Stefansfixes

setup.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+
+from setuptools import find_packages, setup
+
+classifiers = [
+    'Development Status :: 1 - Pre-Alpha',
+    'License :: OSI Approved :: BSD License',
+    'Environment :: Console',
+    'Topic :: Software Development :: Libraries :: Application Frameworks',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Bio-Informatics',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.3',
+    'Programming Language :: Python :: 3.4',
+    'Operating System :: Unix',
+    'Operating System :: POSIX',
+    'Operating System :: MacOS :: MacOS X',
+    'Operating System :: Microsoft :: Windows']
+
+
+description = 'VXdetector'
+
+
+setup(name='vxdetector',
+      version='1.0.0',
+      license='BSD',
+      #description=description,
+      #long_description=long_description,
+      #keywords=keywords,
+      classifiers=classifiers,
+      author="Johannes Groos",
+      author_email="Johannes.Groos@bio.uni-giessen.de",
+      maintainer="http://jlab.bio",
+      maintainer_email="stefan.m.janssen@gmail.com",
+      url='https://github.com/jlab/algorithm_vxdetector/',
+      test_suite='nose.collector',
+      packages=find_packages(),
+      install_requires=[
+          #'click >= 6',
+          #'scikit-bio >= 0.4.0',
+      ],
+      #extras_require={'test': ["nose", "pep8", "flake8"],
+      #                      'coverage': ["coverage"]}
+)

vxdetector/VXdetector.py

@@ -2,10 +2,10 @@
 
 import argparse
 import os
-import interact_bowtie2
-import interact_bedtools
-import Output_counter
-import files_manager
+from vxdetector.interact_bowtie2 import mapbowtie2, buildbowtie2
+from vxdetector.interact_bedtools import overlap
+from vxdetector import Output_counter
+import vxdetector.files_manager
 import pandas as pd
 
 output = pd.DataFrame({'Read-file': [], 'Number of Reads': [],
@@ -43,18 +43,18 @@ def do_statistic():
 
 def workflow(path, temp_path, file_path, file_type, old_file_name,
              file_name, dir_name, dir_path, mode, read2_file):
-    interact_bowtie2.buildbowtie2(path)
+    buildbowtie2(path)
     if file_type is not None:
-        aligned_path = interact_bowtie2.mapbowtie2(file_path, read2_file,
+        aligned_path = mapbowtie2(file_path, read2_file,
                                                    path, temp_path, mode,
                                                    file_type)
     else:
-        aligned_path = interact_bowtie2.mapbowtie2(file_path, read2_file,
+        aligned_path = mapbowtie2(file_path, read2_file,
                                                    path, temp_path, mode,
                                                    file_type=' -q')
     # The Programm bowtie2 is used to align the Reads to a reference
     # 16S database.
-    interact_bedtools.overlap(path, temp_path, aligned_path)
+    overlap(path, temp_path, aligned_path)
     # look which reads intersect with which variable Region
     if file_type is not None:
         global output

vxdetector/__init__.py

@@ -0,0 +1 @@
+