Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add/feature(repeats+doube_runs) #45

Merged
merged 9 commits into from
Jan 28, 2025
Merged
Changes from 8 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -6,6 +6,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

## [Unreleased]
### Added
- `double_runs` property
- `repeats` method
- `name` property
### Changed
- Test system modified
14 changes: 14 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -92,6 +92,20 @@
>>> primer1.single_runs
{'A': 2, 'T': 0, 'C': 0, 'G': 2}
```
#### Double run length
```pycon
>>> primer1.double_runs
{'AT': 0, 'AG': 4, 'AC': 0, 'TA': 0, 'TG': 0, 'TC': 0, 'GA': 5, 'GT': 0, 'GC': 0, 'CA': 0, 'CT': 0, 'CG': 0}
```
#### Repeats
```pycon
>>> primer1.repeats(sequence="GG", consecutive=False)
4
```
```pycon
>>> primer1.repeats(sequence="GG", consecutive=True)
0
```
#### Melting temperature
```pycon
>>> primer1.melting_temperature()
40 changes: 40 additions & 0 deletions opr/primer.py
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
# -*- coding: utf-8 -*-
"""OPR primer."""
import re
import itertools
from enum import Enum
from warnings import warn
from .errors import OPRBaseError
@@ -44,6 +46,7 @@ def __init__(self, sequence, name=DEFAULT_PRIMER_NAME):
self._gc_content = None
self._gc_clamp = None
self._single_runs = None
self._double_runs = None
self._melting_temperature = {
MeltingTemperature.BASIC: None,
MeltingTemperature.SALT_ADJUSTED: None,
@@ -225,6 +228,43 @@ def single_runs(self):
self._single_runs[base] = single_run_length(self._sequence, base)
return self._single_runs

@property
def double_runs(self):
sepandhaghighi marked this conversation as resolved.
Show resolved Hide resolved
"""
Calculate Double Runs of the primer.

It refers to how many times each 2-base pairs occurs consecutively in the primer.

:return: Dictionary of double runs (2-base pairs) and their counts in the primer
"""
if self._double_runs is None:
pairs = [''.join(pair) for pair in itertools.product(VALID_BASES, repeat=2) if pair[0] != pair[1]]
counts = {pair: 0 for pair in pairs}
for pair in counts:
counts[pair] = self.repeats(pair, consecutive=True)
self._double_runs = counts
return self._double_runs

def repeats(self, sequence, consecutive=False):
"""
Count occurrences of a subsequence in a given sequence.

:param sequence: The sequence to search within.
:type sequence: str
:param consecutive: Whether to count only consecutive repeats.
:type consecutive: bool
:return: The count of occurrences.
"""
if consecutive:
pattern = f"(?:{re.escape(sequence)})+"
matches = re.findall(f"({pattern})+", self.sequence)
result = max((len(match) // len(sequence) for match in matches), default=0)
if result == 1:
result = 0
return result
else:
return self.sequence.count(sequence)

def melting_temperature(self, method=MeltingTemperature.BASIC):
"""
Calculate(if needed) the melting temperature.
32 changes: 32 additions & 0 deletions tests/test_calculations.py
Original file line number Diff line number Diff line change
@@ -66,3 +66,35 @@ def test_single_runs_3(): # Reference: https://www.oligoevaluator.com/OligoCalc
oprimer = Primer("AAAAATTCGGGGATCCCCG")
runs = oprimer.single_runs
assert runs['A'] == 5 and runs['T'] == 2 and runs['C'] == 4 and runs['G'] == 4


def test_double_runs():
p1 = Primer("ATATCGAACACACACACA")
double_runs = p1.double_runs
print(double_runs)
true_answer = {'GT': 0, 'CA': 5, 'AT': 2, 'TA': 0, 'GC': 0, 'GA': 0, 'AG': 0, 'TG': 0, 'CG': 0, 'TC': 0, 'AC': 5, 'CT': 0}
assert len(true_answer) == len(double_runs) and all(double_runs[pair] == true_answer[pair] for pair in double_runs)


def test_repeats_1():
p = Primer("ATCG")
assert (
p.repeats(sequence="A", consecutive=False) == 1 and
p.repeats(sequence="AT", consecutive=False) == 1 and
p.repeats(sequence="AC", consecutive=False) == 0 and
p.repeats(sequence="A", consecutive=True) == 0 and
p.repeats(sequence="AT", consecutive=True) == 0
)


def test_repeats_2():
p = Primer("AAAATCGTGT")
assert (
p.repeats(sequence="AA", consecutive=True) == 2 and
p.repeats(sequence="GT", consecutive=True) == 2
)


def test_repeats_3():
p = Primer("ATCGATCGATCG")
assert p.repeats(sequence="ATCG", consecutive=True) == 3