updating the drug retrieval to use the latest files

build/broad_sanger/03a-nci60Drugs.py

@@ -13,10 +13,23 @@
 
 ##drug files
 smi_strings='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_smiles.csv?version=1&modificationDate=1710381820000&api=v2&download=true'
+#oct 2024
+smi_strings = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_smiles.csv?version=3&modificationDate=1727924130457&api=v2&download=true'
+
 pc_ids='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_sid_cid.csv?version=2&modificationDate=1712766341112&api=v2&download=true'
+pc_ids = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_sid_cid.csv?version=4&modificationDate=1727924129121&api=v2&download=true'
+
+#oct 2024
 chemnames='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemcal_name.csv?version=1&modificationDate=1710382716000&api=v2&download=true'
+
+chemnames='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_chemical_name.csv?version=1&modificationDate=1727924127004&api=v2'
+#oct 2024
 cas='https://wiki.nci.nih.gov/download/attachments/155844992/nsc_cas.csv?version=1&modificationDate=1710381783000&api=v2&download=true'
+#oct 2024
+cas = 'https://wiki.nci.nih.gov/download/attachments/155844992/nsc_cas.csv?version=3&modificationDate=1727924126194&api=v2&download=true'
 conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=11&modificationDate=1712351454136&api=v2'
+##OCT 2024
+conc_data = 'https://wiki.nci.nih.gov/download/attachments/147193864/DOSERESP.zip?version=13&modificationDate=1727922354561&api=v2'
 
 
 def main():    
@@ -39,7 +52,7 @@ def main():
     if not os.path.exists('DOSERESP.csv'):
         resp = request.urlretrieve(conc_data,'doseresp.zip')
         os.system('unzip doseresp.zip')
-    dose_resp = pl.read_csv("DOSERESP.csv",quote_char='"',infer_schema_length=10000000)
+    dose_resp = pl.read_csv("DOSERESP.csv",quote_char='"',infer_schema_length=10000000,ignore_errors=True)
     pubchems = pubchems.filter(pl.col('NSC').is_in(dose_resp['NSC']))
     ##first retreive pubchem data
     if opts.test:

build/broad_sanger/04b-nci60-updated.py

@@ -1,5 +1,5 @@
 '''
-gets nci60 data from 10/2023 release
+gets nci60 data from 10/2024 release
 
 '''
 

build/utils/fit_curve.py

@@ -42,7 +42,7 @@ def hs_response_curve_original(x, einf, ec50, hs):
 
 HS_BOUNDS = ([0, 0, 0], [1, 12, 4]) 
 #HS_BOUNDS_NEG = ([0, -3,-1],[1,8,0]) ## made hill slope forced to be negative
-HS_BOUNDS_NEG = ([0, -11,-1],[1,10,0]) ## made hill slope forced to be negative  ##20241017 updated to make ec50 go lower
+HS_BOUNDS_NEG = ([0, -5,-1],[1,3,0]) ## made hill slope forced to be negative  ##20241017 updated to shift EC50 range
 def response_curve(x, einf, ec50, hs):
     """ transformed the original function with ec50 in -log10(M) instead of M
     """