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drop undeclared dependency on six #91

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8 changes: 1 addition & 7 deletions mirtop/exporter/vcf.py
Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -133,14 +129,12 @@ def create_vcf(mirgff3, precursor, gtf, vcffile):
"""
#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")
Expand Down
8 changes: 3 additions & 5 deletions mirtop/libs/do.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,6 @@
import subprocess
import logging

import six


logger = logging.getLogger("run")

Expand All @@ -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:
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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()
Expand Down
1 change: 0 additions & 1 deletion requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,3 @@ pandas
biopython
pyyaml
pybedtools
six
1 change: 0 additions & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -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'
],
Expand Down