unite result classes to Design_Signle and Design_Plate

ribokit · Mar 16, 2016 · 3f30afe · 3f30afe
1 parent f4d561d
commit 3f30afe
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diff --git a/primerize/__init__.py b/primerize/__init__.py
@@ -1,7 +1,7 @@
 from .thermo import Nearest_Neighbor
 from .util import Assembly, Plate_96Well, Mutation, Construct_List
-from .primerize_1d import Primerize_1D
-from .primerize_2d import Primerize_2D
+from .primerize_1d import Primerize_1D, Design_Single
+from .primerize_2d import Primerize_2D, Design_Plate
 from .primerize_3d import Primerize_3D
 
-__version__ = '1.2.0'
+__version__ = '1.2.1'
diff --git a/primerize/primerize_1d.py b/primerize/primerize_1d.py
@@ -16,9 +16,11 @@
     from .util import *
 
 
-class Design_1D(object):
-    def __init__(self, sequence, name, is_success, primer_set, params, data):
-        (self.sequence, self.name, self.is_success, self.primer_set, self._params, self._data) = (sequence, name, is_success, primer_set, params, data)
+class Design_Single(object):
+    def __init__(self, init_dict):
+        for key in init_dict:
+            key_rename = '_' + key if key in ['params', 'data'] else key
+            setattr(self, key_rename, init_dict[key])
 
     def __repr__(self):
         return '\033[94m%s\033[0m {\n\033[95msequence\033[0m = \'%s\', \n\033[95mname\033[0m = \'%s\', \n\033[95mis_success\033[0m = \033[41m%s\033[0m, \n\033[95mprimer_set\033[0m = %s, \n\033[95mparams\033[0m = %s, \n\033[95mdata\033[0m = {\n    \033[92m\'misprime_score\'\033[0m: %s, \n    \033[92m\'assembly\'\033[0m: %s, \n    \033[92m\'warnings\'\033[0m: %s\n}' % (self.__class__, self.sequence, self.name, self.is_success, repr(self.primer_set), repr(self._params), repr(self._data['misprime_score']), repr(self._data['assembly']), repr(self._data['warnings']))
@@ -208,7 +210,7 @@ def design(self, sequence, MIN_TM=None, NUM_PRIMERS=None, MIN_LENGTH=None, MAX_L
 
         params = {'MIN_TM': MIN_TM, 'NUM_PRIMERS': NUM_PRIMERS, 'MIN_LENGTH': MIN_LENGTH, 'MAX_LENGTH': MAX_LENGTH, 'N_BP': N_BP, 'COL_SIZE': self.COL_SIZE, 'WARN_CUTOFF': self.WARN_CUTOFF}
         data = {'misprime_score': misprime_score, 'assembly': assembly, 'warnings': warnings}
-        return Design_1D(sequence, name, is_success, primer_set, params, data)
+        return Design_Single({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'params': params, 'data': data})
 
 
 

diff --git a/primerize/primerize_2d.py b/primerize/primerize_2d.py
@@ -5,16 +5,19 @@
 
 if __package__ is None or not __package__:
     from util import *
-    from primerize_1d import Primerize_1D, Design_1D
+    from primerize_1d import Primerize_1D, Design_Single
 else:
     from .util import *
-    from .primerize_1d import Primerize_1D, Design_1D
+    from .primerize_1d import Primerize_1D, Design_Single
 
 
-class Design_2D(object):
-    def __init__(self, sequence, name, is_success, primer_set, params, data):
-        (self.sequence, self.name, self.is_success, self.primer_set, self._params, self._data) = (sequence, name, is_success, primer_set, params, data)
-        self._data['illustration'] = draw_region(self.sequence, self._params)
+class Design_Plate(object):
+    def __init__(self, init_dict):
+        for key in init_dict:
+            key_rename = '_' + key if key in ['params', 'data'] else key
+            setattr(self, key_rename, init_dict[key])
+        if self.get('TYPE') == 'Mutate-and-Map':
+            self._data['illustration'] = draw_region(self.sequence, self._params)
 
     def __repr__(self):
         return '\033[94m%s\033[0m {\n\033[95msequence\033[0m = \'%s\', \n\033[95mname\033[0m = \'%s\', \n\033[95mis_success\033[0m = \033[41m%s\033[0m, \n\033[95mprimer_set\033[0m = %s, \n\033[95mparams\033[0m = %s, \n\033[95mdata\033[0m = {\n    \033[92m\'constructs\'\033[0m: %s, \n    \033[92m\'assembly\'\033[0m: %s, \n    \033[92m\'plates\'\033[0m: %s\n}' % (self.__class__, self.sequence, self.name, self.is_success, repr(self.primer_set), repr(self._params), repr(self._data['constructs']), repr(self._data['assembly']), repr(self._data['plates']))
@@ -71,7 +74,7 @@ def echo(self, key=''):
                 return output[:-1]
             elif key == 'assembly':
                 return self._data['assembly'].echo()
-            elif key == 'region':
+            elif key == 'region' and self.get('TYPE') == 'Mutate-and-Map':
                 return '\n'.join(self._data['illustration']['lines'])
 
             elif not key:
@@ -136,7 +139,7 @@ def reset(self):
 
 
     def design(self, sequence, primer_set=[], offset=None, which_muts=None, which_lib=None, prefix=None, is_force=False):
-        if isinstance(sequence, Design_1D):
+        if isinstance(sequence, Design_Single):
             design_1d = sequence
             sequence = design_1d.sequence
             primer_set = design_1d.primer_set
@@ -172,9 +175,9 @@ def design(self, sequence, primer_set=[], offset=None, which_muts=None, which_li
                 is_success = False
 
         if not is_success:
-            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_BP': N_BP}
+            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_BP': N_BP, 'type': 'Mutate-and-Map'}
             data = {'plates': [], 'assembly': [], 'constructs': []}
-            return Design_2D(sequence, name, is_success, primer_set, params, data)
+            return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'params': params, 'data': data})
 
         if not which_muts:
             which_muts = list(range(1 - offset, N_BP + 1 - offset))
@@ -189,9 +192,9 @@ def design(self, sequence, primer_set=[], offset=None, which_muts=None, which_li
         (primers, is_success) = get_primer_index(primer_set, sequence)
         if not is_success:
             print('\033[41mFAIL\033[0m: \033[91mMismatch\033[0m of given \033[92mprimer_set\033[0m for given \033[92msequence\033[0m.\n')
-            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP}
+            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP, 'type': 'Mutate-and-Map'}
             data = {'plates': [], 'assembly': [], 'constructs': []}
-            return Design_2D(sequence, name, is_success, primer_set, params, data)
+            return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'params': params, 'data': data})
 
         assembly = Assembly(sequence, primers, name, self.COL_SIZE)
         constructs = Construct_List()
@@ -212,9 +215,9 @@ def design(self, sequence, primer_set=[], offset=None, which_muts=None, which_li
             print(traceback.format_exc())
             print('\033[41mERROR\033[0m: Primerize 2D design() encountered error.\n')
 
-        params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP}
+        params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP, 'type': 'Mutate-and-Map'}
         data = {'plates': plates, 'assembly': assembly, 'constructs': constructs}
-        return Design_2D(sequence, name, is_success, primer_set, params, data)
+        return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'params': params, 'data': data})
 
 
 

diff --git a/primerize/primerize_3d.py b/primerize/primerize_3d.py
@@ -5,69 +5,12 @@
 
 if __package__ is None or not __package__:
     from util import *
-    from primerize_1d import Primerize_1D, Design_1D
+    from primerize_1d import Primerize_1D, Design_Single
+    from primerize_2d import Design_Plate
 else:
     from .util import *
-    from .primerize_1d import Primerize_1D, Design_1D
-
-
-class Design_3D(object):
-    def __init__(self, sequence, name, is_success, primer_set, structures, params, data):
-        (self.sequence, self.name, self.is_success, self.primer_set, self.structures, self._params, self._data) = (sequence, name, is_success, primer_set, structures, params, data)
-
-    def __repr__(self):
-        pass
-
-    def __str__(self):
-        return self.echo()
-
-
-    def get(self, key):
-        pass
-
-
-    def save(self, key='', path='./', name=None):
-        if self.is_success:
-            if name is None: name = self.name
-            key = key.lower()
-            if key == 'table':
-                save_plates_excel(self._data['plates'], self._params['N_PLATE'], self._params['N_PRIMER'], name, path)
-            elif key == 'image':
-                save_plate_layout(self._data['plates'], self._params['N_PLATE'], self._params['N_PRIMER'], name, path)
-            elif key == 'construct':
-                save_construct_key(self._data['constructs'], name, path, self._params['which_lib'])
-            elif key == 'assembly':
-                self._data['assembly'].save(path, name)
-
-            elif not key:
-                for key in ['table', 'image', 'construct', 'assembly']:
-                    self.save(key, path, name)
-            else:
-                raise AttributeError('\033[41mERROR\033[0m: Unrecognized key \033[92m%s\033[0m for \033[94m%s.save()\033[0m.\n' % (key, self.__class__))
-        else:
-            raise UnboundLocalError('\033[41mFAIL\033[0m: Result of key \033[92m%s\033[0m unavailable for \033[94m%s\033[0m where \033[94mis_cucess\033[0m = \033[41mFalse\033[0m.\n' % (key, self.__class__))
-
-
-    def echo(self, key=''):
-        if self.is_success:
-            key = key.lower()
-            if key == 'plate':
-                output = ''
-                for i in range(len(self._data['plates'][0])):
-                    for j in range(len(self._data['plates'])):
-                        output += 'Plate \033[95m%d\033[0m; Primer \033[92m%d\033[0m\n' % (i + 1, j + 1)
-                        output += self._data['plates'][j][i].echo(self.primer_set[j])
-                return output[:-1]
-            elif key == 'assembly':
-                return self._data['assembly'].echo()
-
-            elif not key:
-                return self.echo('assembly') + '\n\n' + self.echo('plate')
-            else:
-                raise AttributeError('\033[41mERROR\033[0m: Unrecognized key \033[92m%s\033[0m for \033[94m%s.echo()\033[0m.\n' % (key, self.__class__))
-        else:
-            raise UnboundLocalError('\033[41mFAIL\033[0m: Result of key \033[92m%s\033[0m unavailable for \033[94m%s\033[0m where \033[94mis_cucess\033[0m = \033[41mFalse\033[0m.\n' % (key, self.__class__))
-
+    from .primerize_1d import Primerize_1D, Design_Single
+    from .primerize_2d import Design_Plate
 
 
 class Primerize_3D(object):
@@ -135,7 +78,7 @@ def reset(self):
 
 
     def design(self, sequence, primer_set=[], offset=None, structures=[], N_mutations=None, which_lib=None, which_muts=[], prefix=None, is_single=None, is_fillWT=False, is_force=False):
-        if isinstance(sequence, Design_1D):
+        if isinstance(sequence, Design_Single):
             design_1d = sequence
             sequence = design_1d.sequence
             primer_set = design_1d.primer_set
@@ -176,9 +119,9 @@ def design(self, sequence, primer_set=[], offset=None, structures=[], N_mutation
                 is_success = False
 
         if not is_success:
-            params = {'offset': offset, 'N_mutations': N_mutations, 'which_lib': which_lib, 'N_BP': N_BP}
+            params = {'offset': offset, 'N_mutations': N_mutations, 'which_lib': which_lib, 'N_BP': N_BP, 'type': 'Mutation/Rescue'}
             data = {'plates': [], 'assembly': [], 'constructs': []}
-            return Design_3D(sequence, name, is_success, primer_set, structures, params, data)
+            return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'structures': structures, 'params': params, 'data': data})
 
         if not which_muts:
             which_muts = list(range(1 - offset, N_BP + 1 - offset))
@@ -190,9 +133,9 @@ def design(self, sequence, primer_set=[], offset=None, structures=[], N_mutation
         (primers, is_success) = get_primer_index(primer_set, sequence)
         if not is_success:
             print('\033[41mFAIL\033[0m: \033[91mMismatch\033[0m of given \033[92mprimer_set\033[0m for given \033[92msequence\033[0m.\n')
-            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_BP': N_BP}
+            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_BP': N_BP, 'type': 'Mutation/Rescue'}
             data = {'plates': [], 'assembly': [], 'constructs': []}
-            return Design_3D(sequence, name, is_success, primer_set, structures, params, data)
+            return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'structures': structures, 'params': params, 'data': data})
 
         assembly = Assembly(sequence, primers, name, self.COL_SIZE)
         constructs = Construct_List()
@@ -203,9 +146,9 @@ def design(self, sequence, primer_set=[], offset=None, structures=[], N_mutation
                 bps.remove(pair)
         if not bps:
             print('\033[41mFAIL\033[0m: \033[91mNo\033[0m base-pairs exist within given \033[92mstructures\033[0m and \033[92mwhich_muts\033[0m.\n')
-            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_BP': N_BP}
+            params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_BP': N_BP, 'type': 'Mutation/Rescue'}
             data = {'plates': [], 'assembly': assembly, 'constructs': constructs}
-            return Design_3D(sequence, name, is_success, primer_set, structures, params, data)
+            return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'structures': structures, 'params': params, 'data': data})
 
 
         N_constructs = (len(bps) - N_mutations + 1) * (is_single * 2 + 1) + 1
@@ -240,8 +183,8 @@ def design(self, sequence, primer_set=[], offset=None, structures=[], N_mutation
             print(traceback.format_exc())
             print('\033[41mERROR\033[0m: Primerize 3D design() encountered error.\n')
 
-        params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP}
+        params = {'offset': offset, 'which_muts': which_muts, 'which_lib': which_lib, 'N_mutations': N_mutations, 'is_single': is_single, 'N_PRIMER': N_primers, 'N_PLATE': N_plates, 'N_CONSTRUCT': N_constructs, 'N_BP': N_BP, 'type': 'Mutation/Rescue'}
         data = {'plates': plates, 'assembly': assembly, 'constructs': constructs}
-        return Design_3D(sequence, name, is_success, primer_set, structures, params, data)
+        return Design_Plate({'sequence': sequence, 'name': name, 'is_success': is_success, 'primer_set': primer_set, 'structures': structures, 'params': params, 'data': data})
 
 
diff --git a/primerize/util.py b/primerize/util.py
@@ -651,3 +651,6 @@ def mutate_primers(plates, primers, primer_set, offset, constructs, which_lib=1,
                 plates[p][plate_num].set(well_tag, well_name, mut_primer)
 
     return plates
+
+
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -651,3 +651,6 @@ def mutate_primers(plates, primers, primer_set, offset, constructs, which_lib=1,
		plates[p][plate_num].set(well_tag, well_name, mut_primer)

		return plates