GC content

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 - `Primer` class
 - Molecular weight calculation
+- GC content calculation
 - Sequence validation
 - Unit tests
 - `complement` method

opr/opr_obj.py

@@ -1,8 +1,9 @@
 # -*- coding: utf-8 -*-
 """OPR modules."""
+from warnings import warn
 from .opr_error import OPRBaseError
 from .opr_param import VALID_BASES
-from .opr_param import PRIMER_SEQUENCE_TYPE_ERROR, PRIMER_SEQUENCE_LENGTH_ERROR, PRIMER_SEQUENCE_VALID_BASES_ERROR, PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_ERROR
+from .opr_param import PRIMER_SEQUENCE_TYPE_ERROR, PRIMER_SEQUENCE_LENGTH_WARNING, PRIMER_SEQUENCE_VALID_BASES_ERROR, PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_WARNING
 from .opr_param import PRIMER_LOWER_LENGTH, PRIMER_HIGHEST_LENGTH, PRIMER_LOWEST_GC_RANGE, PRIMER_HIGHEST_GC_RANGE
 from .opr_param import PRIMER_READ_ONLY_ATTRIBUTE_ERROR, PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR
 from .opr_param import A_WEIGHT, T_WEIGHT, C_WEIGHT, G_WEIGHT, ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
@@ -27,6 +28,7 @@ def __init__(self, primer_sequence):
         """
         self._sequence = Primer.validate_primer(primer_sequence)
         self._molecular_weight = None
+        self._gc_content = None
 
     def reverse(self, inplace=False):
         """
@@ -72,16 +74,10 @@ def validate_primer(primer_sequence):
         primer_sequence = primer_sequence.upper()
 
         if len(primer_sequence) < PRIMER_LOWER_LENGTH or len(primer_sequence) > PRIMER_HIGHEST_LENGTH:
-            raise OPRBaseError(PRIMER_SEQUENCE_LENGTH_ERROR)
+            warn(PRIMER_SEQUENCE_LENGTH_WARNING, RuntimeWarning)
 
         if not all(base in VALID_BASES for base in primer_sequence):
             raise OPRBaseError(PRIMER_SEQUENCE_VALID_BASES_ERROR)
-
-        gc_count = primer_sequence.count('G') + primer_sequence.count('C')
-        gc_content = gc_count / len(primer_sequence)
-
-        if gc_content < PRIMER_LOWEST_GC_RANGE or gc_content > PRIMER_HIGHEST_GC_RANGE:
-            raise OPRBaseError(PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_ERROR)
         return primer_sequence
 
     @property
@@ -126,3 +122,25 @@ def molecular_weight(self, _):
     @molecular_weight.deleter
     def molecular_weight(self, _):
         self._molecular_weight = None
+
+    @property
+    def gc_content(self):
+        """
+        Calculate gc content.
+
+        :return: gc content
+        """
+        if self._gc_content is None:
+            gc_count = self._sequence.count('G') + self._sequence.count('C')
+            self._gc_content = gc_count / len(self._sequence)
+        if self._gc_content < PRIMER_LOWEST_GC_RANGE or self._gc_content > PRIMER_HIGHEST_GC_RANGE:
+            warn(PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_WARNING, RuntimeWarning)
+        return self._gc_content
+
+    @gc_content.setter
+    def gc_content(self, _):
+        raise OPRBaseError(PRIMER_READ_ONLY_ATTRIBUTE_ERROR)
+
+    @gc_content.deleter
+    def gc_content(self, _):
+        raise OPRBaseError(PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR)

opr/opr_param.py

@@ -16,8 +16,8 @@
 ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT = 61.96
 
 PRIMER_SEQUENCE_TYPE_ERROR = "Primer sequence should be a string variable."
-PRIMER_SEQUENCE_LENGTH_ERROR = "Primer length should be between 18 and 30 nucleotides."
+PRIMER_SEQUENCE_LENGTH_WARNING = "The recommended range for primer length is between 18 and 30."
 PRIMER_SEQUENCE_VALID_BASES_ERROR = "Primer sequence should only contain the nucleotide bases A, T, C, and G."
-PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_ERROR = "Primer GC content should be between 30% and 80%."
+PRIMER_SEQUENCE_VALID_GC_CONTENT_RANGE_WARNING = "The recommended range for GC content is between 30% and 80%."
 PRIMER_READ_ONLY_ATTRIBUTE_ERROR = "This attribute is read-only."
 PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR = "This attribute is not removable."

tests/test_calculations.py

@@ -0,0 +1,21 @@
+from opr import Primer
+
+TEST_CASE_NAME = "Calculations tests"
+
+def test_mwc():
+    oprimer = Primer("ATCGATCGATCGATCGAT")
+    assert round(oprimer.molecular_weight, 1) == 5498.7
+
+
+def test_gc_content_1(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+    oprimer = Primer("ATCG")
+    assert oprimer.gc_content == 0.5
+
+
+def test_gc_content_2(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+    oprimer = Primer("ATTCG")
+    assert oprimer.gc_content == 0.4
+
+def test_gc_content_3(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
+    oprimer = Primer("ATTTTTT")
+    assert oprimer.gc_content == 0