Merge branch 'novartisPDX-drugs-experiments' of https://github.com/PNNL-CompBio/coderdata into novartisPDX-omics

Pulling from Novartis experiments and drugs branch to get updated experiments file

Author: alexandriai168

build/novartispdx/01-samples-novartispdx.py

@@ -44,7 +44,6 @@ def get_complete_novartispdx_sample_sheet(synObject):
     print("Logging into Synapse")
     PAT = args.token
     synObject = synapseclient.login(authToken=PAT)
-
     samplesheet = get_complete_novartispdx_sample_sheet(synObject)
 
     if (args.prevSamples):

build/novartispdx/04-experiments-novartispdx.py

@@ -20,7 +20,7 @@ def get_novartis_pdx_experiments_file(synObject, samples_df):
     novartispdx_curvefile['treatment']=novartispdx_curvefile['treatment'].str.replace('untreated', 'control')
     novartispdx_curvefile['experiment'] = novartispdx_curvefile.groupby(['model_id']).ngroup()+1
     # remove triple combination(s)
-    novartispdx_curvefile = novartispdx_curvefile[~novartispdx_curvefile['treatment'].str.contains(r'\+.*\+')]
+    novartispdx_curvefile = novartispdx_curvefile[~novartispdx_curvefile['treatment'].str.contains(r'\+')]
     # remove dose information appended to some drugs in the treatment column and include in dose colum
     druganddose = novartispdx_curvefile['treatment'].str.split('-', expand=True)
     druganddose = druganddose.rename({0: 'treatment', 1:'dose'}, axis=1)
@@ -39,12 +39,9 @@ def get_novartis_pdx_experiments_file(synObject, samples_df):
     #merge on drug names done in calc_pdx_metrics.py
     #final_w_drugIDs = finaldf.merge(drug_df, how='left',right_on='chem_name', left_on="treatment")
     final_allIDs = nomissingcontrols.merge(samples_df, how='left', right_on='common_name', left_on='model_id') 
-    print(final_allIDs.head)
     final_allIDs = final_allIDs.drop('model_id', axis=1)
     finalDF = final_allIDs.rename({'improve_sample_id':'model_id'}, axis=1)
-    print(finalDF.head)
     finalcurvefile = finalDF[['model_id', 'time', 'volume', 'treatment', 'experiment', 'dose']]
-    print(finalcurvefile.head)
     return finalcurvefile
 
 
@@ -59,7 +56,6 @@ def get_novartis_pdx_experiments_file(synObject, samples_df):
     print("Logging into Synapse")
     PAT = args.token
     synObject = synapseclient.login(authToken=PAT)
-    #drug_df = pd.read_csv(args.drugfile, sep='\t')
     samples_df = pd.read_csv(args.curSampleFile)
 
     doseresponse_data = get_novartis_pdx_experiments_file(synObject, samples_df)

build/novartispdx/build_experiments.sh

@@ -2,4 +2,4 @@
 #python3 04-experiments-novartispdx.py --token $SYNAPSE_AUTH_TOKEN 
 
 python3 -m novartispdx.04-experiments-novartispdx --token $SYNAPSE_AUTH_TOKEN -o ~/Projects/CoderData/dev-environment/novartispdx/novartispdx_curvedata.tsv
-python3 utils/calc_pdx_metrics.py /tmp/novartispdx_curvedata.tsv --drugfile=/tmp/novartispdx_drugs.tsv --outprefix=/tmp/novartispdx
+python3 utils/calc_pdx_metrics.py /tmp/novartispdx_curvedata.tsv --drugfile=/tmp/novartispdx_drugs.tsv --outprefix=/tmp/novartispdx --study='Novartis PDX Gao etal 2015' --source='Synapse'

build/utils/calc_pdx_metrics.py

@@ -184,12 +184,12 @@ def AUC(time, volume, time_normalize=True):
     dict: Dictionary containing the AUC value.
     """
     auc = trapz_auc(time, volume)
-    print('at line 187')
-    print(time.shape)
-    print(time.dtype)
-    print(np.max(time.astype(int)))
-    print('auc is : ')
-    print(auc)
+    #print('at line 187')
+    #print(time.shape)
+    #print(time.dtype)
+    #print(np.max(time.astype(int)))
+    #print('auc is : ')
+    #print(auc)
     if time_normalize:
         auc = auc/np.max(time)
     return {"metric": "auc", "value": auc, 'time':np.max(time)}
@@ -292,7 +292,7 @@ def lmm(time, volume, treatment, drug_name):
     #interaction_term = 'time:exp_type'
 #    if interaction_term in fit.params:
 #    time_coef_value = fit.params['time']
-    print(fit.params)
+    #print(fit.params)
     i_coef_value = fit.params['time:exp_type[T.'+drug_name+']']
     #i_coef_value = fit.params['time:exp_type['+drug_name+']']
    # else:
@@ -312,6 +312,8 @@ def main():
     parser.add_argument('curvefile')
     parser.add_argument('--drugfile')
     parser.add_argument('--outprefix',default='/tmp/')
+    parser.add_argument('--study')
+    parser.add_argument('--source')
 
     args = parser.parse_args()
 
@@ -325,22 +327,21 @@ def main():
     expsing = expsing.dropna()
 
     # source	improve_sample_id	improve_drug_id	study	time	time_unit	dose_response_metric	dose_response_value
-
-    combos[['drug1','drug2']]=combos.drug.str.split('+',expand=True)
-    print('COMBOS ARE: ')
-    print(combos[['drug1', 'drug2']])
-    combos = combos.rename({'metric':'drug_combination_metric','value':'drug_combination_value','sample':'improve_sample_id'},axis=1).dropna()
-
-    expcomb = combos.rename({'drug1':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_1'},axis=1)[['improve_drug_1','drug2','improve_sample_id','time_unit','time','drug_combination_metric','drug_combination_value']]
-    expcomb = expcomb.rename({'drug2':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_2'},axis=1)[['improve_drug_1','improve_drug_2','improve_sample_id','time_unit','time','drug_combination_metric','drug_combination_value']]
-    print(expcomb[['improve_drug_1', 'improve_drug_2']])
-    expcomb[['source']]='Synapse'
-    expcomb[['study']]='MPNST PDX in vivo'
-
-    expsing[['source']]='Synapse'
-    expsing[['study']]='MPNST PDX in vivo'
+    if combos.shape[0]> 0:
+        combos[['drug1','drug2']]=combos['drug'].str.split('+',expand=True)
+        
+        combos = combos.rename({'metric':'drug_combination_metric','value':'drug_combination_value','sample':'improve_sample_id'},axis=1).dropna()
+        
+        expcomb = combos.rename({'drug1':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_1'},axis=1)[['improve_drug_1','drug2','improve_sample_id','time_unit','time','drug_combination_metric','drug_combination_value']]
+        expcomb = expcomb.rename({'drug2':'chem_name'},axis=1).merge(drugs,on='chem_name',how='left').rename({'improve_drug_id':'improve_drug_2'},axis=1)[['improve_drug_1','improve_drug_2','improve_sample_id','time_unit','time','drug_combination_metric','drug_combination_value']]
+        expcomb[['source']]=args.source
+        expcomb[['study']]=args.study
+        expcomb.to_csv(args.outprefix+'_combinations.tsv',index=False, sep="\t")
+
+    expsing[['source']]=args.source
+    expsing[['study']]=args.study
     expsing.to_csv(args.outprefix+'_experiments.tsv',index=False, sep="\t")
-    expcomb.to_csv(args.outprefix+'_combinations.tsv',index=False, sep="\t")
+    #expcomb.to_csv(args.outprefix+'_combinations.tsv',index=False, sep="\t")