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This is the input CSV. Note the name of the column Metadata_dose_recode
Metadata_dose_recode
cat /tmp/a.csv Metadata_Plate_Map_Name,Metadata_broad_sample,Metadata_pert_well,Metadata_mmoles_per_liter,Metadata_dose_recode,Cells_AreaShape_Area C-7161-01-LM6-001,BRD-A25234499-001-18-3,B13, 10,6,0.590843 C-7161-01-LM6-001,BRD-A25234499-001-18-3,B14,3.3333,5,0.953997 C-7161-01-LM6-001,BRD-A25234499-001-18-3,B15,1.1111,4,1.10022 C-7161-01-LM6-001,BRD-A25234499-001-18-3,B16,0.37037,3,0.616491
Convert
import pandas import pycytominer pandas.read_csv("/tmp/a.csv") pycytominer.write_gct(a, "/tmp/a.gct")
This is the output GCT. Note the name of the column Metadata_ose_recode
Metadata_ose_recode
$ cat /tmp/a.gct #1.3 1 4 1 5 id cp_feature_name SAMPLE_0 SAMPLE_1 SAMPLE_2 SAMPLE_3 Plate_Map_Name nan C-7161-01-LM6-001 C-7161-01-LM6-001 C-7161-01-LM6-001 C-7161-01-LM6-001 broad_sample nan BRD-A25234499-001-18-3 BRD-A25234499-001-18-3 BRD-A25234499-001-18-3 BRD-A25234499-001-18-3 pert_well nan B13 B14 B15 B16 mmoles_per_liter nan 10.0 3.3333 1.1111 0.37037 ose_recode nan 6 5 4 3 Cells_AreaShape_Area Cells_AreaShape_Area 0.590843 0.953997 1.10022 0.616491
The text was updated successfully, but these errors were encountered:
write_gct
see #70 - it seems now is the time to make this fix!
Sorry, something went wrong.
fixed in #87
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This is the input CSV. Note the name of the column
Metadata_dose_recode
Convert
This is the output GCT. Note the name of the column
Metadata_ose_recode
The text was updated successfully, but these errors were encountered: