added pdcli as a separate module

sdm/static/sdm/scripts/pdcli.py → pdcli.py

@@ -5,7 +5,8 @@
 from Bio.Seq import Seq
 from Bio.Alphabet import IUPAC
 from Bio.SeqRecord import SeqRecord
-from primerclass import *
+from pdcli.primerclass import *
+from pdcli.input_handler import *
 
 
 def main():
@@ -18,63 +19,17 @@ def main():
     parser.add_argument('-p', '--position', help='Target base position', type=int)
     parser.add_argument('-i', '--interactive', help='Interactive mode', action='store_true')
     args = parser.parse_args()
-    args_dict = dict()
 
     if args.interactive:
-        print('')
-        print('====================================')
-        print('======                        ======')
-        print('===     PrimerDriver v0.1.2      ===')
-        print('======                        ======')
-        print('====================================\n')
-        print('(c) 2020 Kenneth Domingo & Nomer Gutierrez\n')
-        args_dict['mode'] = input('Enter primer mode [dna/pro/char]: ')
-        if args_dict['mode'].upper() == 'DNA':
-            args_dict['sequence'] = input('Enter DNA sequence: ')
-            PrimerChecks(args_dict['sequence']).check_sequence_length()
-            PrimerChecks(args_dict['sequence']).check_valid_base()
-            args_dict['mutation_type'] = input('Enter mutation type [s/i/d]: ')
-            if args_dict['mutation_type'].upper() in ['S', 'SUB']:
-                args_dict['target'] = input('Enter target base: ')
-                args_dict['destination'] = input('Enter replacement for target base: ')
-                args_dict['position'] = int(input('Enter position of target: '))
-            elif args_dict['mutation_type'].upper() in ['I', 'INS']:
-                args_dict['target'] = None
-                args_dict['destination'] = input('Enter insertion sequence: ')
-                args_dict['position'] = int(input('Enter insertion position: '))
-            elif args_dict['mutation_type'].upper() in ['I', 'INS']:
-                args_dict['target'] = None
-                args_dict['destination'] = input('Enter starting position to delete: ')
-            else:
-                raise ValueError("Invalid argument passed to 'MUTATION_TYPE'")
-        elif args_dict['mode'].upper() == 'CHAR':
-            args_dict['sequence'] = input('Enter primer sequence: ')
-            args_dict['mutation_type'] = input('Enter mutation type [s/i/d]: ')
-            args_dict['mismatched_bases'] = input('Enter number of mismatched bases: ')
-        else:
-            raise NotImplementedError(f"{args_dict['mode']} mode not implemented (yet).")
-
+        args_dict = interactive_handler()
     else:
-        args_dict['mode'] = args.mode
-        if args.mode.upper() =='DNA':
-            args_dict['sequence'] = args.sequence
-            PrimerChecks(args.sequence).check_sequence_length()
-            PrimerChecks(args.sequence).check_valid_base()
-            args_dict['mutation_type'] = args.mutation_type
-            args_dict['position'] = args.position
-            args_dict['destination'] = args.destination
-            if args.mutation_type.upper() in ['S', 'SUB']:
-                args_dict['target'] = args.target
-            else:
-                raise ValueError("Invalid argument passed to 'MUTATION_TYPE'")
-        else:
-            raise NotImplementedError(f"{args_dict['mode']} mode not implemented (yet).")
+        args_dict = singleCommand_handler(args)
 
     res = PrimerDesign(**args_dict)
     if args_dict['mode'].upper() == 'CHAR':
         res.characterize_primer()
         df = res.df
-    else:
+    elif args_dict['mode'].upper() == 'DNA':
         res.main()
         idx = [
             'Forward',
@@ -94,7 +49,10 @@ def main():
             index=idx,
             dtype=str,
         )
-    save = input("Save? [y/n] ")
+    else:
+        raise NotImplementedError
+
+    save = input("\nSave? [y/n] ")
     if save.upper() == "Y":
         while True:
             savename = input("Enter filename: ")

pdcli/input_handler.py

@@ -0,0 +1,54 @@
+def singleCommand_handler(args):
+    args_dict = dict()
+    args_dict['mode'] = args.mode
+    if args.mode.upper() =='DNA':
+        args_dict['sequence'] = args.sequence
+        PrimerChecks(args.sequence).check_sequence_length()
+        PrimerChecks(args.sequence).check_valid_base()
+        args_dict['mutation_type'] = args.mutation_type
+        args_dict['position'] = args.position
+        args_dict['destination'] = args.destination
+        if args.mutation_type.upper() in ['S', 'SUB']:
+            args_dict['target'] = args.target
+        else:
+            raise ValueError("Invalid argument passed to 'MUTATION_TYPE'")
+    else:
+        raise NotImplementedError(f"{args_dict['mode']} mode not implemented (yet).")
+    return args_dict
+
+def interactive_handler():
+    args_dict = dict()
+    print('')
+    print('====================================')
+    print('======                        ======')
+    print('===     PrimerDriver v0.1.2      ===')
+    print('======                        ======')
+    print('====================================\n')
+    print('(c) 2020 Kenneth Domingo & Nomer Gutierrez\n')
+    args_dict['mode'] = input('Enter primer mode [dna/pro/char]: ')
+    if args_dict['mode'].upper() == 'DNA':
+        args_dict['sequence'] = input('Enter DNA sequence: ')
+        PrimerChecks(args_dict['sequence']).check_sequence_length()
+        PrimerChecks(args_dict['sequence']).check_valid_base()
+        args_dict['mutation_type'] = input('Enter mutation type [s/i/d]: ')
+        if args_dict['mutation_type'].upper() in ['S', 'SUB']:
+            args_dict['target'] = input('Enter target base: ')
+            args_dict['destination'] = input('Enter replacement for target base: ')
+            args_dict['position'] = int(input('Enter position of target: '))
+        elif args_dict['mutation_type'].upper() in ['I', 'INS']:
+            args_dict['target'] = None
+            args_dict['destination'] = input('Enter insertion sequence: ')
+            args_dict['position'] = int(input('Enter insertion position: '))
+        elif args_dict['mutation_type'].upper() in ['I', 'INS']:
+            args_dict['target'] = None
+            args_dict['destination'] = input('Enter starting position to delete: ')
+        else:
+            raise ValueError("Invalid argument passed to 'MUTATION_TYPE'")
+    elif args_dict['mode'].upper() == 'CHAR':
+        args_dict['sequence'] = input('Enter primer sequence: ')
+        args_dict['mutation_type'] = input('Enter mutation type [s/i/d]: ')
+        args_dict['mismatched_bases'] = input('Enter number of mismatched bases: ')
+    else:
+        raise NotImplementedError(f"{args_dict['mode']} mode not implemented (yet).")
+
+    return args_dict

sdm/static/sdm/scripts/primerclass.py → pdcli/primerclass.py

@@ -78,7 +78,7 @@ def deletion(self):
         self.forward = ''.join(seq)
 
     def characterize_primer(self):
-        with open("lut.json", "r", encoding="utf-8") as f:
+        with open("pdcli/lut.json", "r", encoding="utf-8") as f:
             lut = load(f)
         mol_weight = lut["mol_weight"]
         complement_dict = lut["complement"]
@@ -109,11 +109,11 @@ def characterize_primer(self):
             f'{self.mismatch*100:.2f}%',
             gc_end
         ]
-        print(tabulate(
+        print('\n', tabulate(
             array([col, dat]).T,
             headers=['Primer 1'],
             tablefmt='orgtbl'
-        ))
+        ), sep="")
         self.df = DataFrame(
             data=dat,
             columns=['Primer 1'],
@@ -130,7 +130,7 @@ def main(self):
         else:
             raise NotImplementedError('Invalid mutation type')
 
-        with open("lut.json", "r", encoding="utf-8") as f:
+        with open("pdcli/lut.json", "r", encoding="utf-8") as f:
             complement_dict = load(f)["complement"]
         self.rev_compl = ''.join([complement_dict[b] for b in list(self.forward[::-1])])
         self.gc_content = (self.forward.count('G') + self.forward.count('C'))/len(self.forward)