTraitsTransform(input_dir, output_dir)
Bases:
TransformBactoTraits transform.
Essentially just ingests and transforms this file: https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv
Columns available in the file: - strain n¡ - Bacdive_ID - culture collection codes - Kingdom - Phylum - Class - Order - Family - Genus - Species - Full_name - pHO_0_to_6 - pHO_6_to_7 - pHO_7_to_8 - pHO_8_to_14 - pHR_0_to_4 - pHR_4_to_6 - pHR_6_to_7 - pHR_7_to_8 - pHR_8_to_10 - 10_to_14 - pHd_<=1 - pHd_1_2 - pHd_2_3 - pHd_3_4 - pHd_4_5 - pHd_5_9 - NaO_<=1 - NaO_1_to_3 - NaO_3_to_8 - NaO_>8 - NaR_<=1 - NaR_1_to_3 - NaR_3_to_8 - NaR_>8 - Nad_<=1 - Nad_1_3 - Nad_3_8 - Nad_>8 - TO_<=10 - TO_10_to_22 - TO_22_to_27 - TO_27_to_30 - TO_30_to_34 - TO_34_to_40 - TO_>40 - TR_<=10 - TR_10_to_22 - TR_22_to_27 - TR_27_to_30 - TR_30_to_34 - TR_34_to_40 - TR_>40 - Td_1_5 - Td_5_10 - Td_10_20 - Td_20_30 - Td_>30 - Ox_anaerobic - Ox_aerobic - Ox_facultative_aerobe_anaerobe - Ox_microerophile - G_negative - G_positive - non-motile - motile - spore - no_spore - GC_<=42.65 - GC_42.65_57.0 - GC_57.0_66.3 - GC_>66.3 - W_<=0.5 - W_0.5_0.65 - W_0.65_0.9 - W_>0.9 - L_<=1.3 - L_1.3_2 - L_2_3 - L_>3 - S_rod - S_sphere - S_curved_spiral - S_filament - S_ovoid - S_star_dumbbell_pleomorphic - TT_heterotroph - TT_autotroph - TT_organotroph - TT_lithotroph - TT_chemotroph - TT_phototroph - TT_copiotroph_diazotroph - TT_methylotroph - TT_oligotroph - Pigment_pink - Pigment_yellow - Pigment_brown - Pigment_black - Pigment_orange - Pigment_white - Pigment_cream - Pigment_red - Pigment_green - Pigment_carotenoid
-
REQUIRED_CONSUMED_INPUTS:
tuple= ('bacdive_taxon_lookup',) Named generated inputs that must actually be read before fresh finalization. Unlike DATA_INPUTS, these are checked after upstream producers have run.
-
TRANSFORM_INPUTS:
tuple= ('bacdive',) The BacDive-produced intermediate TSV supplies strain-taxid mappings (#1091).
- run(data_file=None, show_status=True)
Run BactoTraitsTransform.
- Return type:
None
-
REQUIRED_CONSUMED_INPUTS:
Module contents
BactoTraits transform.
- class kg_microbe.transform_utils.bactotraits.BactoTraitsTransform(input_dir, output_dir)
Bases:
TransformBactoTraits transform.
Essentially just ingests and transforms this file: https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv
Columns available in the file: - strain n¡ - Bacdive_ID - culture collection codes - Kingdom - Phylum - Class - Order - Family - Genus - Species - Full_name - pHO_0_to_6 - pHO_6_to_7 - pHO_7_to_8 - pHO_8_to_14 - pHR_0_to_4 - pHR_4_to_6 - pHR_6_to_7 - pHR_7_to_8 - pHR_8_to_10 - 10_to_14 - pHd_<=1 - pHd_1_2 - pHd_2_3 - pHd_3_4 - pHd_4_5 - pHd_5_9 - NaO_<=1 - NaO_1_to_3 - NaO_3_to_8 - NaO_>8 - NaR_<=1 - NaR_1_to_3 - NaR_3_to_8 - NaR_>8 - Nad_<=1 - Nad_1_3 - Nad_3_8 - Nad_>8 - TO_<=10 - TO_10_to_22 - TO_22_to_27 - TO_27_to_30 - TO_30_to_34 - TO_34_to_40 - TO_>40 - TR_<=10 - TR_10_to_22 - TR_22_to_27 - TR_27_to_30 - TR_30_to_34 - TR_34_to_40 - TR_>40 - Td_1_5 - Td_5_10 - Td_10_20 - Td_20_30 - Td_>30 - Ox_anaerobic - Ox_aerobic - Ox_facultative_aerobe_anaerobe - Ox_microerophile - G_negative - G_positive - non-motile - motile - spore - no_spore - GC_<=42.65 - GC_42.65_57.0 - GC_57.0_66.3 - GC_>66.3 - W_<=0.5 - W_0.5_0.65 - W_0.65_0.9 - W_>0.9 - L_<=1.3 - L_1.3_2 - L_2_3 - L_>3 - S_rod - S_sphere - S_curved_spiral - S_filament - S_ovoid - S_star_dumbbell_pleomorphic - TT_heterotroph - TT_autotroph - TT_organotroph - TT_lithotroph - TT_chemotroph - TT_phototroph - TT_copiotroph_diazotroph - TT_methylotroph - TT_oligotroph - Pigment_pink - Pigment_yellow - Pigment_brown - Pigment_black - Pigment_orange - Pigment_white - Pigment_cream - Pigment_red - Pigment_green - Pigment_carotenoid
-
REQUIRED_CONSUMED_INPUTS:
tuple= ('bacdive_taxon_lookup',) Named generated inputs that must actually be read before fresh finalization. Unlike DATA_INPUTS, these are checked after upstream producers have run.
-
TRANSFORM_INPUTS:
tuple= ('bacdive',) The BacDive-produced intermediate TSV supplies strain-taxid mappings (#1091).
- run(data_file=None, show_status=True)
Run BactoTraitsTransform.
- Return type:
None
-
REQUIRED_CONSUMED_INPUTS: