diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt
index 3bd4c942944..c8faba1b706 100644
--- a/.ci/flake8_lint_include_list.txt
+++ b/.ci/flake8_lint_include_list.txt
@@ -53,8 +53,10 @@ lib/galaxy/datatypes/dataproviders/__init__.py
 lib/galaxy/datatypes/data.py
 lib/galaxy/datatypes/display_applications/__init__.py
 lib/galaxy/datatypes/display_applications/util.py
+lib/galaxy/datatypes/genetics.py
 lib/galaxy/datatypes/images.py
 lib/galaxy/datatypes/__init__.py
+lib/galaxy/datatypes/interval.py
 lib/galaxy/datatypes/metadata.py
 lib/galaxy/datatypes/msa.py
 lib/galaxy/datatypes/ngsindex.py
diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt
index 68fd3d55315..a17447b9d75 100644
--- a/.ci/py3_sources.txt
+++ b/.ci/py3_sources.txt
@@ -13,7 +13,9 @@ lib/galaxy/datatypes/constructive_solid_geometry.py
 lib/galaxy/datatypes/converters/
 lib/galaxy/datatypes/dataproviders/
 lib/galaxy/datatypes/data.py
+lib/galaxy/datatypes/genetics.py
 lib/galaxy/datatypes/images.py
+lib/galaxy/datatypes/interval.py
 lib/galaxy/datatypes/msa.py
 lib/galaxy/datatypes/ngsindex.py
 lib/galaxy/datatypes/proteomics.py
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 24900beebe7..ee5b5980739 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -11,18 +11,18 @@ subsequent row values are all numeric ! Will fail if any non numeric (eg '+' or
 ross lazarus for rgenetics
 august 20 2007
 """
-
 import logging
 import os
 import re
 import sys
-import urllib
 from cgi import escape
 
+from six.moves.urllib.parse import quote_plus
+
 from galaxy.datatypes import metadata
-from galaxy.datatypes.text import Html
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.text import Html
 from galaxy.util import nice_size
 from galaxy.web import url_for
 
@@ -95,9 +95,9 @@ class GenomeGraphs( Tabular ):
                                                    action='display_at',
                                                    filename='ucsc_' + site_name )
                     display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type)
-                    display_url = urllib.quote_plus( display_url )
-                    # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
-                    # redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
+                    display_url = quote_plus( display_url )
+                    # was display_url = quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) )
+                    # redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) )
                     sl = ["%sdb=%s" % (site_url, dataset.dbkey ), ]
                     # sl.append("&hgt.customText=%s")
                     sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data'))
@@ -106,7 +106,7 @@ class GenomeGraphs( Tabular ):
                     sl.append("&hgGenome_doSubmitUpload=submit")
                     sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url)
                     s = ''.join(sl)
-                    s = urllib.quote_plus(s)
+                    s = quote_plus(s)
                     redirect_url = s
                     link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
                     ret_val.append( (site_name, link) )
@@ -117,17 +117,17 @@ class GenomeGraphs( Tabular ):
         Create HTML table, used for displaying peek
         """
         out = ['<table cellspacing="0" cellpadding="3">']
-        f = open(dataset.file_name, 'r')
-        d = f.readlines()[:5]
-        if len(d) == 0:
-            out = "Cannot find anything to parse in %s" % dataset.name
-            return out
-        hasheader = 0
-        try:
-            ['%f' % x for x in d[0][1:]]  # first is name - see if starts all numerics
-        except:
-            hasheader = 1
         try:
+            with open(dataset.file_name, 'r') as f:
+                d = f.readlines()[:5]
+            if len(d) == 0:
+                out = "Cannot find anything to parse in %s" % dataset.name
+                return out
+            hasheader = 0
+            try:
+                ['%f' % x for x in d[0][1:]]  # first is name - see if starts all numerics
+            except:
+                hasheader = 1
             # Generate column header
             out.append( '<tr>' )
             if hasheader:
@@ -150,16 +150,16 @@ class GenomeGraphs( Tabular ):
         Validate a gg file - all numeric after header row
         """
         errors = list()
-        infile = open(dataset.file_name, "r")
-        infile.next()  # header
-        for i, row in enumerate(infile):
-            ll = row.strip().split('\t')[1:]  # first is alpha feature identifier
-            badvals = []
-            for j, x in enumerate(ll):
-                try:
-                    x = float(x)
-                except:
-                    badvals.append('col%d:%s' % (j + 1, x))
+        with open(dataset.file_name, "r") as infile:
+            next(infile)  # header
+            for i, row in enumerate(infile):
+                ll = row.strip().split('\t')[1:]  # first is alpha feature identifier
+                badvals = []
+                for j, x in enumerate(ll):
+                    try:
+                        x = float(x)
+                    except:
+                        badvals.append('col%d:%s' % (j + 1, x))
         if len(badvals) > 0:
             errors.append('row %d, %s' % (' '.join(badvals)))
             return errors
@@ -219,7 +219,7 @@ class rgTabList(Tabular):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+        return self.make_html_table( dataset, column_names=self.column_names )
 
     def get_mime(self):
         """Returns the mime type of the datatype"""
@@ -246,8 +246,8 @@ class rgSampleList(rgTabList):
         # this is what Plink wants as at 2009
 
     def sniff(self, filename):
-        infile = open(filename, "r")
-        header = infile.next()  # header
+        with open(filename, "r") as infile:
+            header = next(infile)  # header
         if header[0] == 'FID' and header[1] == 'IID':
             return True
         else:
@@ -287,7 +287,7 @@ class Rgenetics(Html):
     def generate_primary_file( self, dataset=None ):
         rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>']
         rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).iteritems():
+        for composite_name, composite_file in self.get_composite_files( dataset=dataset ).items():
             fn = composite_name
             opt_text = ''
             if composite_file.optional:
@@ -617,7 +617,7 @@ class RexpBase( Html ):
             del useConc[i]  # get rid of concordance
             del useCols[i]  # and usecols entry
         for i, conc in enumerate(useConc):  # these are all unique columns for the design matrix
-                ccounts = sorted([(conc.get(code, 0), code) for code in conc.keys()])  # decorate
+                ccounts = sorted((conc.get(code, 0), code) for code in conc.keys())  # decorate
                 cc = [(x[1], x[0]) for x in ccounts]  # list of code count tuples
                 codeDetails = (head[useCols[i]], cc)  # ('foo',[('a',3),('b',11),..])
                 listCol.append(codeDetails)
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 2305d3c4a75..2db26f1628f 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -6,10 +6,10 @@ import math
 import os
 import sys
 import tempfile
-import urllib
 
 import numpy
 from bx.intervals.io import GenomicIntervalReader, ParseError
+from six.moves.urllib.parse import quote_plus
 
 from galaxy import util
 from galaxy.datatypes import metadata
@@ -19,8 +19,10 @@ from galaxy.datatypes.tabular import Tabular
 from galaxy.datatypes.util.gff_util import parse_gff_attributes
 from galaxy.web import url_for
 
-import data
-import dataproviders
+from . import (
+    data,
+    dataproviders
+)
 
 log = logging.getLogger(__name__)
 
@@ -86,7 +88,7 @@ class Interval( Tabular ):
                         self.init_meta( dataset )
                         line = line.strip( '#' )
                         elems = line.split( '\t' )
-                        for meta_name, header_list in alias_spec.iteritems():
+                        for meta_name, header_list in alias_spec.items():
                             for header_val in header_list:
                                 if header_val in elems:
                                     # found highest priority header to meta_name
@@ -239,7 +241,7 @@ class Interval( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'endCol': 'End', 'strandCol': 'Strand', 'nameCol': 'Name'} )
+        return self.make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'endCol': 'End', 'strandCol': 'Strand', 'nameCol': 'Name'} )
 
     def ucsc_links( self, dataset, type, app, base_url ):
         """
@@ -263,10 +265,10 @@ class Interval( Tabular ):
         for site_name, site_url in valid_sites:
             internal_url = url_for( controller='dataset', dataset_id=dataset.id,
                                     action='display_at', filename='ucsc_' + site_name )
-            display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at"
-                                             % (base_url, url_for( controller='root' ), dataset.id, type) )
-            redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s"
-                                              % (site_url, dataset.dbkey, chrom, start, stop ) )
+            display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
+                                      (base_url, url_for( controller='root' ), dataset.id, type) )
+            redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
+                                       (site_url, dataset.dbkey, chrom, start, stop ) )
             link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
             ret_val.append( ( site_name, link ) )
         return ret_val
@@ -286,7 +288,7 @@ class Interval( Tabular ):
 
         while True:
             try:
-                reader.next()
+                next(reader)
             except ParseError as e:
                 errors.append(e)
             except StopIteration:
@@ -635,8 +637,8 @@ class _RemoteCallMixin:
         """
         internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='%s_%s' % ( type, site_name ) )
         base_url = app.config.get( "display_at_callback", base_url )
-        display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
-                                         ( base_url, url_for( controller='root' ), dataset.id, type ) )
+        display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" %
+                                  ( base_url, url_for( controller='root' ), dataset.id, type ) )
         link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
         return link
 
@@ -723,7 +725,7 @@ class Gff( Tabular, _RemoteCallMixin ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return Tabular.make_html_table( self, dataset, column_names=self.column_names )
+        return self.make_html_table( dataset, column_names=self.column_names )
 
     def get_estimated_display_viewport( self, dataset ):
         """
@@ -808,7 +810,7 @@ class Gff( Tabular, _RemoteCallMixin ):
         if seqid is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
                 if site_name in app.datatypes_registry.get_display_sites('ucsc'):
-                    redirect_url = urllib.quote_plus(
+                    redirect_url = quote_plus(
                         "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" %
                         ( site_url, dataset.dbkey, seqid, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
@@ -823,7 +825,7 @@ class Gff( Tabular, _RemoteCallMixin ):
                 if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if seqid.startswith( 'chr' ) and len( seqid ) > 3:
                         seqid = seqid[3:]
-                    redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
+                    redirect_url = quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, seqid, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
         return ret_val
@@ -1170,7 +1172,7 @@ class Wiggle( Tabular, _RemoteCallMixin ):
                 if site_name in app.datatypes_registry.get_display_sites('gbrowse'):
                     if chrom.startswith( 'chr' ) and len( chrom ) > 3:
                         chrom = chrom[3:]
-                    redirect_url = urllib.quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
+                    redirect_url = quote_plus( "%s/?q=%s:%s..%s&eurl=%%s" % ( site_url, chrom, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
         return ret_val
@@ -1181,14 +1183,14 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         if chrom is not None:
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey ):
                 if site_name in app.datatypes_registry.get_display_sites('ucsc'):
-                    redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
+                    redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) )
                     link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url )
                     ret_val.append( ( site_name, link ) )
         return ret_val
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
+        return self.make_html_table( dataset, skipchars=['track', '#'] )
 
     def set_meta( self, dataset, overwrite=True, **kwd ):
         max_data_lines = None
@@ -1266,7 +1268,7 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         x = numpy.arange( t_start, t_end ) * resolution
         y = data[ t_start : t_end ]
 
-        return zip(x.tolist(), y.tolist())
+        return list(zip(x.tolist(), y.tolist()))
 
     def get_track_resolution( self, dataset, start, end):
         range = end - start
@@ -1305,7 +1307,7 @@ class CustomTrack ( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] )
+        return self.make_html_table( dataset, skipchars=['track', '#'] )
 
     def get_estimated_display_viewport( self, dataset, chrom_col=None, start_col=None, end_col=None ):
         """Return a chrom, start, stop tuple for viewing a file."""
@@ -1372,8 +1374,8 @@ class CustomTrack ( Tabular ):
             for site_name, site_url in app.datatypes_registry.get_legacy_sites_by_build('ucsc', dataset.dbkey):
                 if site_name in app.datatypes_registry.get_display_sites('ucsc'):
                     internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name )
-                    display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
-                    redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
+                    display_url = quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) )
+                    redirect_url = quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) )
                     link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url )
                     ret_val.append( (site_name, link) )
         return ret_val
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index eb22d3be33d..2bf02043848 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -61,12 +61,12 @@ class PepXmlReport(Tabular):
     file_ext = "pepxml.tsv"
 
     def __init__(self, **kwd):
-        Tabular.__init__(self, **kwd)
+        super(PepXmlReport, self).__init__(**kwd)
         self.column_names = ['Protein', 'Peptide', 'Assumed Charge', 'Neutral Pep Mass (calculated)', 'Neutral Mass', 'Retention Time', 'Start Scan', 'End Scan', 'Search Engine', 'PeptideProphet Probability', 'Interprophet Probabaility']
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return Tabular.make_html_table(self, dataset, column_names=self.column_names)
+        return self.make_html_table(dataset, column_names=self.column_names)
 
 
 class ProtXmlReport(Tabular):
@@ -76,7 +76,7 @@ class ProtXmlReport(Tabular):
     comment_lines = 1
 
     def __init__(self, **kwd):
-        Tabular.__init__(self, **kwd)
+        super(ProtXmlReport, self).__init__(**kwd)
         self.column_names = [
             "Entry Number", "Group Probability",
             "Protein", "Protein Link", "Protein Probability",
@@ -91,7 +91,7 @@ class ProtXmlReport(Tabular):
 
     def display_peek(self, dataset):
         """Returns formated html of peek"""
-        return Tabular.make_html_table(self, dataset, column_names=self.column_names)
+        return self.make_html_table(dataset, column_names=self.column_names)
 
 
 class ProteomicsXml(GenericXml):
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index b52a1e491a0..34bcff7152b 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -408,7 +408,7 @@ class Taxonomy( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return super(Taxonomy, self).make_html_table( dataset, column_names=self.column_names )
+        return self.make_html_table( dataset, column_names=self.column_names )
 
 
 @dataproviders.decorators.has_dataproviders
@@ -428,7 +428,7 @@ class Sam( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return super( Sam, self ).make_html_table( dataset, column_names=self.column_names )
+        return self.make_html_table( dataset, column_names=self.column_names )
 
     def sniff( self, filename ):
         """
@@ -614,7 +614,7 @@ class Pileup( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return super( Pileup, self ).make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
+        return self.make_html_table( dataset, column_parameter_alias={'chromCol': 'Chrom', 'startCol': 'Start', 'baseCol': 'Base'} )
 
     def repair_methods( self, dataset ):
         """Return options for removing errors along with a description"""
@@ -691,7 +691,7 @@ class Vcf( Tabular ):
 
     def display_peek( self, dataset ):
         """Returns formated html of peek"""
-        return super( Vcf, self ).make_html_table( dataset, column_names=self.column_names )
+        return self.make_html_table( dataset, column_names=self.column_names )
 
     def set_meta( self, dataset, **kwd ):
         super( Vcf, self ).set_meta( dataset, **kwd )