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MICS_Biomathematics
bioinfo
VariantAnnotator
Commits
8dc9bb3d
Commit
8dc9bb3d
authored
Feb 17, 2021
by
Pradat Yoann
Browse files
v1.1 change setup.py and update ensembl-vep
parent
4f4c4bae
Changes
20
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Makefile
View file @
8dc9bb3d
PYTHON
?=
python
PYTEST
?=
pytest
CTAGS
?=
ctags
PIP
?=
pip
# .PHONY defines parts of the makefile that are not dependant on any specific file
# This is most often used to store functions
.PHONY
=
h
elp
test
tags
clean
.PHONY
=
clean dev
el
o
p
install
tags
test
# Defines the default target that `make` will to try to make, or in the case of a phony target, execute the specified commands
# This target is executed whenever we just type `make`
.DEFAULT_GOAL
=
help
develop
:
@
echo
"---------------Install varannot in develop mode-----------------"
$(PYTHON)
-m
pip
install
-e
.
# The @ makes sure that the command itself isn't echoed in the terminal
help
:
@
echo
"---------------HELP-----------------"
@
echo
"make setup to setup the project"
@
echo
"make test to run the tests"
@
echo
"make clean to remove build/dev files"
@
echo
"make install to install"
@
echo
"------------------------------------"
install
:
@
echo
"---------------Install varannot-----------------"
$(PYTHON)
setup.py
install
tags
:
$(CTAGS)
--python-kinds
=
-i
--exclude
=
*
/tests/
*
-R
.
test
:
$(PIP)
install
--upgrade
pytest pytest-cov
@
echo
"---------------Run varannot tests-----------------"
$(PYTHON)
-m
pip
install
pytest pytest-cov
$(PYTEST)
--cov-config
=
.coveragerc
--cov-report
term-missing
--cov
.
.
codecov
:
bash <
(
curl
-s
https://codecov.io/bash
)
-t
c8bcf054-f0cb-4bf1-8866-1b862905ef89
build
:
@
echo
"---------------Build variant_annotator-----------------"
$(PYTHON)
-m
pip
install
--user
--upgrade
setuptools wheel
$(PYTHON)
setup.py sdist bdist_wheel
install
:
@
echo
"---------------Install variant_annotator-----------------"
git submodule update
--init
$(PIP)
install
--upgrade
pip setuptools wheel
$(PIP)
install
-r
reqs/requirements.txt
$(PIP)
install
.
update
:
@
echo
"---------------Update vcf2maf-----------------"
cd
tools/vcf2maf
...
...
@@ -56,3 +42,6 @@ clean:
rm
-rf
build
rm
-rf
dist
rm
-rf
*
.egg-info
rm
-rf
./
*
.pyc
rm
-rf
./
*
.tgz
examples/run_example_tcga_GA.py
View file @
8dc9bb3d
...
...
@@ -27,7 +27,7 @@ import sys
if
"."
not
in
sys
.
path
:
sys
.
path
.
append
(
"."
)
from
var
iant_
annot
ator
import
run_annotator
,
Vcf2mafConfig
,
VepConfig
from
varannot
import
run_annotator
,
Vcf2mafConfig
,
VepConfig
#### # SCRIPT PARAMETERS
#### #####################################################################################################
...
...
examples/run_example_tcga_HS.py
View file @
8dc9bb3d
...
...
@@ -27,7 +27,7 @@ import sys
if
"."
not
in
sys
.
path
:
sys
.
path
.
append
(
"."
)
from
var
iant_
annot
ator
import
run_annotator
,
Vcf2mafConfig
,
VepConfig
from
varannot
import
run_annotator
,
Vcf2mafConfig
,
VepConfig
#### # SCRIPT PARAMETERS
#### #####################################################################################################
...
...
pyproject.toml
0 → 100644
View file @
8dc9bb3d
[build-system]
requires
=
[
"setuptools"
,
"wheel"
]
build-backend
=
"setuptools.build_meta"
reqs/requirements.txt
deleted
100644 → 0
View file @
4f4c4bae
numpy>=1.14.0
pandas>=0.23.0
reqs/requirements.yml
deleted
100644 → 0
View file @
4f4c4bae
channels
:
-
defaults
dependencies
:
-
numpy
-
pandas
-
pytest
-
pytest-cov
-
ipython
setup.cfg
0 → 100644
View file @
8dc9bb3d
[metadata]
name = varannot
description = "Variant annotation with VEP and vcf2maf"
license = BSD 2-Clause License
version = 1.1
classifiers =
Topic :: Scientific/Engineering :: Bio-Informatics
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Programming Language :: Python :: 3
[options]
packages =
varannot
install_requires =
numpy >= 1.14.0
pandas >= 0.23.0
setup.py
View file @
8dc9bb3d
import
os
from
setuptools
import
setup
,
Command
class
CleanCommand
(
Command
):
user_options
=
[]
def
initialize_options
(
self
):
self
.
cwd
=
None
def
finalize_options
(
self
):
self
.
cwd
=
os
.
getcwd
()
def
run
(
self
):
assert
os
.
getcwd
()
==
self
.
cwd
,
'Must be in package root: %s'
%
self
.
cwd
os
.
system
(
'rm -rf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info'
)
setup
(
name
=
"variant_annotator"
,
version
=
"1.0.0"
,
author
=
"Yoann Pradat"
,
author_email
=
"yoann.pradat@centralesupelec.fr"
,
install_requires
=
[
"numpy"
,
"pandas"
,
],
cmdclass
=
{
'clean'
:
CleanCommand
}
)
import
setuptools
setuptools
.
setup
()
var
iant_
annot
ator
/__init__.py
→
varannot/__init__.py
View file @
8dc9bb3d
"""
The :mod:`var
iant_
annot
ator
` module defines functions for annotating variants using a combination of manual, vep and
The :mod:`varannot` module defines functions for annotating variants using a combination of manual, vep and
vcf2maf annotations.
"""
...
...
var
iant_
annot
ator
/_main.py
→
varannot/_main.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/_manual.py
→
varannot/_manual.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/_util.py
→
varannot/_util.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/_vcf2maf.py
→
varannot/_vcf2maf.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/_vep.py
→
varannot/_vep.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/__init__.py
→
varannot/tests/__init__.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/test_main.py
→
varannot/tests/test_main.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/test_manual.py
→
varannot/tests/test_manual.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/test_util.py
→
varannot/tests/test_util.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/test_vcf2maf.py
→
varannot/tests/test_vcf2maf.py
View file @
8dc9bb3d
File moved
var
iant_
annot
ator
/tests/test_vep.py
→
varannot/tests/test_vep.py
View file @
8dc9bb3d
File moved
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