add experiments python script, edits for testing with docker

wrote a full Dockerfile, edits to build_drugs.sh to reflect position of utils scripts in docker container. Adding the 03_createSarcPDOExperimentFIle.py to the repo.

Author: RubyFore

build/docker/Dockerfile.sarcpdo

@@ -3,11 +3,19 @@ FROM python:3.9
 WORKDIR /usr/src/app
 
 
-COPY build/sarcpdo/00_createSarcPDOSampleFile.py . 
+COPY build/sarcpdo/00_createSarcPDOSampleFile.py .
+COPY build/sarcpdo/01_createSarcPDOOmicsFiles.py .
+COPY build/sarcpdo/02_createSarcPDODrugsFile.py .
+COPY build/sarcpdo/03_createSarcPDOExperimentFile.py . 
 COPY build/sarcpdo/requirements.txt .
+COPY build/sarcpdo/*sh ./
+COPY build/utils/* ./
+
+# Set MPLCONFIGDIR to a writable directory
+ENV MPLCONFIGDIR=/app/tmp/matplotlib
+RUN mkdir -p /app/tmp/matplotlib
 
 RUN pip install --no-cache-dir -r requirements.txt
 
-VOLUM ['/tmp']
+VOLUME  ['/tmp']
 
-CMD python 

build/sarcpdo/03_createSarcPDOExperimentFile.py

@@ -0,0 +1,56 @@
+import synapseclient
+import pandas as pd
+import numpy as np
+import argparse
+import os
+
+
+if __name__ == "__main__":
+   
+    parser = argparse.ArgumentParser(description="This script handles downloading, processing and formatting of drug information for the Sarcoma PDO project into an experiments file")
+    
+    parser.add_argument('-t', '--token', type=str, help='Synapse Token')
+    parser.add_argument('-s', '--samplesFile', nargs = "?", type=str, default = "", help = "Use this to provide previously generated sample file for this dataset to link to experiment data.")
+    parser.add_argument('-d', '--drugFile', nargs = "?", type=str, default = "", help = "Use this to provide previously generated drugs file for this dataset to link with to experiment data.")
+
+    args = parser.parse_args()
+    print(args)
+    print("Logging into Synapse")
+    PAT = args.token
+    synObject = synapseclient.login(authToken=PAT)
+
+    drug_query = synObject.tableQuery("select * from syn61892224")
+    drug_data = drug_query.asDataFrame()
+
+    # convert Drug_Name to lowercase for merge with drug info files
+    drug_data['chem_name'] = drug_data['Drug_Name'].str.lower()
+
+    sarcpdo_samples = pd.read_csv(args.samplesFile)
+
+    sarcpdo_drugs = pd.read_csv(args.drugFile, sep="\t")
+    # reformat 'other_id', specifically, alter underscores before '1' to dashes so we can split on "_" and retain appended numbers
+    # rename to "Sample_ID" for merging with drug_data
+    sarcpdo_samples['Sample_ID'] = sarcpdo_samples['other_id'].str.lower()
+    sarcpdo_samples["Sample_ID"] = sarcpdo_samples["Sample_ID"].str.replace("_1", "-1")
+    sarcpdo_samples['Sample_ID'] = sarcpdo_samples["Sample_ID"].str.split("_", expand =True)[0]
+    # and change dashes back to underscores to merge with drug_data's Sample_ID
+    sarcpdo_samples["Sample_ID"] = sarcpdo_samples["Sample_ID"].str.replace("-", "_")
+
+    # inner merge with samples because there are samples without experiment info and many Sample_ID's in experiments data without sample info
+    experiments = drug_data.merge(sarcpdo_drugs, how='left').merge(sarcpdo_samples, how='inner')
+
+    final_experiment = experiments[['improve_sample_id', 'improve_drug_id', 'Viability_Score']]
+    final_experiment.loc[:,['study']] = 'Landscape of Sarcoma'
+    final_experiment.loc[:,['source']] = 'pharmacoGX'
+    final_experiment.loc[:,['time']] = None
+    final_experiment.loc[:,['time_unit']]= None
+    final_experiment.loc[:,['dose_response_metric']] = 'published_auc' 
+    final_experiment.loc[:,['dose_response_value']] = final_experiment['Viability_Score']
+
+    toReturn = final_experiment[['source', 'improve_sample_id', 'improve_drug_id', 'study', 'time', 'time_unit', 'dose_response_metric', 'dose_response_value']]
+
+    toReturn.to_csv('/tmp/sarcpdo_experiments.tsv', sep='\t', index=False)
+
+
+    # to test run
+    #  python3 03_createSarcPDOExperimentFile.py -t $SYNAPSE_AUTH_TOKEN -s sarcpdo_samples.csv -d sarcpdo_drugs.tsv

build/sarcpdo/build_drugs.sh

@@ -4,7 +4,7 @@ set -euo pipefail
 trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
 
 echo "Running script with token and drugFile $1"
-python3 02_createSarcPDODrugsFile.py --token $SYNAPSE_AUTH_TOKEN -d $1 -o /tmp/sarcpdo_drugs.tsv
+python3 02_createSarcPDODrugsFile --token $SYNAPSE_AUTH_TOKEN -d $1 -o /tmp/sarcpdo_drugs.tsv
 
 echo "Running build_drug_desc.py..."
 python3 build_drug_desc.py --drugtable /tmp/sarcpdo_drugs.tsv --desctable /tmp/sarcpdo_drug_descriptors.tsv.gz

build/sarcpdo/build_exp.sh

@@ -4,4 +4,4 @@ set -euo pipefail
 trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
 
 echo "Running script with token and curSamples $1 and drugFile $2."
-python3 03_createSarcPDOExperimentFile.py -t $SYNAPSE_AUTH_TOKEN -s sarcpdo_samples.csv -d sarcpdo_drugs.tsv
+python3 03_createSarcPDOExperimentFile.py -t $SYNAPSE_AUTH_TOKEN -s $1 -d $2