Test file locations

setup.cfg

@@ -14,3 +14,6 @@ ignore =
     # E128: continuation line under-indented for visual indent
     # E127,E128
 max_complexity = 10
+
+[tool:pytest]
+addopts = --verbose

setup.py

@@ -4,9 +4,8 @@
 
 setup(
     use_scm_version=True,
-    setup_requires=['setuptools_scm', 'setuptools_scm_git_archive',
-                    'isort', 'pytest-runner'],
-    install_requires=['setuptools_scm', 'biopython'],
+    setup_requires=['setuptools_scm', 'setuptools_scm_git_archive', 'pytest-runner'],
+    install_requires=['setuptools_scm'],
     tests_require=['pytest', 'flake8'],
     name='MinVar',
     description='Minority variants in HIV',
@@ -16,7 +15,7 @@
     packages=find_packages('src'),  # include all packages under src
     package_dir={'': 'src'},  # tell setuptools packages are under src
     # scripts=['bin/minvar', 'src/scripts/blast2sam.py'],
-    package_data={'minvar': ['src/minvar/db/*']},
+    package_data={'minvar': ['db/HIV/*', 'db/HCV/*']},
     entry_points={
         'console_scripts': ['minvar = minvar.cli:main',
                             'blast2sam = scripts.blast2sam:main'],

src/minvar/cli.py

@@ -18,11 +18,12 @@
 import os
 import sys
 
-from pkg_resources import (DistributionNotFound, get_distribution)
+from pkg_resources import (get_distribution, DistributionNotFound, resource_exists)
 # resource_filename)
 
 try:
     __version__ = get_distribution('minvar').version
+    HCV_references = resource_exists(__name__, 'db/HCV/subtype_references.fasta')
 
 except DistributionNotFound:
     # package is not installed

src/minvar/reportdrm.py

@@ -216,7 +216,7 @@ def main(org=None, fastq=None, version='unknown', mut_file='final.csv', subtype_
         logging.info('Shape of elaborated merged is: %s', str(drms.shape))
         # os.remove('merged_muts.csv')
 
-        drms.drop(['', 'commented', 'mut_y'], axis=1, inplace=True)
+        drms.drop(['commented', 'mut_y'], axis=1, inplace=True)
         drms.rename(columns={'mut_x': 'mut'}, inplace=True)
 
         cols = ['gene', 'pos', 'mut', 'freq', 'category']