Merge pull request #17 from GertjanBisschop/bugfix-lib

Bugfix lib

gimbleprep.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import os
-from cli.interface import main
+from gimbleprep.interface import main
 
 if __name__ == '__main__':
     main(os.path.dirname(os.path.realpath(__file__)))

gimbleprep/preprocess.py

@@ -15,7 +15,6 @@
         -h, --help                       Show this
 """
 
-import gimbleprep.runargs
 import numpy as np
 import tempfile
 import pathlib
@@ -26,6 +25,9 @@
 from tqdm import tqdm
 import pysam
 import pandas as pd
+
+import gimbleprep.runargs as runargs
+
 from timeit import default_timer as timer
 from docopt import docopt
 
@@ -68,7 +70,7 @@ def fix_permissions(path):
             os.chmod(_f, 0o664)
         #os.chmod(root, 0o775)
 
-class PreprocessParameterObj(lib.runargs.RunArgs):
+class PreprocessParameterObj(runargs.RunArgs):
     '''Sanitises command line arguments and stores parameters'''
     def __init__(self, params, args):
         super().__init__(params)
@@ -271,7 +273,7 @@ def main(params):
         parameterObj = PreprocessParameterObj(params, args)
         print("[+] Running 'gimble-preprocess'...")
         preprocess(parameterObj)
-        print("[*] Total runtime was %s" % (lib.runargs.format_time(timer() - start_time)))
+        print("[*] Total runtime was %s" % (runargs.format_time(timer() - start_time)))
     except KeyboardInterrupt:
-        print("\n[X] Interrupted by user after %s !\n" % (lib.runargs.format_time(timer() - start_time)))
+        print("\n[X] Interrupted by user after %s !\n" % (runargs.format_time(timer() - start_time)))
         exit(-1)

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='gimbleprep',
-    version='0.0.2b4',
+    version='0.0.2b5',
     description='Preprocess fasta, bam and vcf files ready to be used by gimble',
     url='http://github.com/LohseLab/gimbleprep',
     author='Lohse Lab',