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Correcting the issue with JC transformation error message
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shahab-sarmashghi committed Mar 22, 2019
1 parent 24daae9 commit ad451a6
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Showing 2 changed files with 7 additions and 7 deletions.
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from setuptools import setup

setup(name='skmer',
version='2.0.1',
version='2.0.2',
description='Assembly-free and alignment-free tool for estimating genomic distances between genome-skims',
author='Shahab Sarmashghi',
author_email='[email protected]',
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12 changes: 6 additions & 6 deletions skmer/__main__.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
import multiprocessing as mp


__version__ = 'skmer 2.0.1'
__version__ = 'skmer 2.0.2'


# Hard-coded param
Expand Down Expand Up @@ -188,8 +188,8 @@ def estimate_dist(sample_1, sample_2, lib_1, lib_2, ce, le, ee, rl, k, cov_thres
if d < 0.75:
d = max(0, -0.75 * np.log(1 - 4.0 * d / 3.0))
else:
raise ValueError('Distance between {0} and {1} is not in range [0, 0.75); Unable to apply Jukes-Cantor ' +
'transformation'.format(sample_1, sample_2))
raise ValueError('Distance between {0} and {1} '.format(sample_1, sample_2) +
'is not in range [0, 0.75); Unable to apply Jukes-Cantor transformation')
return sample_1, sample_2, d


Expand Down Expand Up @@ -427,15 +427,15 @@ def query(args):

def main():
# Input arguments parser
parser = argparse.ArgumentParser(description='{} - Estimating gonomic distances between '
'genome-skims'.format(__version__),
parser = argparse.ArgumentParser(description='{0} - Estimating gonomic distances between '.format(__version__) +
'genome-skims',
formatter_class=argparse.RawDescriptionHelpFormatter)
# parser.add_argument('-v', '--version', action='store_true', help='print the current version')
parser.add_argument('--debug', action='store_true', help='Print the traceback when an exception is raised')
subparsers = parser.add_subparsers(title='commands',
description='reference Process a library of reference genome-skims or assemblies\n'
'distance Compute pairwise distances for a processed library\n'
'query Compare a genome-skim or assembly against a reference ' +
'query Compare a genome-skim or assembly against a reference '
'library',
help='Run skmer {commands} [-h] for additional help',
dest='{commands}')
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