From ad451a695120c829aae0e3a415045b6fc1e7f04b Mon Sep 17 00:00:00 2001 From: Shahab Sarmashghi Date: Thu, 21 Mar 2019 17:08:50 -0700 Subject: [PATCH] Correcting the issue with JC transformation error message --- setup.py | 2 +- skmer/__main__.py | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/setup.py b/setup.py index 514bf08..efa254e 100644 --- a/setup.py +++ b/setup.py @@ -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='ssarmash@ucsd.edu', diff --git a/skmer/__main__.py b/skmer/__main__.py index e8b0b99..3417833 100644 --- a/skmer/__main__.py +++ b/skmer/__main__.py @@ -15,7 +15,7 @@ import multiprocessing as mp -__version__ = 'skmer 2.0.1' +__version__ = 'skmer 2.0.2' # Hard-coded param @@ -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 @@ -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}')