GC Clamp Property Added to Primer Class

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [Unreleased]
 ### Added
 - `equality` operator overload
+- `gc_clamp` property
 ## [0.1] - 2024-11-27
 ### Added
 - `MeltingTemperature` enum

README.md

@@ -82,6 +82,11 @@
 >>> primer1.gc_content
 0.5217391304347826
 ```
+#### GC clamp
+```pycon
+>>> primer1.gc_clamp
+1
+```
 #### Melting temperature
 ```pycon
 >>> primer1.melting_temperature()

opr/functions.py

@@ -1,6 +1,8 @@
 # -*- coding: utf-8 -*-
 """OPR functions."""
 from .params import A_WEIGHT, T_WEIGHT, C_WEIGHT, G_WEIGHT, ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
+from .params import PRIMER_SEQUENCE_VALID_RANGE_FOR_GC_CLAMP_WARNING
+from warnings import warn
 
 
 def molecular_weight_calc(sequence):
@@ -36,3 +38,17 @@ def basic_melting_temperature_calc(sequence):
     else:
         melting_temperature = 64.9 + 41 * ((g_count + c_count - 16.4) / (a_count + t_count + g_count + c_count))
     return melting_temperature
+
+
+def gc_clamp_calc(sequence):
+    """
+    Calculate GC clamp.
+
+    :param sequence: primer nucleotides sequence
+    :type sequence: str
+    :return: Number of guanine (G) or cytosine (C) bases in the last 5 bases of a primer.
+    """
+    if len(sequence) < 5:
+        warn(PRIMER_SEQUENCE_VALID_RANGE_FOR_GC_CLAMP_WARNING, RuntimeWarning)
+        return 0
+    return sequence[-5:].count('G') + sequence[-5:].count('C')

opr/params.py

@@ -19,6 +19,7 @@
 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_WARNING = "The recommended range for GC content is between 30% and 80%."
+PRIMER_SEQUENCE_VALID_RANGE_FOR_GC_CLAMP_WARNING = "The primer sequence should have at least 5 bases. GC clamp is set to 0."
 PRIMER_READ_ONLY_ATTRIBUTE_ERROR = "This attribute is read-only."
 PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR = "This attribute is not removable."
 

opr/primer.py

@@ -10,7 +10,7 @@
 from .params import DNA_COMPLEMENT_MAP
 from .params import PRIMER_ADDITION_ERROR, PRIMER_MULTIPLICATION_ERROR
 from .params import PRIMER_MELTING_TEMPERATURE_NOT_IMPLEMENTED_ERROR
-from .functions import molecular_weight_calc, basic_melting_temperature_calc
+from .functions import molecular_weight_calc, basic_melting_temperature_calc, gc_clamp_calc
 
 
 class MeltingTemperature(Enum):
@@ -40,6 +40,7 @@ def __init__(self, sequence):
         self._sequence = Primer.validate_primer(sequence)
         self._molecular_weight = None
         self._gc_content = None
+        self._gc_clamp = None
         self._melting_temperature = {
             MeltingTemperature.BASIC: None,
             MeltingTemperature.SALT_ADJUSTED: None,
@@ -197,6 +198,25 @@ def gc_content(self, _):
     def gc_content(self, _):
         raise OPRBaseError(PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR)
 
+    @property
+    def gc_clamp(self):
+        """
+        Calculate GC clamp of the primer.
+
+        :return: GC clamp of the primer
+        """
+        if self._gc_clamp is None:
+            self._gc_clamp = gc_clamp_calc(self._sequence)
+        return self._gc_clamp
+
+    @gc_clamp.setter
+    def gc_clamp(self, _):
+        raise OPRBaseError(PRIMER_READ_ONLY_ATTRIBUTE_ERROR)
+
+    @gc_clamp.deleter
+    def gc_clamp(self, _):
+        raise OPRBaseError(PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR)
+
     def melting_temperature(self, method=MeltingTemperature.BASIC):
         """
         Calculate(if needed) the melting temperature.

tests/test_calculations.py

@@ -19,6 +19,14 @@ def test_gc_content_3(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.h
     oprimer = Primer("ATTTTTT")
     assert oprimer.gc_content == 0
 
+def test_gc_clamp_1(): #Reference: https://www.oligoevaluator.com/OligoCalcServlet
+    oprimer = Primer("ATCGATCGATCGATCGATCG")
+    assert oprimer.gc_clamp == 2
+
+def test_gc_clamp_2(): #Reference: https://www.oligoevaluator.com/OligoCalcServlet
+    oprimer = Primer("ATCG")
+    assert oprimer.gc_clamp == 0
+
 def test_melt_temp_1(): #Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
     oprimer = Primer("ATCGATCGATCGATCGATCG")
     basic_melt_temp = oprimer.melting_temperature(MeltingTemperature.BASIC)