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backtranslate
Commits
591b3e30
Unverified
Commit
591b3e30
authored
Jun 19, 2020
by
Jeroen F.J. Laros
Browse files
Package rename.
parent
d60c01b3
Changes
15
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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
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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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This diff is collapsed.
Click to expand it.
backtranslate/__init__.py
→
mutalyzer_
backtranslate/__init__.py
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591b3e30
File moved
backtranslate/backtranslate.py
→
mutalyzer_
backtranslate/backtranslate.py
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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
)
...
...
backtranslate/cli.py
→
mutalyzer_
backtranslate/cli.py
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591b3e30
File moved
backtranslate/util.py
→
mutalyzer_
backtranslate/util.py
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591b3e30
File moved
setup.cfg
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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
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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
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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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