codeine 0.0.0__tar.gz → 0.1.0__tar.gz

codeine-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Michael Dunne
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

codeine-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: codeine
+Version: 0.1.0
+Author: Michael Peter Dunne
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+# 🧬 Codeine
+
+**Codeine** is a Python library for generating synonymous protein-coding sequences under biological constraints.
+
+
+## Installation & documentation
+
+**Codeine** is available on PyPI:
+
+```bash
+pip install codeine
+```
+
+Full documentation: **https://codeine.readthedocs.io/**.
+
+## Quick start
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTIIALSYIFCLVF')
+
+print(space.n_valid_sequences)
+print(space.sample())
+```
+
+
+## Overview
+
+A protein sequence can typically be encoded by an enormous number of synonymous DNA/RNA coding sequences.
+
+For biotechnological applications such as recombinant expression, we typically must choose a coding sequence while respecting one or more practical constraints, for example:
+- avoiding restriction enzyme sites,
+- avoiding nucleotide homopolymers,
+- fixing specific codons,
+- mutating relative to a reference sequence.
+
+Identifying valid coding sequences under such constraints quickly becomes challenging, especially for longer protein sequences.
+
+**Codeine** represents the complete space of valid coding sequences for a given protein and experimental setup. It enables highly efficient sampling, enumeration and mutation library design while guaranteeing that the generated sequences satisfy user-specified constraints.
+
+## Examples
+
+Count valid sequences:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+print(space.n_valid_sequences)
+```
+
+Sample a single valid sequences:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+seq = space.sample()
+print(seq)
+```
+
+Sample many:
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+for seq in space.sample(n=5):
+    print(seq)
+```
+
+Apply restrictions:
+
+```python
+from codeine import CodingSpace, RestrictionSite
+
+space = CodingSpace(
+    'MKTLEFQNGSCPRYKKL',
+    forbidden_motifs=[
+        RestrictionSite.EcoRI,
+        RestrictionSite.BamHI,
+        'CTGCAG',
+    ],
+    codon_restrictions={
+        2: 'AAG',
+        16: 'AAG',
+    },
+    max_homopolymer=4,
+)
+
+print(space.n_valid_sequences)
+print(space.sample())
+```
+
+Use custom codon weights to change sampling distribution:
+
+```python
+from codeine import CodingSpace, CodonWeights
+
+weights = CodonWeights.ecoli()
+
+space = CodingSpace("MKTLEFQNGSCPRYKKL", codon_weights=weights)
+
+seq = space.sample()
+print(seq)
+```
+
+Nonstandard translation tables and RNA:
+
+```python
+from codeine import CodingSpace, TranslationTable
+
+table = TranslationTable(table_id=2, rna=True)
+
+space = CodingSpace("MKTLEFQNGSCPRYKKL", translation_table=table)
+
+seq = space.sample()
+print(seq)
+```
+
+Enumerate all sequences (only recommended for small spaces):
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('CYIQNCPLG')
+
+for sequence in space:
+    print(sequence)
+```
+
+Explore mutants of a chosen reference sequence:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+reference = space.sample()
+
+mutants = space.mutants(
+    reference,
+    free_positions=range(5, 14),
+    min_nts=2,
+    max_nts=5,
+)
+
+mutant = mutants.sample()
+print(mutant)
+```

codeine-0.1.0/README.md

@@ -0,0 +1,153 @@
+# 🧬 Codeine
+
+**Codeine** is a Python library for generating synonymous protein-coding sequences under biological constraints.
+
+
+## Installation & documentation
+
+**Codeine** is available on PyPI:
+
+```bash
+pip install codeine
+```
+
+Full documentation: **https://codeine.readthedocs.io/**.
+
+## Quick start
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTIIALSYIFCLVF')
+
+print(space.n_valid_sequences)
+print(space.sample())
+```
+
+
+## Overview
+
+A protein sequence can typically be encoded by an enormous number of synonymous DNA/RNA coding sequences.
+
+For biotechnological applications such as recombinant expression, we typically must choose a coding sequence while respecting one or more practical constraints, for example:
+- avoiding restriction enzyme sites,
+- avoiding nucleotide homopolymers,
+- fixing specific codons,
+- mutating relative to a reference sequence.
+
+Identifying valid coding sequences under such constraints quickly becomes challenging, especially for longer protein sequences.
+
+**Codeine** represents the complete space of valid coding sequences for a given protein and experimental setup. It enables highly efficient sampling, enumeration and mutation library design while guaranteeing that the generated sequences satisfy user-specified constraints.
+
+## Examples
+
+Count valid sequences:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+print(space.n_valid_sequences)
+```
+
+Sample a single valid sequences:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+seq = space.sample()
+print(seq)
+```
+
+Sample many:
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+for seq in space.sample(n=5):
+    print(seq)
+```
+
+Apply restrictions:
+
+```python
+from codeine import CodingSpace, RestrictionSite
+
+space = CodingSpace(
+    'MKTLEFQNGSCPRYKKL',
+    forbidden_motifs=[
+        RestrictionSite.EcoRI,
+        RestrictionSite.BamHI,
+        'CTGCAG',
+    ],
+    codon_restrictions={
+        2: 'AAG',
+        16: 'AAG',
+    },
+    max_homopolymer=4,
+)
+
+print(space.n_valid_sequences)
+print(space.sample())
+```
+
+Use custom codon weights to change sampling distribution:
+
+```python
+from codeine import CodingSpace, CodonWeights
+
+weights = CodonWeights.ecoli()
+
+space = CodingSpace("MKTLEFQNGSCPRYKKL", codon_weights=weights)
+
+seq = space.sample()
+print(seq)
+```
+
+Nonstandard translation tables and RNA:
+
+```python
+from codeine import CodingSpace, TranslationTable
+
+table = TranslationTable(table_id=2, rna=True)
+
+space = CodingSpace("MKTLEFQNGSCPRYKKL", translation_table=table)
+
+seq = space.sample()
+print(seq)
+```
+
+Enumerate all sequences (only recommended for small spaces):
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('CYIQNCPLG')
+
+for sequence in space:
+    print(sequence)
+```
+
+Explore mutants of a chosen reference sequence:
+
+```python
+from codeine import CodingSpace
+
+space = CodingSpace('MKTLEFQNGSCPRYKKL')
+
+reference = space.sample()
+
+mutants = space.mutants(
+    reference,
+    free_positions=range(5, 14),
+    min_nts=2,
+    max_nts=5,
+)
+
+mutant = mutants.sample()
+print(mutant)
+```

codeine-0.1.0/codeine/__init__.py

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+from codeine.space.coding import CodingSpace
+from codeine.space.mutation import MutationSpace
+
+from codeine.translation.tables import TranslationTable
+from codeine.translation.weights import CodonWeights
+
+from codeine.motifs.restriction import RestrictionSite
+
+__all__ = [
+    'CodingSpace',
+    'CodonWeights',
+    'MutationSpace',
+    'RestrictionSite',
+    'TranslationTable'
+]