Commit 1185db42 authored by Jakub Horváth's avatar Jakub Horváth
Browse files

skipped fixing packaging issues, will focus on building the program and extending behavior

parent b39300ee

TEster/__init__.py

+1 −0
Original line number Original line Diff line number Diff line 
__name__ = "TEster"

__version__ = '1.0.0'

__version__ = '1.0.0'

__author__ = 'Jakub Horvath'
 
__author__ = 'Jakub Horvath'

TEster/setup.py

+5 −5
Original line number Original line Diff line number Diff line 
from setuptools import setup, find_packages

from setuptools import setup, find_packages



import TEster

setup(

setup(

    name='TEster',

    name='TEster',

    version='1.0.0',

    version=TEster.__version__,

    description='Nested description',

    description='nester testing tool',

    author='Jakub Horvath',

    author=TEster.__author__,

    packages=find_packages(),

    packages=find_packages(),

    install_requires=[

    install_requires=[

        'bcbio-gff==0.6.4',

        'bcbio-gff==0.6.4',
@@ -15,7 +15,7 @@ setup( 
    ],

    ],

    entry_points={

    entry_points={

        'console_scripts': [

        'console_scripts': [

            'TEster=toolchain.TEster:main'

            'TEster = TEster.toolchain.TEster:main'

        ]

        ]

    }

    }

)
 
)

TEster/setup.sh

0 → 100644
+3 −0
Original line number Original line Diff line number Diff line 
python3 setup.py install



rm -r TEster/TEster.egg-info

TEster/toolchain/TEster.py

+3 −3
Original line number Original line Diff line number Diff line
@@ -21,8 +21,8 @@ 








import click

import click

from toolchain.sequence_generator import sequence_generator

from sequence_generator import sequence_generator

from toolchain.analyser import parametrisation

from analyser import parametrisation









@click.command()

@click.command()
@@ -46,7 +46,7 @@ def main(input_file, sequence_database, generate_analysis=False): 
        # call a class from database loader

        # call a class from database loader





    # run the parametrisation from analyser.py

    # run the parametrisation from analyser.py

    parametrisation(input_file)

    parametrisation(generated_file)





    # setup the config file

    # setup the config file

TEster/toolchain/analyser.py

+1 −1
Original line number Original line Diff line number Diff line
@@ -16,7 +16,7 @@ 
# -p min length of exact match pair

# -p min length of exact match pair

# -S output score limit [0..10]

# -S output score limit [0..10]





from toolchain.nester_run import run_nester

from nester_run import run_nester









class Parameter:

class Parameter: