remove six dependency

gffutils/attributes.py

@@ -1,4 +1,3 @@
-import six
 import collections
 
 try:
@@ -95,7 +94,7 @@ def __str__(self):
         return "\n".join(s)
 
     def update(self, *args, **kwargs):
-        for k, v in six.iteritems(dict(*args, **kwargs)):
+        for k, v in dict(*args, **kwargs).items():
             self[k] = v
 
 

gffutils/biopython_integration.py

@@ -2,7 +2,6 @@
 Module for integration with BioPython, specifically SeqRecords and SeqFeature
 objects.
 """
-import six
 
 try:
     from Bio.SeqFeature import SeqFeature, FeatureLocation
@@ -15,7 +14,8 @@
 _biopython_strand = {
     "+": 1,
     "-": -1,
-    ".": 0,
+    ".": None,
+    "?": 0,
 }
 _feature_strand = dict((v, k) for k, v in _biopython_strand.items())
 
@@ -33,7 +33,7 @@ def to_seqfeature(feature):
         If string, assume it is a GFF or GTF-format line; otherwise just use
         the provided feature directly.
     """
-    if isinstance(feature, six.string_types):
+    if isinstance(feature, str):
         feature = feature_from_line(feature)
 
     qualifiers = {
@@ -68,7 +68,7 @@ def from_seqfeature(s, **kwargs):
     score = s.qualifiers.get("score", ".")[0]
     seqid = s.qualifiers.get("seqid", ".")[0]
     frame = s.qualifiers.get("frame", ".")[0]
-    strand = _feature_strand[s.strand]
+    strand = _feature_strand[s.location.strand]
 
     # BioPython parses 1-based GenBank positions into 0-based for use within
     # Python.  We need to convert back to 1-based GFF format here.

gffutils/convert.py

@@ -2,7 +2,6 @@
 Conversion functions that operate on :class:`FeatureDB` classes.
 """
 
-import six
 
 
 def to_bed12(f, db, child_type="exon", name_field="ID"):
@@ -22,7 +21,7 @@ def to_bed12(f, db, child_type="exon", name_field="ID"):
         Attribute to be used in the "name" field of the BED12 entry.  Usually
         "ID" for GFF; "transcript_id" for GTF.
     """
-    if isinstance(f, six.string_types):
+    if isinstance(f, str):
         f = db[f]
     children = list(db.children(f, featuretype=child_type, order_by="start"))
     sizes = [len(i) for i in children]

gffutils/create.py

@@ -5,7 +5,6 @@
 import sys
 import os
 import sqlite3
-import six
 from textwrap import dedent
 from gffutils import constants
 from gffutils import version
@@ -119,7 +118,7 @@ def __init__(
                 os.unlink(dbfn)
         self.dbfn = dbfn
         self.id_spec = id_spec
-        if isinstance(dbfn, six.string_types):
+        if isinstance(dbfn, str):
             conn = sqlite3.connect(dbfn)
         else:
             conn = dbfn
@@ -171,7 +170,7 @@ def _id_handler(self, f):
         """
 
         # If id_spec is a string or callable, convert to iterable for later
-        if isinstance(self.id_spec, six.string_types):
+        if isinstance(self.id_spec, str):
             id_key = [self.id_spec]
         elif hasattr(self.id_spec, "__call__"):
             id_key = [self.id_spec]
@@ -181,7 +180,7 @@ def _id_handler(self, f):
         elif isinstance(self.id_spec, dict):
             try:
                 id_key = self.id_spec[f.featuretype]
-                if isinstance(id_key, six.string_types):
+                if isinstance(id_key, str):
                     id_key = [id_key]
 
             # Otherwise, use default auto-increment.
@@ -684,7 +683,7 @@ def _update_relations(self):
         # c.execute('CREATE INDEX childindex ON relations (child)')
         # self.conn.commit()
 
-        if isinstance(self._keep_tempfiles, six.string_types):
+        if isinstance(self._keep_tempfiles, str):
             suffix = self._keep_tempfiles
         else:
             suffix = ".gffutils"
@@ -883,7 +882,7 @@ def _update_relations(self):
             msg = "transcript"
         logger.info("Inferring %s extents " "and writing to tempfile" % msg)
 
-        if isinstance(self._keep_tempfiles, six.string_types):
+        if isinstance(self._keep_tempfiles, str):
             suffix = self._keep_tempfiles
         else:
             suffix = ".gffutils"

gffutils/feature.py

@@ -1,5 +1,4 @@
 from pyfaidx import Fasta
-import six
 import simplejson as json
 from gffutils import constants
 from gffutils import helpers
@@ -166,7 +165,7 @@ def __init__(
         # for testing.
         attributes = attributes or dict_class()
 
-        if isinstance(attributes, six.string_types):
+        if isinstance(attributes, str):
             try:
                 attributes = helpers._unjsonify(attributes, isattributes=True)
 
@@ -182,7 +181,7 @@ def __init__(
         # If string, then try un-JSONifying it into a list; if that doesn't
         # work then assume it's tab-delimited and convert to a list.
         extra = extra or []
-        if isinstance(extra, six.string_types):
+        if isinstance(extra, str):
             try:
                 extra = helpers._unjsonify(extra)
             except json.JSONDecodeError:
@@ -254,10 +253,7 @@ def __setitem__(self, key, value):
             self.attributes[key] = value
 
     def __str__(self):
-        if six.PY3:
-            return self.__unicode__()
-        else:
-            return unicode(self).encode("utf-8")
+        return self.__unicode__()
 
     def __unicode__(self):
 
@@ -387,7 +383,7 @@ def sequence(self, fasta, use_strand=True):
         -------
         string
         """
-        if isinstance(fasta, six.string_types):
+        if isinstance(fasta, str):
             fasta = Fasta(fasta, as_raw=False)
 
         # recall GTF/GFF is 1-based closed;  pyfaidx uses Python slice notation

gffutils/gffwriter.py

@@ -1,7 +1,6 @@
 ##
 ## GFF Writer (writer): serializing gffutils records as GFF text files.
 ##
-import six
 import tempfile
 import shutil
 from time import strftime, localtime
@@ -41,7 +40,7 @@ def __init__(self, out, with_header=True, in_place=False):
         self.temp_file = None
         # Output stream to write to
         self.out_stream = None
-        if isinstance(out, six.string_types):
+        if isinstance(out, str):
             if self.in_place:
                 # Use temporary file
                 self.temp_file = tempfile.NamedTemporaryFile(delete=False)

gffutils/helpers.py

@@ -4,7 +4,6 @@
 import simplejson as json
 import time
 import tempfile
-import six
 from gffutils import constants
 from gffutils import bins
 import gffutils
@@ -202,7 +201,7 @@ def make_query(
         # e.g., "featuretype = 'exon'"
         #
         # or, "featuretype IN ('exon', 'CDS')"
-        if isinstance(featuretype, six.string_types):
+        if isinstance(featuretype, str):
             d["FEATURETYPE"] = "features.featuretype = ?"
             args.append(featuretype)
         else:
@@ -218,7 +217,7 @@ def make_query(
         # `limit` is a string or a tuple of (chrom, start, stop)
         #
         # e.g., "seqid = 'chr2L' AND start > 1000 AND end < 5000"
-        if isinstance(limit, six.string_types):
+        if isinstance(limit, str):
             seqid, startstop = limit.split(":")
             start, end = startstop.split("-")
         else:
@@ -257,7 +256,7 @@ def make_query(
         # Default is essentially random order.
         #
         # e.g. "ORDER BY seqid, start DESC"
-        if isinstance(order_by, six.string_types):
+        if isinstance(order_by, str):
             _order_by.append(order_by)
 
         else:
@@ -387,7 +386,7 @@ def merge_attributes(attr1, attr2, numeric_sort=False):
         if not isinstance(v, list):
             new_d[k] = [v]
 
-    for k, v in six.iteritems(attr1):
+    for k, v in attr1.items():
         if k in attr2:
             if not isinstance(v, list):
                 v = [v]
@@ -507,9 +506,9 @@ def is_gff_db(db_fname):
 
 
 def to_unicode(obj, encoding="utf-8"):
-    if isinstance(obj, six.string_types):
-        if not isinstance(obj, six.text_type):
-            obj = six.text_type(obj, encoding)
+    if isinstance(obj, str):
+        if not isinstance(obj, str):
+            obj = str(obj, encoding)
     return obj
 
 

gffutils/interface.py

@@ -1,6 +1,5 @@
 import collections
 import os
-import six
 import sqlite3
 import shutil
 import warnings
@@ -694,7 +693,7 @@ def region(
                     "If region is supplied, do not supply seqid, "
                     "start, or end as separate kwargs"
                 )
-            if isinstance(region, six.string_types):
+            if isinstance(region, str):
                 toks = region.split(":")
                 if len(toks) == 1:
                     seqid = toks[0]
@@ -774,7 +773,7 @@ def region(
 
         # Add the featuretype clause
         if featuretype is not None:
-            if isinstance(featuretype, six.string_types):
+            if isinstance(featuretype, str):
                 featuretype = [featuretype]
             feature_clause = " or ".join(["featuretype = ?" for _ in featuretype])
             query += " AND (%s) " % feature_clause
@@ -994,7 +993,7 @@ def delete(self, features, make_backup=True, **kwargs):
         FeatureDB object, with features deleted.
         """
         if make_backup:
-            if isinstance(self.dbfn, six.string_types):
+            if isinstance(self.dbfn, str):
                 shutil.copy2(self.dbfn, self.dbfn + ".bak")
 
         c = self.conn.cursor()
@@ -1006,12 +1005,12 @@ def delete(self, features, make_backup=True, **kwargs):
         """
         if isinstance(features, FeatureDB):
             features = features.all_features()
-        if isinstance(features, six.string_types):
+        if isinstance(features, str):
             features = [features]
         if isinstance(features, Feature):
             features = [features]
         for feature in features:
-            if isinstance(feature, six.string_types):
+            if isinstance(feature, str):
                 _id = feature
             else:
                 _id = feature.id
@@ -1060,7 +1059,7 @@ def update(self, data, make_backup=True, **kwargs):
         from gffutils import iterators
 
         if make_backup:
-            if isinstance(self.dbfn, six.string_types):
+            if isinstance(self.dbfn, str):
                 shutil.copy2(self.dbfn, self.dbfn + ".bak")
 
         # get iterator-specific kwargs
@@ -1139,9 +1138,9 @@ def child_func(parent, child):
         -------
         FeatureDB object with new relations added.
         """
-        if isinstance(parent, six.string_types):
+        if isinstance(parent, str):
             parent = self[parent]
-        if isinstance(child, six.string_types):
+        if isinstance(child, str):
             child = self[child]
 
         c = self.conn.cursor()

gffutils/iterators.py

@@ -16,13 +16,8 @@
 from gffutils.interface import FeatureDB
 from gffutils import helpers
 from textwrap import dedent
-import six
-from six.moves.urllib.request import urlopen
-
-if six.PY3:
-    from urllib import parse as urlparse
-else:
-    import urlparse
+from urllib.request import urlopen
+from urllib import parse as urlparse
 
 
 class Directive(object):
@@ -133,7 +128,7 @@ def _custom_iter(self):
         valid_lines = 0
         with self.open_function(self.data) as fh:
             for i, line in enumerate(fh):
-                if isinstance(line, six.binary_type):
+                if isinstance(line, bytes):
                     line = line.decode("utf-8")
                 line = line.rstrip("\n\r")
                 self.current_item = line
@@ -295,11 +290,11 @@ def DataIterator(
         force_dialect_check=force_dialect_check,
         **kwargs,
     )
-    if isinstance(data, six.string_types):
+    if isinstance(data, str):
         if from_string:
             tmp = tempfile.NamedTemporaryFile(delete=False)
             data = dedent(data)
-            if isinstance(data, six.text_type):
+            if isinstance(data, str):
                 data = data.encode("utf-8")
             tmp.write(data)
             tmp.close()

gffutils/parser.py

@@ -3,7 +3,7 @@
 import re
 import copy
 import collections
-from six.moves import urllib
+import urllib
 from gffutils import constants
 from gffutils.exceptions import AttributeStringError
 

gffutils/pybedtools_integration.py

@@ -6,7 +6,6 @@
 import pybedtools
 from pybedtools import featurefuncs
 from gffutils import helpers
-import six
 
 
 def to_bedtool(iterator):
@@ -210,7 +209,7 @@ def gen():
 
     if merge_overlapping or as_bed6:
 
-        if isinstance(attrs, six.string_types):
+        if isinstance(attrs, str):
             attrs = [attrs]
 
         def to_bed(f):

gffutils/scripts/gffutils-cli

@@ -1,7 +1,5 @@
 #!/usr/bin/python
 
-from __future__ import print_function
-
 """
 Command line interface for gffutils.