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|
--- a/mirtop/exporter/vcf.py
+++ b/mirtop/exporter/vcf.py
@@ -4,7 +4,6 @@
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
@@ -133,14 +132,12 @@
"""
#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")
--- a/mirtop/libs/do.py
+++ b/mirtop/libs/do.py
@@ -5,7 +5,6 @@
import subprocess
import logging
-import six
logger = logging.getLogger("run")
@@ -16,7 +15,7 @@
"""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 +43,7 @@
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 +73,7 @@
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()
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,5 +3,4 @@
pandas
biopython
pyyaml
-six
pytest
|
