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Copy pathprism_pipeline.cfg
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prism_pipeline.cfg
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#####################################################################
[PrismCell column headers]
analyte_id = analyte
pool_id = pool_id
davepool_id = davepool_id
id = feature_id
name = cell_iname
minipool_id = minipool_id
ccle_name = ccle_name
lua = barcode_
cell_lineage = cell_lineage
cell_culture = cell_culture
#####################################################################
[PrismCell database file]
prism_cell_database_filepath = /cmap/data/vdb/PRISM/cell_set_definitions/PRISM_CS1.2_definition.txt
#####################################################################
[DavepoolAnalyteMapping column headers]
analyte_id = analyte_id
id = feature_id
cell_name = cell_iname
davepool_id = davepool_id
pool_ID = pool_id
#####################################################################
[Perturbagen CM input column headers]
well_id = well_position
pert_mfc_id = broad_sample
pert_vendor_id = vendor_catalog_id
pert_type = role
pert_mfc_desc = compound_name
pert_vehicle = solvent
#dose concentration
compound_well_mmoles_per_liter = compound_well_mmoles_per_liter
dilution_factor = dilution_factor
#sample physical properties
avg_mol_weight = avg_mol_weight
SMILES = smiles
purity = purity
purity_annotation = annotation
#plate information
mfc_plate_id = cpd_plate_barcode
mfc_plate_name = plate_map_name
assay_plate_barcode = assay_plate_barcode
#####################################################################
[Perturbagen CMap input column headers]
well_id = pert_well
#####################################################################
[Perturbagen values]
pert_type_mapping = {"PosCon":"trt_poscon", "Test":"trt_cp"}
pert_type_vehicle = ctl_vehicle
default_pert_time = 120
default_pert_time_unit = h
pert_dose_unit_uM = uM
pert_id_DMSO = DMSO
#####################################################################
[Assay Plate column headers]
assay_plate_barcode = assay_plate_barcode
det_plate = det_plate
pool_id = pool_id
#####################################################################
[Perturbagen output column header renaming map]
well_id = pert_well