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Unverified Commit 591b3e30 authored by Jeroen F.J. Laros's avatar Jeroen F.J. Laros
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Package rename.

parent d60c01b3
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.gitignore
View file @ 591b3e30
*.egg-info
*.pyc
.cache/
.tox/
build/
dist/
docs/Makefile
docs/_build/
examples/.ipynb_checkpoints/
mutalyzer_backtranslate.egg-info
README.rst
View file @ 591b3e30
......@@ -5,14 +5,14 @@ Back translation
:target: https://github.com/mutalyzer/backtranslate/graphs/commit-activity
.. image:: https://travis-ci.org/mutalyzer/backtranslate.svg?branch=master
:target: https://travis-ci.org/mutalyzer/backtranslate
.. image:: https://readthedocs.org/projects/simplerpc/badge/?version=latest
:target: https://backtranslate.readthedocs.io/en/latest
.. image:: https://readthedocs.org/projects/mutalyzer-backtranslate/badge/?version=latest
:target: https://mutalyzer-backtranslate.readthedocs.io/en/latest
.. image:: https://img.shields.io/github/release-date/mutalyzer/backtranslate.svg
:target: https://github.com/mutalyzer/backtranslate/releases
.. image:: https://img.shields.io/github/release/mutalyzer/backtranslate.svg
:target: https://github.com/mutalyzer/backtranslate/releases
.. image:: https://img.shields.io/pypi/v/backtranslate.svg
:target: https://pypi.org/project/backtranslate/
.. image:: https://img.shields.io/pypi/v/mutalyzer-backtranslate.svg
:target: https://pypi.org/project/mutalyzer-backtranslate/
.. image:: https://img.shields.io/github/languages/code-size/mutalyzer/backtranslate.svg
:target: https://github.com/mutalyzer/backtranslate
.. image:: https://img.shields.io/github/languages/count/mutalyzer/backtranslate.svg
......@@ -30,4 +30,4 @@ nucleotides.
Please see ReadTheDocs_ for the latest documentation.
.. _ReadTheDocs: https://backtranslate.readthedocs.io
.. _ReadTheDocs: https://mutalyzer-backtranslate.readthedocs.io
docs/api.rst 0 → 100644
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API documentation
=================
Main library
------------
.. automodule:: mutalyzer_backtranslate.backtranslate
:members:
Utils
-----
.. automodule:: mutalyzer_backtranslate.util
:members:
docs/conf.py 0 → 100644
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import os
import subprocess
import sys
subprocess.call('pip install ..', shell=True)
from mutalyzer_backtranslate import _get_metadata
author = _get_metadata('Author')
copyright = _get_metadata('Author')
project = _get_metadata('Name')
release = _get_metadata('Version')
autoclass_content = 'both'
extensions = ['sphinx.ext.autodoc']
master_doc = 'index'
docs/index.rst
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......@@ -8,4 +8,5 @@
install
usage
library
api
credits
docs/install.rst
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......@@ -5,7 +5,7 @@ The software is distributed via PyPI_, it can be installed with ``pip``:
::
pip install backtranslate
pip install mutalyzer-backtranslate
From source
......@@ -21,5 +21,5 @@ the following commands.
pip install .
.. _PyPI: https://pypi.org/project/backtranslate/
.. _PyPI: https://pypi.org/project/mutalyzer-backtranslate/
.. _GitHub: https://github.com/mutalyzer/backtranslate
docs/library.rst
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......@@ -6,7 +6,7 @@ nucleotides.
.. code:: python
>>> from backtranslate import BackTranslate
>>> from mutalyzer_backtranslate import BackTranslate
>>>
>>> # Create a class instance, optionally giving the translation table id.
>>> bt = BackTranslate()
......@@ -41,7 +41,7 @@ To get substitutions in a readable format, we can use the following:
.. code:: python
>>> from backtranslate.util import subst_to_cds
>>> from mutalyzer_backtranslate.util import subst_to_cds
>>>
>>> substitutions = bt.without_dna('W', '*')
>>>
......
examples/heatmap.ipynb
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......@@ -10,9 +10,7 @@
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [
{
"name": "stdout",
......@@ -29,15 +27,13 @@
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [],
"source": [
"from collections import defaultdict\n",
"\n",
"from backtranslate import BackTranslate\n",
"from backtranslate.util import protein_letters"
"from mutalyzer_backtranslate import BackTranslate\n",
"from mutalyzer_backtranslate.util import protein_letters"
]
},
{
......@@ -50,9 +46,7 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"metadata": {},
"outputs": [],
"source": [
"bt = BackTranslate()"
......@@ -67,10 +61,8 @@
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"table = []\n",
......@@ -90,14 +82,12 @@
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
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\n",
"image/png": 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\n",
"text/plain": [
"<Figure size 432x288 with 2 Axes>"
]
......@@ -125,14 +115,12 @@
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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jVdUjVfWaqprtvn72A+d1f1dPqGZD3/2Q5sjbMOwB7prCt2G4ELia3lHyQ93HpZMe6mXsD4E7kjwMbAD+fMLzvEj3r41PAw8Cj9D7+pv8qyaTO4EvA69Psj/JNcBW4C1JnqT3L5GtUzjjXwOnATu7r52/m8IZp4KvjJWkxjV7RC9J6jH0ktQ4Qy9JjTP0ktQ4Qy9JjTP0ktQ4Qy9JjTP0ktS4/wezN8bS38P1PgAAAABJRU5ErkJggg==\n",
"image/png": 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EvcBdY34LhEEuAK6idzT8SPdxybiHehX7I+COJI8Cm4A/H/M8P6H7W8XngYeBx+h9/439JfRJ7gS+Cpyd5ECSq4HtwNuTPE3vbxxj/Z/UZpnxr4BTgd3d987frsAZxzfPyvubjCRpWM0euUvSa5lxl6QGGXdJapBxl6QGGXdJapBxl6QGGXdJatD/AT89wfiOemvIAAAAAElFTkSuQmCC\n",
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
......@@ -167,10 +155,8 @@
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
......@@ -219,9 +205,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.3"
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 0
"nbformat_minor": 1
}
%% Cell type:markdown id: tags:
# Back translation
%% Cell type:code id: tags:
``` python
%pylab inline
```
%%%% Output: stream
Populating the interactive namespace from numpy and matplotlib
%% Cell type:code id: tags:
``` python
from collections import defaultdict
from backtranslate import BackTranslate
from backtranslate.util import protein_letters
from mutalyzer_backtranslate import BackTranslate
from mutalyzer_backtranslate.util import protein_letters
```
%% Cell type:markdown id: tags:
Create a reverse translation class instance.
%% Cell type:code id: tags:
``` python
bt = BackTranslate()
```
%% Cell type:markdown id: tags:
For each pair of amino acids, calculate the number of one-nucleotide substitutions that transform one amino acid into the other.
%% Cell type:code id: tags:
``` python
table = []
for i in protein_letters:
table.append([])
for j in protein_letters:
s = bt.without_dna(i, j)
table[-1].append(int(sum(list(map(len, s.values())))))
```
%% Cell type:markdown id: tags:
Visualise the resutling matrix.
%% Cell type:code id: tags:
``` python
imshow(table, interpolation='nearest')
xticks(range(21), protein_letters)
yticks(range(21), protein_letters)
set_cmap('cool')
colorbar();
```
%%%% Output: display_data
[Hidden Image Output]
%% Cell type:markdown id: tags:
Visualise the distribution of values in the matrix.
%% Cell type:code id: tags:
``` python
d = defaultdict(int)
for row in table:
for element in row:
d[element] += 1
ind = sorted(d.keys())
values = []
for i in ind:
values.append(d[i])
bar(ind, values);
```
%%%% Output: display_data
[Hidden Image Output]
%% Cell type:markdown id: tags:
Print some summaries.
%% Cell type:code id: tags:
``` python
total = 21 ** 2
total_p = total / 100
imperfect = sum(values[2:])
print('\n{} substitutions in total.'.format(total))
print('{:3} impossible substitutions ({:.2f}%).'.format(values[0], values[0] / total_p))
print('{:3} perfect substitutions ({:.2f}%).'.format(values[1], values[1] / total_p))
print('{:3} imperfect substitutions ({:.2f}%).'.format(imperfect, imperfect / total_p))
possible = sum(values[1:])
possible_p = possible / 100
print('\n{:3} possible substitutions, of which {:.2f}% is perfect and {:.2f}% is imperfect.'.format(
possible, values[1] / possible_p, imperfect / possible_p))
```
%%%% Output: stream
441 substitutions in total.
252 impossible substitutions (57.14%).
130 perfect substitutions (29.48%).
59 imperfect substitutions (13.38%).
189 possible substitutions, of which 68.78% is perfect and 31.22% is imperfect.
......
backtranslate/backtranslate.py → mutalyzer_backtranslate/backtranslate.py
View file @ 591b3e30
......@@ -43,8 +43,7 @@ def reverse_translation_table(table_id=1):
class BackTranslate(object):
"""Back translation."""
def __init__(self, table_id=1):
"""Initialise the class.
"""
:arg int table_id: Translation table id.
"""
self._back_table = reverse_translation_table(table_id)
......
setup.cfg
View file @ 591b3e30
[metadata]
name = backtranslate
version = 0.1.2
name = mutalyzer_backtranslate
version = 0.1.3
description = Functions for reverse translation.
long_description = file: README.rst
author = LUMC, Jeroen F.J. Laros
......@@ -28,4 +28,4 @@ tests_require =
[options.entry_points]
console_scripts =
backtranslate = backtranslate.cli:main
backtranslate = mutalyzer_backtranslate.cli:main
tests/test_backtranslate.py
View file @ 591b3e30
"""Tests for the backtranslate.backtranslate module."""
from backtranslate.backtranslate import BackTranslate, cmp_subst
"""Tests for the backtranslate module."""
from mutalyzer_backtranslate.backtranslate import BackTranslate, cmp_subst
class TestParser(object):
......
tests/test_cli.py
View file @ 591b3e30
......@@ -6,7 +6,7 @@ from io import StringIO
from fake_open import md5_check
from backtranslate import cli
from mutalyzer_backtranslate import cli
class TestParser(object):
......
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