created get omics data function

Author: alexandriai168

build/novartispdx/02-omics-novartispdx.py

@@ -4,3 +4,47 @@
 import math
 import argparse
 
+def download_parse_omics_novPDX(synID:str , save_path:str = None, synToken:str = None):
+    """ 
+    Download omics data from Synapse at synapseID syn66364488. Requires a synapse token, which requires you to make a Synapse account
+    and create a Personal Access Token.  More information here: https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens 
+    Omics data is an excel file.  The excel file is then parsed for the RNAseq, copy number, and mutations data.
+    
+    Parameters
+    ----------
+    synID : string
+        SynapseID of dataset to download. Default is synapseID of the sequencing dataset.
+        
+    save_path : string
+        Local path where the downloaded file will be saved.
+
+    synToken : string
+        Synapse Personal Access Token of user.  Requires a Synapse account. More information at: https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens
+        
+    Returns
+    -------
+    mutations_data : pd.DataFrame
+        A DataFrame containing mutations data.
+
+    copy_number_data : pd.DataFrame
+        A DataFrame containing copy number data.
+
+    rnaseq_data : pd.DataFrame
+        A DataFrame containing RNAseq data.
+    """
+
+    syn = synapseclient.Synapse() 
+    syn.login(authToken=synToken) 
+    
+    # Obtain a pointer and download the data 
+    syn66364488 = syn.get(entity=synID, downloadLocation = save_path) 
+
+    # Get the path to the local copy of the data file 
+    sequencing_filepath = syn66364488.path
+    all_omics_excel = pd.ExcelFile(open(sequencing_filepath, 'rb'))
+    mutations_data = pd.read_excel(all_omics_excel, 'pdxe_mut_and_cn2') # table with somatic mutation information 
+    copy_number_data = pd.read_excel(all_omics_excel, 'copy number') # table with copy number information
+    rnaseq_data = pd.read_excel(all_omics_excel, 'RNAseq_fpkm')
+
+
+    return(rnaseq_data, copy_number_data, mutations_data)