Feature/base arch

.github/dependabot.yml

@@ -9,3 +9,4 @@ updates:
   target-branch: dev
   assignees:
       - "sadrasabouri"
+      - "AHReccese"

.github/workflows/test.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-latest, macOS-latest]
+        os: [ubuntu-20.04, windows-2022, macOS-13]
         python-version: [3.6, 3.7, 3.8, 3.9, 3.10.0, 3.11.0, 3.12.0]
     steps:
       - uses: actions/checkout@v2

AUTHORS.md

@@ -1,7 +1,9 @@
 # Authors #
 
 ----------
-- Sadra Sabouri  - Open Science Laboratory ([Github](https://github.com/sadrasabouri)) **
+- Sepand Haghighi - Open Science Laboratory ([Github](https://github.com/sepandhaghighi))
+- Sadra Sabouri - Open Science Laboratory ([Github](https://github.com/sadrasabouri))
+- AmirHosein Rostami  - Open Science Laboratory ([Github](https://github.com/AHReccese))
 
 ** **Maintainer**
 

CHANGELOG.md

@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [Unreleased]
 ### Added
 ### Changed
+## [0.1] - 2024-06-05
+### Added
+- Molecular Weight Calculation
+- Sequence Validation
+- OPR class
 
 [Unreleased]: https://github.com/openscilab/opr/compare/v0.1...dev
 [0.1]: https://github.com/openscilab/opr/compare/3598e8b...v0.1

dev-requirements.txt

@@ -0,0 +1,6 @@
+setuptools>=40.8.0
+vulture>=1.0
+bandit>=1.5.1
+pydocstyle>=3.0.0
+pytest>=4.3.1
+pytest-cov>=2.6.1

opr/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """OPR modules."""
 from .opr_param import OPR_VERSION
+from .opr_obj import OPR
 
 __version__ = OPR_VERSION

opr/opr_error.py

@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+"""OPR errors."""
+
+
+class OPRBaseError(Exception):
+    """OPR base error class."""
+
+    pass

opr/opr_obj.py

@@ -0,0 +1,95 @@
+# -*- coding: utf-8 -*-
+"""OPR modules."""
+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_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
+
+class OPR:
+    """
+    The OPR class facilitates working with the primer sequence.
+
+    >>> oprimer = OPR("ATCGATCGATCGATCGAT")
+    >>> oprimer.molecular_weight
+    """
+
+    def __init__(self, primer_sequence):
+        """
+        Initialize the Optimized Primer(OPR) instance.
+
+        :param primer_sequence: primer nucleotides sequence
+        :type primer_sequence: str
+        :return: an instance of the OPR class
+        """
+        self._sequence = OPR.validate_primer(primer_sequence)
+        self._molecular_weight = None
+
+    @staticmethod
+    def validate_primer(primer_sequence):
+        """
+        Validate the given primer sequence.
+
+        :param primer_sequence: primer nucleotides sequence
+        :type primer_sequence: any
+        :return: an uppercased primer sequence
+        """
+        if not isinstance(primer_sequence, str):
+            raise OPRBaseError(PRIMER_SEQUENCE_TYPE_ERROR)
+        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)
+
+        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
+    def sequence(self):
+        """
+        Return the primer sequence.
+
+        :return: primer sequence
+        """
+        return self._sequence
+
+    @sequence.setter
+    def sequence(self, _):
+        raise OPRBaseError(PRIMER_READ_ONLY_ATTRIBUTE_ERROR)
+
+    @sequence.deleter
+    def sequence(self, _):
+        raise OPRBaseError(PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR)
+
+    @property
+    def molecular_weight(self):
+        """
+        Calculate(if needed) the molecular weight.
+
+        :return: molecular weight
+        """
+        if self._molecular_weight:
+            return self._molecular_weight
+        a_count = self._sequence.count('A')
+        t_count = self._sequence.count('T')
+        c_count = self._sequence.count('C')
+        g_count = self._sequence.count('G')
+        # Anhydrous Molecular Weight = (An x 313.21) + (Tn x 304.2) + (Cn x 289.18) + (Gn x 329.21) - 61.96
+        self._molecular_weight = (a_count * A_WEIGHT) + (t_count * T_WEIGHT) + (c_count * C_WEIGHT) + (g_count * G_WEIGHT) - ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
+        return self._molecular_weight    
+
+    @molecular_weight.setter
+    def molecular_weight(self, _):
+        raise OPRBaseError(PRIMER_READ_ONLY_ATTRIBUTE_ERROR)
+
+    @molecular_weight.deleter
+    def molecular_weight(self, _):
+        self._molecular_weight = None

opr/opr_param.py

@@ -1,3 +1,23 @@
 # -*- coding: utf-8 -*-
 """Parameters and constants."""
 OPR_VERSION = "0.1"
+VALID_BASES = set('ATCG')
+
+PRIMER_LOWER_LENGTH = 18
+PRIMER_HIGHEST_LENGTH = 30
+PRIMER_LOWEST_GC_RANGE = 0.3
+PRIMER_HIGHEST_GC_RANGE = 0.8
+
+A_WEIGHT = 313.21
+T_WEIGHT = 304.2
+C_WEIGHT = 289.18
+G_WEIGHT = 329.21
+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_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_READ_ONLY_ATTRIBUTE_ERROR = "This attribute is read-only."
+PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR = "This attribute is not removable."
+

otherfiles/meta.yaml

@@ -31,4 +31,6 @@ about:
         Repo: https://github.com/openscilab/opr
 extra:
     recipe-maintainers:
+        - sepandhaghighi
+        - AHReccese
         - sadrasabouri

tests/test_molecular_weight.py

@@ -0,0 +1,7 @@
+from opr.opr_obj import OPR
+
+TEST_CASE_NAME = "molecular weight calculation testcase"
+
+def test_mwc():
+    oprimer = OPR("ATCGATCGATCGATCGAT")
+    assert round(oprimer.molecular_weight, 1) == 5498.7