drop undeclared dependency on six

mirtop/exporter/vcf.py

@@ -1,11 +1,7 @@
-from __future__ import print_function
-
 import datetime
 import sys
 import os.path as op
 
-import six
-
 from mirtop.mirna.fasta import read_precursor
 from mirtop.mirna.mapper import read_gtf_to_precursor, read_gtf_to_mirna
 from mirtop.gff.body import read_gff_line
@@ -133,14 +129,12 @@ def create_vcf(mirgff3, precursor, gtf, vcffile, database):
     """
     #Check if the input files exist:
     try:
-        gff3_file = open(mirgff3, "r", encoding="utf-8") if six.PY3 else open(mirgff3, "r")
+        gff3_file = open(mirgff3, "r", encoding="utf-8")
     except IOError:
         print ("Can't read the file", end=mirgff3)
         sys.exit()
     with gff3_file:
         data = gff3_file.read()
-        if six.PY2:
-            data = data.decode("utf-8-sig").encode("utf-8")
 
     gff3_data = data.split("\n")
     vcf_file = open(vcffile, "w")

mirtop/libs/do.py

@@ -5,8 +5,6 @@
 import subprocess
 import logging
 
-import six
-
 
 logger = logging.getLogger("run")
 
@@ -16,7 +14,7 @@ def run(cmd, data=None, checks=None, region=None, log_error=True,
     """Run the provided command, logging details and checking for errors.
     """
     try:
-        logger.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, six.string_types) else cmd)
+        logger.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, str) else cmd)
         _do_run(cmd, checks, log_stdout)
     except:
         if log_error:
@@ -44,7 +42,7 @@ def _normalize_cmd_args(cmd):
     Piped commands set pipefail and require use of bash to help with debugging
     intermediate errors.
     """
-    if isinstance(cmd, six.string_types):
+    if isinstance(cmd, str):
         # check for standard or anonymous named pipes
         if cmd.find(" | ") > 0 or cmd.find(">(") or cmd.find("<("):
             return "set -o pipefail; " + cmd, True, find_bash()
@@ -74,7 +72,7 @@ def _do_run(cmd, checks, log_stdout=False):
             for line in s.stdout:
                 debug_stdout.append(line)
             if exitcode is not None and exitcode != 0:
-                error_msg = " ".join(cmd) if not isinstance(cmd, six.string_types) else cmd
+                error_msg = " ".join(cmd) if not isinstance(cmd, str) else cmd
                 error_msg += "\n"
                 error_msg += "".join(debug_stdout)
                 s.communicate()

requirements.txt

@@ -3,5 +3,6 @@ pybedtools
 pandas
 biopython
 pyyaml
+pybedtools
 six
 pytest

setup.py

@@ -29,7 +29,6 @@ def write_version_py():
       long_description_content_type="text/markdown",
       classifiers=[
         'License :: OSI Approved :: MIT License',
-        'Programming Language :: Python :: 2.7',
         "Programming Language :: Python :: 3",
         'Topic :: Scientific/Engineering :: Bio-Informatics'
       ],