Ubuntu 1404 py3

setup.py

@@ -13,7 +13,7 @@
 setup(
   name = 'stringMLST',
   scripts = ['stringMLST.py'], 
-  version = '0.4',
+  version = '0.4.1,
   description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.',
   long_description=long_description,
   author = 'Jordan Lab',

stringMLST.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 import getopt
 import sys
 import logging
@@ -16,7 +15,7 @@
 except ImportError:
         from urllib import urlopen, urlretrieve
 import argparse
-version = """ stringMLST v0.4 (updated : May 17, 2017) """
+version = """ stringMLST v0.4.1 (updated : May 21, 2017) """
 """
 
 stringMLST free for academic users and requires permission before any commercial 
@@ -38,7 +37,7 @@
 the Licensor receives from making the Licensed Material available under these
 terms and conditions.
 
-Section 1 – Definitions.
+Section 1 - Definitions.
 
 Adapted Material means material subject to Copyright and Similar Rights that is
 derived from or based upon the Licensed Material and in which the Licensed
@@ -87,7 +86,7 @@
 of databases, as amended and/or succeeded, as well as other essentially
 equivalent rights anywhere in the world. You means the individual or entity
 exercising the Licensed Rights under this Public License. Your has a
-corresponding meaning. Section 2 – Scope.
+corresponding meaning. Section 2 - Scope.
 
 License grant. Subject to the terms and conditions of this Public License, the
 Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-
@@ -106,10 +105,10 @@
 including technical modifications necessary to circumvent Effective
 Technological Measures. For purposes of this Public License, simply making
 modifications authorized by this Section 2(a)(4) never produces Adapted
-Material. Downstream recipients. Offer from the Licensor – Licensed Material.
+Material. Downstream recipients. Offer from the Licensor - Licensed Material.
 Every recipient of the Licensed Material automatically receives an offer from
 the Licensor to exercise the Licensed Rights under the terms and conditions of
-this Public License. Additional offer from the Licensor – Adapted Material.
+this Public License. Additional offer from the Licensor - Adapted Material.
 Every recipient of Adapted Material from You automatically receives an offer
 from the Licensor to exercise the Licensed Rights in the Adapted Material under
 the conditions of the Adapter’s License You apply. No downstream restrictions.
@@ -133,7 +132,7 @@
 voluntary or waivable statutory or compulsory licensing scheme. In all other
 cases the Licensor expressly reserves any right to collect such royalties,
 including when the Licensed Material is used other than for NonCommercial
-purposes. Section 3 – License Conditions.
+purposes. Section 3 - License Conditions.
 
 Your exercise of the Licensed Rights is expressly made subject to the following
 conditions.
@@ -168,7 +167,7 @@
 medium, means, and context in which You Share Adapted Material. You may not
 offer or impose any additional or different terms or conditions on, or apply any
 Effective Technological Measures to, Adapted Material that restrict exercise of
-the rights granted under the Adapter's License You apply. Section 4 – Sui
+the rights granted under the Adapter's License You apply. Section 4 - Sui
 Generis Database Rights.
 
 Where the Licensed Rights include Sui Generis Database Rights that apply to Your
@@ -184,7 +183,7 @@
 Share all or a substantial portion of the contents of the database. For the
 avoidance of doubt, this Section 4 supplements and does not replace Your
 obligations under this Public License where the Licensed Rights include other
-Copyright and Similar Rights. Section 5 – Disclaimer of Warranties and
+Copyright and Similar Rights. Section 5 - Disclaimer of Warranties and
 Limitation of Liability.
 
 Unless otherwise separately undertaken by the Licensor, to the extent possible,
@@ -205,7 +204,7 @@
 limitation may not apply to You. The disclaimer of warranties and limitation of
 liability provided above shall be interpreted in a manner that, to the extent
 possible, most closely approximates an absolute disclaimer and waiver of all
-liability. Section 6 – Term and Termination.
+liability. Section 6 - Term and Termination.
 
 This Public License applies for the term of the Copyright and Similar Rights
 licensed here. However, if You fail to comply with this Public License, then
@@ -220,13 +219,13 @@
 Material under separate terms or conditions or stop distributing the Licensed
 Material at any time; however, doing so will not terminate this Public License.
 Sections 1, 5, 6, 7, and 8 survive termination of this Public License. Section 7
-– Other Terms and Conditions.
+- Other Terms and Conditions.
 
 The Licensor shall not be bound by any additional or different terms or
 conditions communicated by You unless expressly agreed. Any arrangements,
 understandings, or agreements regarding the Licensed Material not stated herein
 are separate from and independent of the terms and conditions of this Public
-License. Section 8 – Interpretation.
+License. Section 8 - Interpretation.
 
 For the avoidance of doubt, this Public License does not, and shall not be
 interpreted to, reduce, limit, restrict, or impose conditions on any use of the
@@ -458,7 +457,10 @@ def singleFileTool(fastq, k):
         print(msg)
 def fileExplorer(file, k, non_overlapping_window):
     if file.endswith('.gz'):
-        f = gzip.open(file, 'rb')
+        if sys.version_info[0] == 3:
+            f = gzip.open(file, 'rt')
+        else:
+            f = gzip.open(file, 'rb')
     else:
         f = open(file)
     msg = "fileExplorer :" + file