diff PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,77 @@
+import modlamp
+from modlamp.datasets import load_AMPvsTM
+from modlamp.datasets import load_AMPvsUniProt
+from modlamp.datasets import load_ACPvsTM
+from modlamp.datasets import load_ACPvsRandom
+from modlamp.database import query_apd
+from modlamp.database import query_camp
+import os
+import pandas as pd
+
+def DataGen(DataBaseType, OutFile, IDs):
+
+    if DataBaseType == 'AMPvsTM':
+        data = load_AMPvsTM()
+
+    elif DataBaseType == 'AMPvsUniProt':
+        data = load_AMPvsUniProt()
+
+    elif DataBaseType == 'ACPvsTM':
+        data = load_ACPvsTM()
+
+    elif DataBaseType == 'ACPvsRandom':
+        data = load_ACPvsRandom()
+
+    elif DataBaseType == 'query_apd':
+
+        data = query_apd([int(i) for i in IDs.split(',')])
+        df = pd.DataFrame(data, columns=['Peptides'])
+        df.to_csv(OutFile, index=False, sep='\t')
+        exit()
+
+    elif DataBaseType == 'query_camp':
+        data = query_camp([int(i) for i in IDs.split(',')])
+        df = pd.DataFrame(data, columns=['Peptides'])
+        df.to_csv(OutFile, index=False, sep='\t')
+        exit()
+
+    else:
+        print ("Enter Correct Values")
+        exit()
+
+    Target = data.target.tolist()
+    Target_list = set(Target)
+    df = data.sequences
+
+
+    Target = pd.DataFrame(Target, columns=['Target'])
+    df = pd.DataFrame(df, columns=['Peptide'])
+    
+    df = pd.DataFrame(df)
+    df = pd.concat([df, Target], axis=1)
+
+    df.to_csv(OutFile, index=False, sep='\t')
+
+
+if __name__=="__main__":
+
+    import argparse
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("-d", "--DataBaseType",
+                        required=True,
+                        default=None,
+                        help="Name of the dataset ")
+                        
+    parser.add_argument("-o", "--OutFile",
+                        required=False,
+                        default='Out.tsv',
+                        help="Out put file name for str descriptors")   
+
+    parser.add_argument("-L", "--List",
+    					required=False,
+    					default=None,
+    					help="List of integer as ID")
+
+    args = parser.parse_args()
+    DataGen(args.DataBaseType, args.OutFile, args.List)