Merge pull request #2983 from nsoranzo/python3

Fix import order and Python3 compatibility for tools/
2026-09-24 16:30:27 +08:00 · 2016-09-30 11:08:27 -04:00
parent 7dadb932d8 11b4f3a60c
commit a1158a7905
67 changed files with 451 additions and 448 deletions
@@ -516,54 +516,4 @@ test/unit/workflows/test_render.py
 test/unit/workflows/test_workflow_progress.py
 test/unit/test_objectstore.py
 tool_list.py
-tools/data_source/fetch.py
-tools/data_source/genbank.py
-tools/data_source/hbvar_filter.py
-tools/data_source/import.py
-tools/data_source/microbial_import_code.py
-tools/data_source/microbial_import.py
-tools/data_source/upload.py
-tools/evolution/
-tools/extract/liftOver_wrapper.py
-tools/filters/axt_to_concat_fasta.py
-tools/filters/axt_to_fasta.py
-tools/filters/axt_to_lav_code.py
-tools/filters/axt_to_lav.py
-tools/filters/bed_to_gff_converter.py
-tools/filters/catWrapper.py
-tools/filters/convert_characters.py
-tools/filters/gff/
-tools/filters/gff_to_bed_converter.py
-tools/filters/gtf_to_bedgraph_converter.py
-tools/filters/join.py
-tools/filters/joinWrapper.py
-tools/filters/lav_to_bed_code.py
-tools/filters/lav_to_bed.py
-tools/filters/mergeCols.py
-tools/filters/randomlines.py
-tools/filters/random_lines_two_pass.py
-tools/filters/secure_hash_message_digest.py
-tools/filters/sff_extract.py
-tools/filters/sorter.py
-tools/filters/trimmer.py
-tools/filters/ucsc_gene_bed_to_exon_bed.py
-tools/filters/ucsc_gene_bed_to_intron_bed.py
-tools/filters/ucsc_gene_table_to_intervals.py
-tools/filters/uniq.py
-tools/filters/wiggle_to_simple.py
-tools/genomespace/
-tools/maf/
-tools/meme/
-tools/metag_tools/
-tools/next_gen_conversion/fastq_conversions.py
-tools/next_gen_conversion/fastq_gen_conv.py
-tools/next_gen_conversion/solid_to_fastq.py
-tools/ngs_simulation/
-tools/phenotype_association/
-tools/plotting/
-tools/solid_tools/
-tools/sr_assembly/
-tools/sr_mapping/
-tools/stats/grouping.py
-tools/stats/gsummary.py
-tools/visualization/
+tools/
@@ -72,8 +72,4 @@ scripts/db_shell.py
 scripts/drmaa_external_runner.py
 test/
 tool_list.py
-tools/data_source/
-tools/evolution/
-tools/sr_mapping/
-tools/stats/aggregate_scores_in_intervals.py
-tools/visualization/
+tools/
@@ -4,14 +4,14 @@
 import os
 import socket
 import sys
-from json import loads, dumps
+from json import dumps, loads

 from six.moves.urllib.parse import urlencode
 from six.moves.urllib.request import urlopen

-from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
+from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
 from galaxy.util import get_charset_from_http_headers

 GALAXY_PARAM_PREFIX = 'GALAXY'
@@ -13,7 +13,7 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
    data_type = param_dict.get( 'type', 'txt' )
    if data_type == 'txt':
        data_type = 'interval'  # All data is TSV, assume interval
-    name, data = list(out_data.items())[0]
+    name, data = next(iter(out_data.items()))
    data = app.datatypes_registry.change_datatype(data, data_type)
    data.name = data_name
    out_data[name] = data
@@ -35,7 +35,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
    except Exception as exc:
        raise Exception('Problems connecting to %s (%s)' % (URL, exc) )

-    name, data = list(out_data.items())[0]
+    data = next(iter(out_data.values()))

    fp = open(data.file_name, 'wb')
    size = 0
@@ -90,7 +90,7 @@ def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):

 # post processing, set build for data and add additional data to history
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    base_dataset = list(out_data.items())[0][1]
+    base_dataset = next(iter(out_data.values()))
    history = base_dataset.history
    if history is None:
        print("unknown history!")
@@ -118,7 +118,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
            chr = fields[2]
            dbkey = fields[3]
            file_type = fields[4]
-            name, data = list(out_data.items())[0]
+            data = next(iter(out_data.values()))
            data.set_size()
            basic_name = data.name
            data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] + " for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")"
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-from __future__ import with_statement
+from __future__ import print_function

 import sys

@@ -7,7 +7,7 @@ from bx.bbi.bigwig_file import BigWigFile


 def die( message ):
-    print >> sys.stderr, message
+    print(message, file=sys.stderr)
    sys.exit(1)


@@ -100,9 +100,9 @@ def main():
                score_val = 'NA'
            else:
                die( '%s line %d: chrom=%s, start=%d, score_list_len = %d' % ( input_filename, line_number, chrom, start, score_list_len ) )
-            print >> ofh, '\t'.join( [line, score_val] )
+            print('\t'.join( [line, score_val] ), file=ofh)
        else:
-            print >> ofh, line
+            print(line, file=ofh)

    bwfh.close()
    ifh.close()
@@ -13,7 +13,7 @@ def validate_input( trans, error_map, param_values, page_param_map ):
    dbkeys = set()
    data_param_names = set()
    data_params = 0
-    for name, param in page_param_map.iteritems():
+    for name, param in page_param_map.items():
        if isinstance( param, DataToolParameter ):
            # for each dataset parameter
            if param_values.get(name, None) is not None:
@@ -9,6 +9,8 @@ usage: %prog $input $out_file1
    -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction
    -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
 """
+from __future__ import print_function
+
 import os
 import subprocess
 import sys
@@ -17,7 +19,7 @@ import tempfile
 import bx.seq.nib
 import bx.seq.twobit
 from bx.cookbook import doc_optparse
-from bx.intervals.io import Header, Comment
+from bx.intervals.io import Comment, Header

 from galaxy.datatypes.util import gff_util
 from galaxy.tools.util.galaxyops import parse_cols_arg
@@ -45,7 +47,7 @@ def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
        if line and not line.startswith( "#" ) and line.startswith( 'seq' ):
            fields = line.split( '\t' )
            if len( fields) >= 3 and fields[1] == dbkey:
-                print "Using *.nib genomic reference files"
+                print("Using *.nib genomic reference files")
                return fields[2].strip()

    # If no entry in aligseq.loc was found, check for the presence of a *.2bit file in twobit.loc
@@ -55,7 +57,7 @@ def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
        if line and not line.startswith( "#" ) and line.endswith( '.2bit' ):
            fields = line.split( '\t' )
            if len(fields) >= 2 and fields[0] == dbkey:
-                print "Using a *.2bit genomic reference file"
+                print("Using a *.2bit genomic reference file")
                return fields[1].strip()

    return ''
@@ -299,10 +301,10 @@ def __main__():
    if warnings:
        warn_msg = "%d warnings, 1st is: " % len( warnings )
        warn_msg += warnings[0]
-        print warn_msg
+        print(warn_msg)
    if skipped_lines:
        # Error message includes up to the first 10 skipped lines.
-        print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) )
+        print('Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) ))

    # Clean up temp file.
    if fasta_file:
@@ -2,6 +2,8 @@
 """
 Adapted from bx/scripts/axt_to_concat_fasta.py
 """
+from __future__ import print_function
+
 import sys

 import bx.align.axt
@@ -40,8 +42,8 @@ def main():
 # TODO: this should be moved to a bx.align.fasta module
 def print_component_as_fasta(text, src):
    header = ">" + src
-    print header
-    print text
+    print(header)
+    print(text)


 if __name__ == "__main__":
@@ -2,6 +2,8 @@
 """
 Adapted from bx/scripts/axt_to_fasta.py
 """
+from __future__ import print_function
+
 import sys

 import bx.align.axt
@@ -34,7 +36,7 @@ def main():
            id = None
        print_component_as_fasta(a.components[0], id)
        print_component_as_fasta(a.components[1], id)
-        print
+        print()


 # TODO: this should be moved to a bx.align.fasta module
@@ -42,8 +44,8 @@ def print_component_as_fasta(c, id=None):
    header = ">%s_%s_%s" % (c.src, c.start, c.start + c.size)
    if id is not None:
        header += " " + id
-    print header
-    print c.text
+    print(header)
+    print(c.text)

 if __name__ == "__main__":
    main()
@@ -9,6 +9,8 @@ Application to convert AXT file to LAV file
 The application reads an AXT file from standard input and writes a LAV file to
 standard out;  some statistics are written to standard error.
 """
+from __future__ import print_function
+
 import sys

 import bx.align.axt
@@ -114,13 +116,13 @@ def main():
        primary_c = axtBlock.get_component_by_src_start(primary)
        secondary_c = axtBlock.get_component_by_src_start(secondary)

-        print >>seq_file1, ">%s_%s_%s_%s" % (primary_c.src, secondary_c.strand, primary_c.start, primary_c.start + primary_c.size)
-        print >>seq_file1, primary_c.text
-        print >>seq_file1
+        print(">%s_%s_%s_%s" % (primary_c.src, secondary_c.strand, primary_c.start, primary_c.start + primary_c.size), file=seq_file1)
+        print(primary_c.text, file=seq_file1)
+        print(file=seq_file1)

-        print >>seq_file2, ">%s_%s_%s_%s" % (secondary_c.src, secondary_c.strand, secondary_c.start, secondary_c.start + secondary_c.size)
-        print >>seq_file2, secondary_c.text
-        print >>seq_file2
+        print(">%s_%s_%s_%s" % (secondary_c.src, secondary_c.strand, secondary_c.start, secondary_c.start + secondary_c.size), file=seq_file2)
+        print(secondary_c.text, file=seq_file2)
+        print(file=seq_file2)
        axtsWritten += 1

    out.close()
@@ -1,8 +1,6 @@

 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    for name, data in out_data.items():
-        if name == "seq_file2":
-            data.dbkey = param_dict['dbkey_2']
-            app.model.context.add( data )
-            app.model.context.flush()
-            break
+    data = out_data["seq_file2"]
+    data.dbkey = param_dict['dbkey_2']
+    app.model.context.add( data )
+    app.model.context.flush()
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # This code exists in 2 places: ~/datatypes/converters and ~/tools/filters
+from __future__ import print_function
+
 import sys

 assert sys.version_info[:2] >= ( 2, 4 )
@@ -69,7 +71,7 @@ def __main__():
    info_msg = "%i lines converted to GFF version 2.  " % ( i + 1 - skipped_lines )
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
-    print info_msg
+    print(info_msg)

 if __name__ == "__main__":
    __main__()
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 # By, Guruprasad Ananda.
+from __future__ import print_function

 import optparse
 import re
@@ -46,7 +47,7 @@ def __main__():
                    skipped += 1

    if skipped:
-        print "Skipped %d lines as invalid." % skipped
+        print("Skipped %d lines as invalid." % skipped)

 if __name__ == "__main__":
    __main__()
@@ -5,6 +5,8 @@ Extract features from GFF file.

 usage: %prog input1 out_file1 column features
 """
+from __future__ import print_function
+
 import sys

 from bx.cookbook import doc_optparse
@@ -45,7 +47,7 @@ def main():
                pass
    fo.close()

-    print 'Column %d features: %s' % ( column + 1, features )
+    print('Column %d features: %s' % ( column + 1, features ))

 if __name__ == "__main__":
    main()
@@ -3,7 +3,7 @@
 # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
 # TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats/). The commonalities should be
 # abstracted and leveraged in each filtering tool.
-from __future__ import division
+from __future__ import division, print_function

 import sys
 from json import loads
@@ -136,7 +136,7 @@ for i, line in enumerate( open( in_fname ) ):

 valid_filter = True
 try:
-    exec code
+    exec(code)
 except Exception as e:
    out.close()
    if str( e ).startswith( 'invalid syntax' ):
@@ -148,10 +148,10 @@ except Exception as e:
 if valid_filter:
    out.close()
    valid_lines = total_lines - skipped_lines
-    print 'Filtering with %s, ' % ( cond_text )
+    print('Filtering with %s, ' % ( cond_text ))
    if valid_lines > 0:
-        print 'kept %4.2f%% of %d lines.' % ( 100.0 * lines_kept / valid_lines, total_lines )
+        print('kept %4.2f%% of %d lines.' % ( 100.0 * lines_kept / valid_lines, total_lines ))
    else:
-        print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text
+        print('Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text)
    if skipped_lines > 0:
-        print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+        print('Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ))
@@ -5,6 +5,8 @@ Filter a gff file using a criterion based on feature counts for a transcript.
 Usage:
 %prog input_name output_name feature_name condition
 """
+from __future__ import print_function
+
 import sys

 from bx.intervals.io import GenomicInterval
@@ -53,7 +55,7 @@ def __main__():
            except:
                number = None
            if empty != "" or not number:
-                print >> sys.stderr, "Invalid condition: %s, cannot filter." % condition
+                print("Invalid condition: %s, cannot filter." % condition, file=sys.stderr)
                return
            break

@@ -84,7 +86,7 @@ def __main__():
        ( kept_features, i, float(kept_features) / i * 100.0, feature_name + condition )
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
-    print info_msg
+    print(info_msg)

 if __name__ == "__main__":
    __main__()
@@ -4,6 +4,7 @@
 # Usage:
 # python gff_filter_by_attribute_values.py <gff_file> <attribute_name> <ids_file> <output_file>
 #
+from __future__ import print_function

 import sys

@@ -45,7 +46,7 @@ def parse_gff_attributes( attr_str ):
    return attributes


-def filter( gff_file, attribute_name, ids_file, output_file ):
+def gff_filter( gff_file, attribute_name, ids_file, output_file ):
    # Put ids in dict for quick lookup.
    ids_dict = {}
    for line in open( ids_file ):
@@ -63,7 +64,7 @@ def filter( gff_file, attribute_name, ids_file, output_file ):
 if __name__ == "__main__":
    # Handle args.
    if len( sys.argv ) != 5:
-        print >> sys.stderr, "usage: python %s <gff_file> <attribute_name> <ids_file> <output_file>" % sys.argv[0]
+        print("usage: python %s <gff_file> <attribute_name> <ids_file> <output_file>" % sys.argv[0], file=sys.stderr)
        sys.exit( -1 )
    gff_file, attribute_name, ids_file, output_file = sys.argv[1:]
-    filter( gff_file, attribute_name, ids_file, output_file )
+    gff_filter( gff_file, attribute_name, ids_file, output_file )
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import sys

 from galaxy.datatypes.util.gff_util import parse_gff_attributes
@@ -19,7 +21,7 @@ def get_bed_line( chrom, name, strand, blocks ):
    #

    # Get transcript start, end.
-    t_start = sys.maxint
+    t_start = sys.maxsize
    t_end = -1
    for block_start, block_end in blocks:
        if block_start < t_start:
@@ -65,8 +67,8 @@ def __main__():
            try:
                # GFF format: chrom source, name, chromStart, chromEnd, score, strand, attributes
                elems = line.split( '\t' )
-                start = str( long( elems[3] ) - 1 )
-                coords = [ long( start ), long( elems[4] ) ]
+                start = str( int( elems[3] ) - 1 )
+                coords = [ int( start ), int( elems[4] ) ]
                strand = elems[6]
                if strand not in ['+', '-']:
                    strand = '+'
@@ -127,7 +129,7 @@ def __main__():
    info_msg = "%i lines converted to BED.  " % ( i + 1 - skipped_lines )
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
-    print info_msg
+    print(info_msg)

 if __name__ == "__main__":
    __main__()
@@ -11,12 +11,13 @@
 # -o Output file
 # -pattern RegEx pattern
 # -v true or false (output NON-matching lines)
+from __future__ import print_function

-import commands
 import os
 import re
+import subprocess
 import sys
-from subprocess import Popen, PIPE
+from subprocess import PIPE, Popen
 from tempfile import NamedTemporaryFile


@@ -38,31 +39,31 @@ def main():
    try:
        opts = getopts(args)
    except IndexError:
-        print "Usage:"
-        print " -i Input file"
-        print " -o Output file"
-        print " -pattern RegEx pattern"
-        print " -v true or false (Invert match)"
+        print("Usage:")
+        print(" -i Input file")
+        print(" -o Output file")
+        print(" -pattern RegEx pattern")
+        print(" -v true or false (Invert match)")
        return 0

    outputfile = opts.get("-o")
    if outputfile is None:
-        print "No output file specified."
+        print("No output file specified.")
        return -1

    inputfile = opts.get("-i")
    if inputfile is None:
-        print "No input file specified."
+        print("No input file specified.")
        return -2

    invert = opts.get("-v")
    if invert is None:
-        print "Match style (Invert or normal) not specified."
+        print("Match style (Invert or normal) not specified.")
        return -3

    pattern = opts.get("-pattern")
    if pattern is None:
-        print "RegEx pattern not specified."
+        print("RegEx pattern not specified.")
        return -4

    # All inputs have been specified at this point, now validate.
@@ -89,22 +90,22 @@ def main():

    # verify that filename and inversion flag are in the correct format
    if not fileRegEx.match(outputfile):
-        print "Illegal output filename."
+        print("Illegal output filename.")
        return -5
    if not fileRegEx.match(inputfile):
-        print "Illegal input filename."
+        print("Illegal input filename.")
        return -6
    if not invertRegEx.match(invert):
-        print "Illegal invert option."
+        print("Illegal invert option.")
        return -7

    # invert grep search?
    if invert == "true":
        invertflag = "-v"
-        print "Not matching pattern: %s" % pattern
+        print("Not matching pattern: %s" % pattern)
    else:
        invertflag = ""
-        print "Matching pattern: %s" % pattern
+        print("Matching pattern: %s" % pattern)

    # set version flag
    versionflag = "-P"
@@ -123,7 +124,7 @@ def main():
    commandline = "grep %s %s -f %s %s > %s" % ( versionflag, invertflag, pattern_file_name, inputfile, outputfile )

    # run grep
-    errorcode, stdout = commands.getstatusoutput(commandline)
+    errorcode = subprocess.call(commandline, shell=True)

    # remove temp pattern file
    os.unlink( pattern_file_name )
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import os
 import sys
 import tempfile
@@ -78,7 +80,7 @@ def __main__():
    info_msg = "%i lines converted to BEDGraph.  " % ( i + 1 - skipped_lines )
    if skipped_lines > 0:
        info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." % ( skipped_lines, first_skipped_line )
-    print info_msg
+    print(info_msg)

 if __name__ == "__main__":
    __main__()
@@ -5,8 +5,8 @@ Script to Join Two Files on specified columns.

 Takes two tab delimited files, two column numbers (base 1) and outputs a new tab delimited file with lines joined by tabs.
 User can also opt to have have non-joining rows of file1 echoed.
-
 """
+from __future__ import print_function

 import json
 import optparse
@@ -24,7 +24,7 @@ class OffsetList:
        self.file = tempfile.NamedTemporaryFile( 'w+b' )
        if fmt:
            self.fmt = fmt
-        elif filesize and filesize <= sys.maxint * 2:
+        elif filesize and filesize <= sys.maxsize * 2:
            self.fmt = 'I'
        else:
            self.fmt = 'Q'
@@ -88,14 +88,14 @@ class SortedOffsets( OffsetList ):
    def merge_with_dict( self, new_offset_dict ):
        if not new_offset_dict:
            return  # no items to merge in
-        keys = new_offset_dict.keys()
+        keys = list(new_offset_dict.keys())
        keys.sort()
        identifier2 = keys.pop( 0 )

        result_offsets = OffsetList( fmt=self.fmt )
        offsets1 = enumerate( self.get_offsets() )
        try:
-            index1, offset1 = offsets1.next()
+            index1, offset1 = next(offsets1)
            identifier1 = self.get_identifier_by_offset( offset1 )
        except StopIteration:
            offset1 = None
@@ -121,7 +121,7 @@ class SortedOffsets( OffsetList ):
            else:
                result_offsets.add_offset( offset1 )
                try:
-                    index1, offset1 = offsets1.next()
+                    index1, offset1 = next(offsets1)
                    identifier1 = self.get_identifier_by_offset( offset1 )
                except StopIteration:
                    offset1 = None
@@ -188,7 +188,7 @@ class OffsetIndex:
            offset_index += 1

    def get_offsets( self ):
-        keys = self._offsets.keys()
+        keys = list(self._offsets.keys())
        keys.sort()
        for key in keys:
            for offset in self._offsets[key].get_offsets():
@@ -199,7 +199,7 @@ class OffsetIndex:
        return self.file.readline()

    def get_identifiers_offsets( self ):
-        keys = self._offsets.keys()
+        keys = list(self._offsets.keys())
        keys.sort()
        for key in keys:
            for offset in self._offsets[key].get_offsets():
@@ -216,7 +216,7 @@ class OffsetIndex:
        if not d:
            return  # no data to merge
        self._index = None
-        keys = d.keys()
+        keys = list(d.keys())
        keys.sort()
        identifier = keys.pop( 0 )
        first_char = identifier[0]
@@ -360,7 +360,7 @@ def main():
        try:
            fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) )  # json.load( open( options.fill_options_file ) )
        except Exception as e:
-            print "Warning: Ignoring fill options due to json error (%s)." % e
+            print("Warning: Ignoring fill options due to json error (%s)." % e)
    if fill_options is None:
        fill_options = Bunch()
    if 'fill_unjoined_only' not in fill_options:
@@ -377,7 +377,7 @@ def main():
        column2 = int( args[3] ) - 1
        out_filename = args[4]
    except:
-        print >> sys.stderr, "Error parsing command line."
+        print("Error parsing command line.", file=sys.stderr)
        sys.exit()

    # Character for splitting fields and joining lines
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # Reads a LAV file and writes two BED files.
+from __future__ import print_function
+
 import sys

 import bx.align.lav
@@ -38,13 +40,13 @@ def main():
        bedsWritten += 1

    for spec, file in species.items():
-        print "#FILE\t%s\t%s" % (file.name, spec)
+        print("#FILE\t%s\t%s" % (file.name, spec))

    lav_file.close()
    bed_file1.close()
    bed_file2.close()

-    print "%d lav blocks read, %d regions written\n" % (lavsRead, bedsWritten)
+    print("%d lav blocks read, %d regions written\n" % (lavsRead, bedsWritten))

 if __name__ == "__main__":
    main()
@@ -8,7 +8,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
            filename_to_build[fields[1]] = fields[2].strip()
        else:
            new_stdout = "%s%s" % ( new_stdout, line )
-    for name, data in out_data.items():
+    for data in out_data.values():
        try:
            data.info = "%s\n%s" % ( new_stdout, stderr )
            data.dbkey = filename_to_build[data.file_name]
@@ -1,3 +1,5 @@
+from __future__ import print_function
+
 import sys


@@ -31,10 +33,10 @@ def __main__():
                except:
                    skipped_lines += 1

-            print >>outfile, line
+            print(line, file=outfile)

    if skipped_lines > 0:
-        print 'Skipped %d invalid lines' % skipped_lines
+        print('Skipped %d invalid lines' % skipped_lines)

 if __name__ == "__main__":
    __main__()
@@ -3,6 +3,7 @@
 # Selects N random lines from a file and outputs to another file, maintaining original line order
 # allows specifying a seed
 # does two passes to determine line offsets/count, and then to output contents
+from __future__ import print_function

 import optparse
 import random
@@ -68,9 +69,9 @@ def __main__():
        writer( readliner() )
    input.close()
    output.close()
-    print "Kept %i of %i total lines." % ( num_lines, total_lines )
+    print("Kept %i of %i total lines." % ( num_lines, total_lines ))
    if options.seed is not None:
-        print 'Used random seed of "%s".' % options.seed
+        print('Used random seed of "%s".' % options.seed)

 if __name__ == "__main__":
    __main__()
@@ -33,14 +33,14 @@ def __main__():
    while True:
        chunk = input.read( CHUNK_SIZE )
        if chunk:
-            for algorithm in algorithms.itervalues():
+            for algorithm in algorithms.values():
                algorithm.update( chunk )
        else:
            break

    output = open( options.output, 'wb' )
    output.write( '#%s\n' % ( '\t'.join( algorithms.keys() ) ) )
-    output.write( '%s\n' % ( '\t'.join( map( lambda x: x.hexdigest(), algorithms.values() ) ) ) )
+    output.write( '%s\n' % ( '\t'.join( x.hexdigest() for x in algorithms.values() ) ) )
    output.close()

 if __name__ == "__main__":
@@ -24,12 +24,7 @@ sequence will be removed, even if occuring multiple times.'''
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.

-__author__ = 'Jose Blanca and Bastien Chevreux'
-__copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'
-__license__ = 'GPLv3 or later'
-__version__ = '0.2.10'
-__email__ = 'jblanca@btc.upv.es'
-__status__ = 'beta'
+from __future__ import print_function

 import os
 import struct
@@ -37,6 +32,12 @@ import subprocess
 import sys
 import tempfile

+__author__ = 'Jose Blanca and Bastien Chevreux'
+__copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'
+__license__ = 'GPLv3 or later'
+__version__ = '0.2.10'
+__email__ = 'jblanca@btc.upv.es'
+__status__ = 'beta'

 fake_sff_name = 'fake_sff_name'

@@ -528,7 +529,7 @@ def fragment_sequences(sequence, qualities, splitchar):
    #  the sequence find find variations and splices on seq and qual

    if len(sequence) != len(qualities):
-        print sequence, qualities
+        print(sequence, qualities)
        raise RuntimeError("Internal error: length of sequence and qualities don't match???")

    retlist = ([])
@@ -985,7 +986,7 @@ def check_for_dubious_startseq(seqcheckstore, sffname, seqdata):
        if not foundinloop:
            break
    if len(foundproblem):
-        print foundproblem
+        print(foundproblem)


 def parse_extra_info(info):
@@ -1094,14 +1095,14 @@ def clip_read(data):
 def tests_for_ssaha():
    '''Tests whether SSAHA2 can be successfully called.'''
    try:
-        print "Testing whether SSAHA2 is installed and can be launched ... ",
+        print("Testing whether SSAHA2 is installed and can be launched ... ", end=' ')
        sys.stdout.flush()
        fh = open('/dev/null', 'w')
        subprocess.call(["ssaha2"], stdout=fh)
        fh.close()
-        print "ok."
+        print("ok.")
    except:
-        print "nope? Uh oh ...\n\n"
+        print("nope? Uh oh ...\n\n")
        raise RuntimeError('Could not launch ssaha2. Have you installed it? Is it in your path?')


@@ -1129,15 +1130,15 @@ def launch_ssaha(linker_fname, query_fname, output_fh):
    tests_for_ssaha()

    try:
-        print "Searching linker sequences with SSAHA2 (this may take a while) ... ",
+        print("Searching linker sequences with SSAHA2 (this may take a while) ... ", end=' ')
        sys.stdout.flush()
        retcode = subprocess.call(["ssaha2", "-output", "ssaha2", "-solexa", "-kmer", "4", "-skip", "1", linker_fname, query_fname], stdout=output_fh)
        if retcode:
            raise RuntimeError('Ups.')
        else:
-            print "ok."
+            print("ok.")
    except:
-        print "\n"
+        print("\n")
        raise RuntimeError('An error occured during the SSAHA2 execution, aborting.')


@@ -1147,14 +1148,14 @@ def read_ssaha_data(ssahadata_fh):
    (ssaha paired-end matches) dictionary'''
    global ssahapematches

-    print "Parsing SSAHA2 result file ... ",
+    print("Parsing SSAHA2 result file ... ", end=' ')
    sys.stdout.flush()

    for line in ssahadata_fh:
        if line.startswith('ALIGNMENT'):
            ml = line.split()
            if len(ml) != 12:
-                print "\n", line,
+                print("\n", line, end=' ')
                raise RuntimeError('Expected 12 elements in the SSAHA2 line with ALIGMENT keyword, but found ' + str(len(ml)))
            if ml[2] not in ssahapematches:
                ssahapematches[ml[2]] = ([])
@@ -1167,7 +1168,7 @@ def read_ssaha_data(ssahadata_fh):
                ml[4], ml[5] = ml[5], ml[4]
                ssahapematches[ml[2]].append(ml[1:-1])

-    print "done."
+    print("done.")


 ##########################################################################
@@ -1326,7 +1327,7 @@ def main():
            raise RuntimeError("No SFF file given?")
        extract_reads_from_sff(config, args)
    except (OSError, IOError, RuntimeError) as errval:
-        print errval
+        print(errval)
        return 1

    if stern_warning:
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function

 import optparse
 import sys
@@ -80,7 +81,7 @@ options (listed below) default to 'None' if omitted
        line = line.rstrip( '\r\n' )
        if line:
            if options.fastq and i % 2 == 0:
-                print line
+                print(line)
                continue

            if line[0] not in invalid_starts:
@@ -105,7 +106,7 @@ options (listed below) default to 'None' if omitted
                    else:
                        fields[col - 1] = fields[col - 1][ int( options.start ) - 1: ]
                    line = '\t'.join(fields)
-            print line
+            print(line)

 if __name__ == "__main__":
    main()
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Read a table dump in the UCSC gene table format and print a tab separated
 list of intervals corresponding to requested features of each gene.
@@ -14,9 +13,9 @@ options:
  -i, --input=inputfile       input file
  -o, --output=outputfile     output file
 """
+from __future__ import print_function

 import optparse
-import string
 import sys

 assert sys.version_info[:2] >= ( 2, 4 )
@@ -40,16 +39,16 @@ def main():
    try:
        out_file = open(options.output, "w")
    except:
-        print >> sys.stderr, "Bad output file."
+        print("Bad output file.", file=sys.stderr)
        sys.exit(0)

    try:
        in_file = open(options.input)
    except:
-        print >> sys.stderr, "Bad input file."
+        print("Bad input file.", file=sys.stderr)
        sys.exit(0)

-    print "Region:", options.region + ";"
+    print("Region:", options.region + ";")
    """print "Only overlap with Exons:",
    if options.exons:
        print "Yes"
@@ -92,10 +91,9 @@ def main():
            # the region of interest, otherwise print the span of the region
        # options.exons is always TRUE
            if options.exons:
-                exon_starts = map( int, fields[11].rstrip( ',\n' ).split( ',' ) )
-                exon_starts = map((lambda x: x + tx_start ), exon_starts)
-                exon_ends = map( int, fields[10].rstrip( ',\n' ).split( ',' ) )
-                exon_ends = map((lambda x, y: x + y ), exon_starts, exon_ends)
+                exon_starts = [int(_) + tx_start for _ in fields[11].rstrip( ',\n' ).split( ',' )]
+                exon_ends = [int(_) for _ in fields[10].rstrip( ',\n' ).split( ',' )]
+                exon_ends = [x + y for x, y in zip(exon_starts, exon_ends)]

        # for Intron regions:
            if options.region == 'intron':
@@ -134,7 +132,7 @@ def main():

 def print_tab_sep(out_file, *args ):
    """Print items in `l` to stdout separated by tabs"""
-    print >>out_file, string.join( [ str( f ) for f in args ], '\t' )
+    print('\t'.join(str( f ) for f in args), file=out_file)

 if __name__ == "__main__":
    main()
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Read a table dump in the UCSC gene table format and print a tab separated
 list of intervals corresponding to requested features of each gene.
@@ -14,9 +13,9 @@ options:
  -i, --input=inputfile       input file
  -o, --output=outputfile     output file
 """
+from __future__ import print_function

 import optparse
-import string
 import sys

 assert sys.version_info[:2] >= ( 2, 4 )
@@ -35,13 +34,13 @@ def main():
    try:
        out_file = open(options.output, "w")
    except:
-        print >> sys.stderr, "Bad output file."
+        print("Bad output file.", file=sys.stderr)
        sys.exit(0)

    try:
        in_file = open(options.input)
    except:
-        print >> sys.stderr, "Bad input file."
+        print("Bad input file.", file=sys.stderr)
        sys.exit(0)

    # Read table and handle each gene
@@ -60,10 +59,9 @@ def main():
            int( fields[6] )
            int( fields[7] )

-            exon_starts = map( int, fields[11].rstrip( ',\n' ).split( ',' ) )
-            exon_starts = map((lambda x: x + tx_start ), exon_starts)
-            exon_ends = map( int, fields[10].rstrip( ',\n' ).split( ',' ) )
-            exon_ends = map((lambda x, y: x + y ), exon_starts, exon_ends)
+            exon_starts = [int(_) + tx_start for _ in fields[11].rstrip( ',\n' ).split( ',' )]
+            exon_ends = [int(_) for _ in fields[10].rstrip( ',\n' ).split( ',' )]
+            exon_ends = [x + y for x, y in zip(exon_starts, exon_ends)]

            i = 0
            while i < len(exon_starts) - 1:
@@ -80,7 +78,7 @@ def main():

 def print_tab_sep(out_file, *args ):
    """Print items in `l` to stdout separated by tabs"""
-    print >>out_file, string.join( [ str( f ) for f in args ], '\t' )
+    print('\t'.join(str( f ) for f in args), file=out_file)

 if __name__ == "__main__":
    main()
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Read a table dump in the UCSC gene table format and print a tab separated
 list of intervals corresponding to requested features of each gene.
@@ -14,9 +13,9 @@ options:
  -i, --input=inputfile       input file
  -o, --output=outputfile     output file
 """
+from __future__ import print_function

 import optparse
-import string
 import sys

 assert sys.version_info[:2] >= ( 2, 4 )
@@ -40,21 +39,21 @@ def main():
    try:
        out_file = open(options.output, "w")
    except:
-        print >> sys.stderr, "Bad output file."
+        print("Bad output file.", file=sys.stderr)
        sys.exit(0)

    try:
        in_file = open(options.input)
    except:
-        print >> sys.stderr, "Bad input file."
+        print("Bad input file.", file=sys.stderr)
        sys.exit(0)

-    print "Region:", options.region + ";"
-    print "Only overlap with Exons:",
+    print("Region:", options.region + ";")
+    print("Only overlap with Exons:", end=' ')
    if options.exons:
-        print "Yes"
+        print("Yes")
    else:
-        print "No"
+        print("No")

    # Read table and handle each gene
    for line in in_file:
@@ -111,7 +110,7 @@ def main():

 def print_tab_sep(out_file, *args ):
    """Print items in `l` to stdout separated by tabs"""
-    print >>out_file, string.join( [ str( f ) for f in args ], '\t' )
+    print('\t'.join(str( f ) for f in args), file=out_file)

 if __name__ == "__main__":
    main()
@@ -15,9 +15,10 @@
 # -o            Output file
 # -d            Delimiter
 # -c            Column list (Comma Seperated)
+from __future__ import print_function

-import commands
 import re
+import subprocess
 import sys


@@ -39,46 +40,46 @@ def main():
    try:
        opts = getopts(args)
    except IndexError:
-        print "Usage:"
-        print " -i        Input file"
-        print " -o        Output file"
-        print " -c        Column list (comma seperated)"
-        print " -d        Delimiter:"
-        print "                     T   Tab"
-        print "                     C   Comma"
-        print "                     D   Dash"
-        print "                     U   Underscore"
-        print "                     P   Pipe"
-        print "                     Dt  Dot"
-        print "                     Sp  Space"
-        print " -s        Sorting: value (default), largest, or smallest"
+        print("Usage:")
+        print(" -i        Input file")
+        print(" -o        Output file")
+        print(" -c        Column list (comma seperated)")
+        print(" -d        Delimiter:")
+        print("                     T   Tab")
+        print("                     C   Comma")
+        print("                     D   Dash")
+        print("                     U   Underscore")
+        print("                     P   Pipe")
+        print("                     Dt  Dot")
+        print("                     Sp  Space")
+        print(" -s        Sorting: value (default), largest, or smallest")
        return 0

    outputfile = opts.get("-o")
    if outputfile is None:
-        print "No output file specified."
+        print("No output file specified.")
        return -1

    inputfile = opts.get("-i")
    if inputfile is None:
-        print "No input file specified."
+        print("No input file specified.")
        return -2

    delim = opts.get("-d")
    if delim is None:
-        print "Field delimiter not specified."
+        print("Field delimiter not specified.")
        return -3

    columns = opts.get("-c")
    if columns is None or columns == 'None':
-        print "Columns not specified."
+        print("Columns not specified.")
        return -4

    sorting = opts.get("-s")
    if sorting is None:
        sorting = "value"
    if sorting not in ["value", "largest", "smallest"]:
-        print "Unknown sorting option %r" % sorting
+        print("Unknown sorting option %r" % sorting)
        return -5

    # All inputs have been specified at this point, now validate.
@@ -86,13 +87,13 @@ def main():
    columnRegEx = re.compile("([0-9]{1,},?)+")

    if not columnRegEx.match(columns):
-        print "Illegal column specification."
+        print("Illegal column specification.")
        return -4
    if not fileRegEx.match(outputfile):
-        print "Illegal output filename."
+        print("Illegal output filename.")
        return -5
    if not fileRegEx.match(inputfile):
-        print "Illegal input filename."
+        print("Illegal input filename.")
        return -6

    column_list = re.split(",", columns)
@@ -130,9 +131,9 @@ def main():
    # uniq -C puts a space between the count and the field, want a tab.
    # To replace just first tab, use sed again with 1 as the index
    commandline += " | sed 's/^\ *//' | sed 's/ /\t/1' > " + outputfile
-    errorcode, stdout = commands.getstatusoutput(commandline)
+    errorcode = subprocess.call(commandline, shell=True)

-    print "Count of unique values in " + columns_for_display
+    print("Count of unique values in " + columns_for_display)
    return errorcode

 if __name__ == "__main__":
@@ -1,10 +1,11 @@
 #!/usr/bin/env python
-
 """
 Read a wiggle track and print out a series of lines containing
 "chrom position score". Ignores track lines, handles bed, variableStep
 and fixedStep wiggle lines.
 """
+from __future__ import print_function
+
 import sys

 import bx.wiggle
@@ -33,7 +34,7 @@ def main():
            out_file.write( "%s\n" % "\t".join( map( str, fields ) ) )
    except UCSCLimitException:
        # Wiggle data was truncated, at the very least need to warn the user.
-        print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
+        print('Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.')
    except ValueError as e:
        in_file.close()
        out_file.close()
@@ -1,8 +1,9 @@
 #!/usr/bin/env python
 # Dan Blankenberg
+from __future__ import print_function
+
 import base64
 import binascii
-import cookielib
 import datetime
 import hashlib
 import json
@@ -10,9 +11,12 @@ import logging
 import optparse
 import os
 import tempfile
-import urllib
-import urllib2
-from urlparse import urljoin
+
+import six
+from six.moves import http_cookiejar
+from six.moves.urllib.error import HTTPError
+from six.moves.urllib.parse import quote, urlencode, urljoin
+from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen

 log = logging.getLogger( "tools.genomespace.genomespace_exporter" )

@@ -56,19 +60,19 @@ def chunk_write( source_stream, target_stream, source_method="read", target_meth

 def get_cookie_opener( gs_username, gs_token, gs_toolname=None ):
    """ Create a GenomeSpace cookie opener """
-    cj = cookielib.CookieJar()
+    cj = http_cookiejar.CookieJar()
    for cookie_name, cookie_value in [ ( 'gs-token', gs_token ), ( 'gs-username', gs_username ) ]:
        # create a super-cookie, valid for all domains
-        cookie = cookielib.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
+        cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
        cj.set_cookie( cookie )
-    cookie_opener = urllib2.build_opener( urllib2.HTTPCookieProcessor( cj ) )
+    cookie_opener = build_opener( HTTPCookieProcessor( cj ) )
    cookie_opener.addheaders.append( ( 'gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME ) )
    return cookie_opener


 def get_genomespace_site_urls():
    genomespace_sites = {}
-    for line in urllib2.urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
+    for line in urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
        line = line.rstrip()
        if not line or line.startswith( "#" ):
            continue
@@ -86,11 +90,11 @@ def get_directory( url_opener, dm_url, path ):
    dir_dict = {}
    for i, sub_path in enumerate( path ):
        url = "%s/%s" % ( url, sub_path )
-        dir_request = urllib2.Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' } )
+        dir_request = Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' } )
        dir_request.get_method = lambda: 'GET'
        try:
            dir_dict = json.loads( url_opener.open( dir_request ).read() )
-        except urllib2.HTTPError:
+        except HTTPError:
            # print "e", e, url #punting, assuming lack of permissions at this low of a level...
            continue
        break
@@ -114,15 +118,15 @@ def create_directory( url_opener, directory_dict, new_dir, dm_url ):
    for dir_slice in new_dir:
        if dir_slice in ( '', '/', None ):
            continue
-        url = '/'.join( ( directory_dict['url'], urllib.quote( dir_slice.replace( '/', '_' ), safe='' ) ) )
-        new_dir_request = urllib2.Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' }, data=json.dumps( payload ) )
+        url = '/'.join( ( directory_dict['url'], quote( dir_slice.replace( '/', '_' ), safe='' ) ) )
+        new_dir_request = Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' }, data=json.dumps( payload ) )
        new_dir_request.get_method = lambda: 'PUT'
        directory_dict = json.loads( url_opener.open( new_dir_request ).read() )
    return directory_dict


 def get_genome_space_launch_apps( atm_url, url_opener, file_url, file_type ):
-    gs_request = urllib2.Request( "%s/%s/webtool/descriptor" % ( atm_url, GENOMESPACE_API_VERSION_STRING ) )
+    gs_request = Request( "%s/%s/webtool/descriptor" % ( atm_url, GENOMESPACE_API_VERSION_STRING ) )
    gs_request.get_method = lambda: 'GET'
    opened_gs_request = url_opener.open( gs_request )
    webtool_descriptors = json.loads( opened_gs_request.read() )
@@ -143,7 +147,7 @@ def get_genome_space_launch_apps( atm_url, url_opener, file_url, file_type ):
                    url_delimiter = "&"
                else:
                    url_delimiter = "?"
-                launch_url = "%s%s%s" % ( base_url, url_delimiter, urllib.urlencode( [ ( file_param_name, file_url ) ] ) )
+                launch_url = "%s%s%s" % ( base_url, url_delimiter, urlencode( [ ( file_param_name, file_url ) ] ) )
                webtools.append( ( launch_url, webtool_name ) )
                break
    return webtools
@@ -153,19 +157,19 @@ def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, va
    if value:
        if isinstance( value, list ):
            value = value[0]  # single select, only 1 value
-        elif not isinstance( value, basestring ):
+        elif not isinstance( value, six.string_types ):
            # unvalidated value
            value = value.value
            if isinstance( value, list ):
                value = value[0]  # single select, only 1 value

    def recurse_directory_dict( url_opener, cur_options, url ):
-        cur_directory = urllib2.Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json, text/plain' } )
+        cur_directory = Request( url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json, text/plain' } )
        cur_directory.get_method = lambda: 'GET'
        # get url to upload to
        try:
            cur_directory = url_opener.open( cur_directory ).read()
-        except urllib2.HTTPError as e:
+        except HTTPError as e:
            log.debug( 'GenomeSpace export tool failed reading a directory "%s": %s' % ( url, e ) )
            return  # bad url, go to next
        cur_directory = json.loads( cur_directory )
@@ -244,11 +248,11 @@ def send_file_to_genomespace( genomespace_site, username, token, source_filename
                    sizes = [ last_size ]
            else:
                sizes.append( last_size )
-        print "Performing multi-part upload in %i parts." % ( len( sizes ) )
+        print("Performing multi-part upload in %i parts." % ( len( sizes ) ))
        # get upload url
        upload_url = "uploadinfo"
-        upload_url = "%s/%s/%s%s/%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], urllib.quote( target_filename, safe='' ) )
-        upload_request = urllib2.Request( upload_url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' } )
+        upload_url = "%s/%s/%s%s/%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], quote( target_filename, safe='' ) )
+        upload_request = Request( upload_url, headers={ 'Content-Type': 'application/json', 'Accept': 'application/json' } )
        upload_request.get_method = lambda: 'GET'
        upload_info = json.loads( url_opener.open( upload_request ).read() )
        conn = S3Connection( aws_access_key_id=upload_info['amazonCredentials']['accessKey'],
@@ -273,15 +277,15 @@ def send_file_to_genomespace( genomespace_site, username, token, source_filename
            fh.close()
        upload_result = mp.complete_upload()
    else:
-        print 'Performing simple put upload.'
+        print('Performing simple put upload.')
        upload_url = "uploadurl"
        content_md5 = hashlib.md5()
        chunk_write( input_file, content_md5, target_method="update" )
        input_file.seek( 0 )  # back to start, for uploading

        upload_params = { 'Content-Length': content_length, 'Content-MD5': base64.standard_b64encode( content_md5.digest() ), 'Content-Type': content_type }
-        upload_url = "%s/%s/%s%s/%s?%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], urllib.quote( target_filename, safe='' ), urllib.urlencode( upload_params ) )
-        new_file_request = urllib2.Request( upload_url )  # , headers = { 'Content-Type': 'application/json', 'Accept': 'application/text' } ) #apparently http://www.genomespace.org/team/specs/updated-dm-rest-api:"Every HTTP request to the Data Manager should include the Accept header with a preference for the media types application/json and application/text." is not correct
+        upload_url = "%s/%s/%s%s/%s?%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], quote( target_filename, safe='' ), urlencode( upload_params ) )
+        new_file_request = Request( upload_url )  # , headers = { 'Content-Type': 'application/json', 'Accept': 'application/text' } ) #apparently http://www.genomespace.org/team/specs/updated-dm-rest-api:"Every HTTP request to the Data Manager should include the Accept header with a preference for the media types application/json and application/text." is not correct
        new_file_request.get_method = lambda: 'GET'
        # get url to upload to
        target_upload_url = url_opener.open( new_file_request ).read()
@@ -289,10 +293,10 @@ def send_file_to_genomespace( genomespace_site, username, token, source_filename
        upload_headers = dict( upload_params )
        # upload_headers[ 'x-amz-meta-md5-hash' ] = content_md5.hexdigest()
        upload_headers[ 'Accept' ] = 'application/json'
-        upload_file_request = urllib2.Request( target_upload_url, headers=upload_headers, data=input_file )
+        upload_file_request = Request( target_upload_url, headers=upload_headers, data=input_file )
        upload_file_request.get_method = lambda: 'PUT'
-        upload_result = urllib2.urlopen( upload_file_request ).read()
-    result_url = "%s/%s" % ( target_directory_dict['url'], urllib.quote( target_filename, safe='' ) )
+        upload_result = urlopen( upload_file_request ).read()
+    result_url = "%s/%s" % ( target_directory_dict['url'], quote( target_filename, safe='' ) )
    # determine available gs launch apps
    web_tools = get_genome_space_launch_apps( genomespace_site_dict['atmServer'], url_opener, result_url, file_type )
    if log_filename:
@@ -326,4 +330,4 @@ if __name__ == '__main__':

    (options, args) = parser.parse_args()

-    send_file_to_genomespace( options.genomespace_site, options.username, options.token, options.dataset, map( binascii.unhexlify, options.subdirectory ), binascii.unhexlify( options.filename ), options.file_type, options.content_type, options.log, options.genomespace_toolname )
+    send_file_to_genomespace( options.genomespace_site, options.username, options.token, options.dataset, [binascii.unhexlify(_) for _ in options.subdirectory], binascii.unhexlify( options.filename ), options.file_type, options.content_type, options.log, options.genomespace_toolname )
@@ -1,11 +1,11 @@
 # Dan Blankenberg
-import cookielib
 import json
 import optparse
 import os
-import urllib
-import urllib2
-import urlparse
+
+from six.moves import http_cookiejar
+from six.moves.urllib.parse import unquote_plus, urlencode, urlparse
+from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen

 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
@@ -61,12 +61,12 @@ def chunk_write( source_stream, target_stream, source_method="read", target_meth

 def get_cookie_opener( gs_username, gs_token, gs_toolname=None ):
    """ Create a GenomeSpace cookie opener """
-    cj = cookielib.CookieJar()
+    cj = http_cookiejar.CookieJar()
    for cookie_name, cookie_value in [ ( 'gs-token', gs_token ), ( 'gs-username', gs_username ) ]:
        # create a super-cookie, valid for all domains
-        cookie = cookielib.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
+        cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
        cj.set_cookie( cookie )
-    cookie_opener = urllib2.build_opener( urllib2.HTTPCookieProcessor( cj ) )
+    cookie_opener = build_opener( HTTPCookieProcessor( cj ) )
    cookie_opener.addheaders.append( ( 'gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME ) )
    return cookie_opener

@@ -83,7 +83,7 @@ def get_galaxy_ext_from_genomespace_format_url( url_opener, file_format_url ):

 def get_genomespace_site_urls():
    genomespace_sites = {}
-    for line in urllib2.urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
+    for line in urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
        line = line.rstrip()
        if not line or line.startswith( "#" ):
            continue
@@ -96,14 +96,14 @@ def get_genomespace_site_urls():


 def set_genomespace_format_identifiers( url_opener, dm_site ):
-    gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
+    gs_request = Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
    gs_request.get_method = lambda: 'GET'
    opened_gs_request = url_opener.open( gs_request )
    genomespace_formats = json.loads( opened_gs_request.read() )
    for format in genomespace_formats:
        GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
    global GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN
-    GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = dict( map( lambda x: ( x[1], x[0] ), GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.iteritems() ) ).get( GENOMESPACE_UNKNOWN_FORMAT_KEY, GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN )
+    GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = dict( ( x[1], x[0] ) for x in GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.items() ).get( GENOMESPACE_UNKNOWN_FORMAT_KEY, GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN )


 def download_from_genomespace_file_browser( json_parameter_file, genomespace_site, gs_toolname ):
@@ -147,19 +147,19 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
        filetype_key = "%s%i" % ( file_type_prefix, file_num )
        filetype_url = datasource_params.get( filetype_key, None )
        galaxy_ext = get_galaxy_ext_from_genomespace_format_url( url_opener, filetype_url )
-        formated_download_url = "%s?%s" % ( download_url, urllib.urlencode( [ ( 'dataformat', filetype_url ) ] ) )
-        new_file_request = urllib2.Request( formated_download_url )
+        formatted_download_url = "%s?%s" % ( download_url, urlencode( [ ( 'dataformat', filetype_url ) ] ) )
+        new_file_request = Request( formatted_download_url )
        new_file_request.get_method = lambda: 'GET'
        target_download_url = url_opener.open( new_file_request )
        filename = None
        if 'Content-Disposition' in target_download_url.info():
            # If the response has Content-Disposition, try to get filename from it
-            content_disposition = dict( map( lambda x: x.strip().split('=') if '=' in x else ( x.strip(), '' ), target_download_url.info()['Content-Disposition'].split( ';' ) ) )
+            content_disposition = dict( x.strip().split('=') if '=' in x else ( x.strip(), '' ) for x in target_download_url.info()['Content-Disposition'].split( ';' ) )
            if 'filename' in content_disposition:
                filename = content_disposition[ 'filename' ].strip( "\"'" )
        if not filename:
-            parsed_url = urlparse.urlparse( download_url )
-            filename = urllib.unquote_plus( parsed_url[2].split( '/' )[-1] )
+            parsed_url = urlparse( download_url )
+            filename = unquote_plus( parsed_url[2].split( '/' )[-1] )
        if not filename:
            filename = download_url
        metadata_dict = None
@@ -1,14 +1,14 @@
 # Dan Blankenberg

-import cookielib
 import json
 import optparse
 import os
 import shutil
 import tempfile
-import urllib
-import urllib2
-import urlparse
+
+from six.moves import http_cookiejar
+from six.moves.urllib.parse import parse_qs, unquote_plus, urlparse
+from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen

 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
@@ -60,12 +60,12 @@ def chunk_write( source_stream, target_stream, source_method="read", target_meth

 def get_cookie_opener( gs_username, gs_token, gs_toolname=None ):
    """ Create a GenomeSpace cookie opener """
-    cj = cookielib.CookieJar()
+    cj = http_cookiejar.CookieJar()
    for cookie_name, cookie_value in [ ( 'gs-token', gs_token ), ( 'gs-username', gs_username ) ]:
        # create a super-cookie, valid for all domains
-        cookie = cookielib.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
+        cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False )
        cj.set_cookie( cookie )
-    cookie_opener = urllib2.build_opener( urllib2.HTTPCookieProcessor( cj ) )
+    cookie_opener = build_opener( HTTPCookieProcessor( cj ) )
    cookie_opener.addheaders.append( ( 'gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME ) )
    return cookie_opener

@@ -82,7 +82,7 @@ def get_galaxy_ext_from_genomespace_format_url( url_opener, file_format_url, def

 def get_genomespace_site_urls():
    genomespace_sites = {}
-    for line in urllib2.urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
+    for line in urlopen( GENOMESPACE_SERVER_URL_PROPERTIES ).read().split( '\n' ):
        line = line.rstrip()
        if not line or line.startswith( "#" ):
            continue
@@ -95,7 +95,7 @@ def get_genomespace_site_urls():


 def set_genomespace_format_identifiers( url_opener, dm_site ):
-    gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
+    gs_request = Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
    gs_request.get_method = lambda: 'GET'
    opened_gs_request = url_opener.open( gs_request )
    genomespace_formats = json.loads( opened_gs_request.read() )
@@ -123,21 +123,21 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
    used_filenames = []
    for download_url in url_param.split( ',' ):
        using_temp_file = False
-        parsed_url = urlparse.urlparse( download_url )
-        query_params = urlparse.parse_qs( parsed_url[4] )
+        parsed_url = urlparse( download_url )
+        query_params = parse_qs( parsed_url[4] )
        # write file to disk
-        new_file_request = urllib2.Request( download_url )
+        new_file_request = Request( download_url )
        new_file_request.get_method = lambda: 'GET'
        target_download_url = url_opener.open( new_file_request )
        filename = None
        if 'Content-Disposition' in target_download_url.info():
-            content_disposition = dict( map( lambda x: x.strip().split('=') if '=' in x else ( x.strip(), '' ), target_download_url.info()['Content-Disposition'].split( ';' ) ) )
+            content_disposition = dict( x.strip().split('=') if '=' in x else ( x.strip(), '' ) for x in target_download_url.info()['Content-Disposition'].split( ';' ) )
            if 'filename' in content_disposition:
                filename = content_disposition[ 'filename' ].strip( "\"'" )
        if not filename:
-            parsed_url = urlparse.urlparse( download_url )
-            query_params = urlparse.parse_qs( parsed_url[4] )
-            filename = urllib.unquote_plus( parsed_url[2].split( '/' )[-1] )
+            parsed_url = urlparse( download_url )
+            query_params = parse_qs( parsed_url[4] )
+            filename = unquote_plus( parsed_url[2].split( '/' )[-1] )
        if not filename:
            filename = download_url
        if output_filename is None:
@@ -157,7 +157,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
            try:
                # get and use GSMetadata object
                download_file_path = download_url.split( "%s/file/" % ( genomespace_site_dict['dmServer'] ), 1)[-1]  # FIXME: This is a very bad way to get the path for determining metadata. There needs to be a way to query API using download URLto get to the metadata object
-                metadata_request = urllib2.Request( "%s/%s/filemetadata/%s" % ( genomespace_site_dict['dmServer'], GENOMESPACE_API_VERSION_STRING, download_file_path ) )
+                metadata_request = Request( "%s/%s/filemetadata/%s" % ( genomespace_site_dict['dmServer'], GENOMESPACE_API_VERSION_STRING, download_file_path ) )
                metadata_request.get_method = lambda: 'GET'
                metadata_url = url_opener.open( metadata_request )
                file_metadata_dict = json.loads( metadata_url.read() )
@@ -25,6 +25,8 @@ usage: %prog maf_file [options]
   -z, --mafIndexFile=z: Directory of local maf index file ( maf_index.loc or maf_pairwise.loc )
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import bx.align.maf
 import bx.intervals.io
 from bx.cookbook import doc_optparse
@@ -132,11 +134,11 @@ def __main__():
    maf_utilities.remove_temp_index_file( index_filename )

    if num_blocks:
-        print "%i MAF blocks extracted for %i regions." % ( num_blocks, ( num_regions + 1 ) )
+        print("%i MAF blocks extracted for %i regions." % ( num_blocks, ( num_regions + 1 ) ))
    elif num_regions is not None:
-        print "No MAF blocks could be extracted for %i regions." % ( num_regions + 1 )
+        print("No MAF blocks could be extracted for %i regions." % ( num_regions + 1 ))
    else:
-        print "No valid regions have been provided."
+        print("No valid regions have been provided.")

 if __name__ == "__main__":
    __main__()
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Reads an interval or gene BED and a MAF Source.
 Produces a FASTA file containing the aligned intervals/gene sequences, based upon the provided coordinates
@@ -24,8 +23,9 @@ usage: %prog maf_file [options]

 usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR
 """
-
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 import bx.intervals.io
@@ -142,7 +142,7 @@ def __main__():
                    primary_name = secondary_name = fields[3]
                    alignment_strand = fields[5]
                except Exception as e:
-                    print "Error loading exon positions from input line %i: %s" % ( line_count, e )
+                    print("Error loading exon positions from input line %i: %s" % ( line_count, e ))
                    continue
            else:  # Process as standard intervals
                try:
@@ -155,7 +155,7 @@ def __main__():
                    secondary_name = ""
                    alignment_strand = line.strand
                except Exception as e:
-                    print "Error loading region positions from input line %i: %s" % ( line_count, e )
+                    print("Error loading region positions from input line %i: %s" % ( line_count, e ))
                    continue

            # Write alignment to output file
@@ -182,7 +182,7 @@ def __main__():
            output.write( "\n" )
            regions_extracted += 1
        except Exception as e:
-            print "Unexpected error from input line %i: %s" % ( line_count, e )
+            print("Unexpected error from input line %i: %s" % ( line_count, e ))
            continue

    # close output file
@@ -193,11 +193,11 @@ def __main__():

    # Print message about success for user
    if regions_extracted > 0:
-        print "%i regions were processed successfully." % ( regions_extracted )
+        print("%i regions were processed successfully." % ( regions_extracted ))
    else:
-        print "No regions were processed successfully."
+        print("No regions were processed successfully.")
        if line_count > 0 and options.geneBED:
-            print "This tool requires your input file to conform to the 12 column BED standard."
+            print("This tool requires your input file to conform to the 12 column BED standard.")

 if __name__ == "__main__":
    __main__()
@@ -4,6 +4,7 @@
 Reads a list of block numbers and a maf. Produces a new maf containing the
 blocks specified by number.
 """
+from __future__ import print_function

 import sys

@@ -18,7 +19,7 @@ def __main__():
    output_filename1 = sys.argv[3].strip()
    block_col = int( sys.argv[4].strip() ) - 1
    if block_col < 0:
-        print >> sys.stderr, "Invalid column specified"
+        print("Invalid column specified", file=sys.stderr)
        sys.exit(0)
    species = maf_utilities.parse_species_option( sys.argv[5].strip() )

@@ -39,10 +40,10 @@ def __main__():
                    maf_writer.write( block )
                    break
        except:
-            print >>sys.stderr, "Your MAF file appears to be malformed."
+            print("Your MAF file appears to be malformed.", file=sys.stderr)
            sys.exit()
    if len( failed_lines ) > 0:
-        print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
+        print("Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) ))

 if __name__ == "__main__":
    __main__()
@@ -1,6 +1,8 @@
 # Dan Blankenberg
 # Filters a MAF file according to the provided code file, which is generated in maf_filter.xml <configfiles>
 # Also allows filtering by number of columns in a block, and limiting output species
+from __future__ import print_function
+
 import os
 import shutil
 import sys
@@ -21,7 +23,7 @@ def main():
        min_size = int( sys.argv.pop( 1 ) )
        max_size = int( sys.argv.pop( 1 ) )
        if max_size < 1:
-            max_size = sys.maxint
+            max_size = sys.maxsize
        min_species_per_block = int( sys.argv.pop( 1 ) )
        exclude_incomplete_blocks = int( sys.argv.pop( 1 ) )
        if species:
@@ -29,7 +31,7 @@ def main():
        else:
            num_species = len( sys.argv.pop( 1 ).split( ',') )
    except:
-        print >>sys.stderr, "One or more arguments is missing.\nUsage: maf_filter.py maf_filter_file input_maf output_maf path_to_save_debug species_to_keep"
+        print("One or more arguments is missing.\nUsage: maf_filter.py maf_filter_file input_maf output_maf path_to_save_debug species_to_keep", file=sys.stderr)
        sys.exit()

    # Open input and output MAF files
@@ -37,7 +39,7 @@ def main():
        maf_reader = bx.align.maf.Reader( open( maf_file, 'r' ) )
        maf_writer = bx.align.maf.Writer( open( out_file, 'w' ) )
    except:
-        print >>sys.stderr, "Your MAF file appears to be malformed."
+        print("Your MAF file appears to be malformed.", file=sys.stderr)
        sys.exit()

    # Save script file for debuging/verification info later
@@ -52,7 +54,7 @@ def main():
    for i, maf_block in enumerate( maf_reader ):
        if min_size <= maf_block.text_size <= max_size:
            local = {'maf_block': maf_block, 'ret_val': False}
-            execfile( script_file, {}, local )
+            exec(compile(open( script_file ).read(), script_file, 'exec'), {}, local)
            if local['ret_val']:
                # Species limiting must be done after filters as filters could be run on non-requested output species
                if species:
@@ -63,9 +65,9 @@ def main():
    maf_writer.close()
    maf_reader.close()
    if i == 0:
-        print "Your file contains no valid maf_blocks."
+        print("Your file contains no valid maf_blocks.")
    else:
-        print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
+        print('Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 ))

 if __name__ == "__main__":
    main()
@@ -3,6 +3,7 @@
 """
 Removes blocks that fall outside of specified size range.
 """
+from __future__ import print_function

 import sys

@@ -15,12 +16,12 @@ def __main__():
    min_size = int( sys.argv[3].strip() )
    max_size = int( sys.argv[4].strip() )
    if max_size < 1:
-        max_size = sys.maxint
+        max_size = sys.maxsize
    maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
    try:
        maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) )
    except:
-        print >>sys.stderr, "Your MAF file appears to be malformed."
+        print("Your MAF file appears to be malformed.", file=sys.stderr)
        sys.exit()

    blocks_kept = 0
@@ -29,7 +30,7 @@ def __main__():
        if min_size <= m.text_size <= max_size:
            maf_writer.write( m )
            blocks_kept += 1
-    print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
+    print('Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 ))

 if __name__ == "__main__":
    __main__()
@@ -7,6 +7,8 @@ columns containing only gaps.
 usage: %prog species,species2,... input_maf output_maf allow_partial min_species_per_block
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 import bx.align.maf
@@ -24,7 +26,7 @@ def main():
        maf_reader = bx.align.maf.Reader( open( sys.argv[2], 'r' ) )
        maf_writer = bx.align.maf.Writer( open( sys.argv[3], 'w' ) )
    except:
-        print >>sys.stderr, "Your MAF file appears to be malformed."
+        print("Your MAF file appears to be malformed.", file=sys.stderr)
        sys.exit()
    allow_partial = False
    if int( sys.argv[4] ):
@@ -44,8 +46,8 @@ def main():
    maf_reader.close()
    maf_writer.close()

-    print "Restricted to species: %s." % ", ".join( species )
-    print "%i MAF blocks have been kept." % maf_blocks_kept
+    print("Restricted to species: %s." % ", ".join( species ))
+    print("%i MAF blocks have been kept." % maf_blocks_kept)

 if __name__ == "__main__":
    main()
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Reads a MAF file. Produces a MAF file containing
 the reverse complement for each block in the source file.
@@ -7,6 +6,8 @@ the reverse complement for each block in the source file.
 usage: %prog input_maf_file output_maf_file
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 import bx.align.maf
@@ -23,7 +24,7 @@ def __main__():
    try:
        maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
    except:
-        print sys.stderr, "Unable to open output file"
+        print(sys.stderr, "Unable to open output file")
        sys.exit()
    try:
        count = 0
@@ -33,9 +34,9 @@ def __main__():
                maf = maf.limit_to_species( species )
            maf_writer.write( maf )
    except:
-        print >>sys.stderr, "Your MAF file appears to be malformed."
+        print("Your MAF file appears to be malformed.", file=sys.stderr)
        sys.exit()
-    print "%i regions were reverse complemented." % count
+    print("%i regions were reverse complemented." % count)
    maf_writer.close()

 if __name__ == "__main__":
@@ -2,6 +2,8 @@
 """
 Read a maf and split blocks by unique species combinations
 """
+from __future__ import print_function
+
 import sys

 from bx.align import maf
@@ -35,9 +37,9 @@ def __main__():
    out.close()

    if end_count:
-        print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 )
+        print("%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 ))
    else:
-        print "No alignment blocks were created."
+        print("No alignment blocks were created.")

 if __name__ == "__main__":
    __main__()
@@ -3,6 +3,8 @@
 """
 Reads a list of intervals and a maf. Outputs a new set of intervals with statistics appended.
 """
+from __future__ import print_function
+
 import sys

 import bx.intervals.io
@@ -22,7 +24,7 @@ def __main__():
        start_col = int( sys.argv[6].strip() ) - 1
        end_col = int( sys.argv[7].strip() ) - 1
    except:
-        print >>sys.stderr, "You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file."
+        print("You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file.", file=sys.stderr)
        sys.exit()
    summary = sys.argv[8].strip()
    if summary.lower() == "true":
@@ -40,16 +42,16 @@ def __main__():
        # index maf for use here
        index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species=[dbkey] )
        if index is None:
-            print >>sys.stderr, "Your MAF file appears to be malformed."
+            print("Your MAF file appears to be malformed.", file=sys.stderr)
            sys.exit()
    elif maf_source_type == "cached":
        # access existing indexes
        index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
        if index is None:
-            print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
+            print("The MAF source specified (%s) appears to be invalid." % ( input_maf_filename ), file=sys.stderr)
            sys.exit()
    else:
-        print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
+        print('Invalid source type specified: %s' % maf_source_type, file=sys.stdout)
        sys.exit()

    out = open(output_filename, 'w')
@@ -91,7 +93,7 @@ def __main__():
            # print coverage for interval
            coverage_sum = coverage[dbkey].count_range()
            out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
-            keys = coverage.keys()
+            keys = list(coverage.keys())
            keys.remove( dbkey )
            keys.sort()
            for key in keys:
@@ -103,9 +105,9 @@ def __main__():
            out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
    out.close()
    if num_region is not None:
-        print "%i regions were processed with a total length of %i." % ( num_region + 1, total_length )
+        print("%i regions were processed with a total length of %i." % ( num_region + 1, total_length ))
    if num_bad_region:
-        print "%i regions were invalid." % ( num_bad_region )
+        print("%i regions were invalid." % ( num_bad_region ))
    maf_utilities.remove_temp_index_file( index_filename )

 if __name__ == "__main__":
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Read a maf file and write out a new maf with only blocks having all of
 the passed in species, after dropping any other species and removing columns
@@ -9,6 +8,8 @@ which are adjacent after the unwanted species have been dropped.
 usage: %prog input_maf output_maf species1,species2
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 import bx.align.maf
@@ -24,12 +25,12 @@ def main():
    try:
        maf_reader = bx.align.maf.Reader( open( input_file ) )
    except:
-        print >> sys.stderr, "Unable to open source MAF file"
+        print("Unable to open source MAF file", file=sys.stderr)
        sys.exit()
    try:
        maf_writer = FusingAlignmentWriter( bx.align.maf.Writer( open( output_file, 'w' ) ) )
    except:
-        print >> sys.stderr, "Unable to open output file"
+        print("Unable to open output file", file=sys.stderr)
        sys.exit()
    try:
        for m in maf_reader:
@@ -42,12 +43,12 @@ def main():
                m.score = 0.0
                maf_writer.write( m )
    except Exception as e:
-        print >> sys.stderr, "Error steping through MAF File: %s" % e
+        print("Error steping through MAF File: %s" % e, file=sys.stderr)
        sys.exit()
    maf_reader.close()
    maf_writer.close()

-    print "Restricted to species: %s." % ", ".join( species )
+    print("Restricted to species: %s." % ", ".join( species ))

 if __name__ == "__main__":
    main()
@@ -1,8 +1,9 @@
 #!/usr/bin/env python
-
 """
 Read a maf and output intervals for specified list of species.
 """
+from __future__ import print_function
+
 import os
 import sys

@@ -22,25 +23,23 @@ def __main__():
    primary_spec = None

    if "None" in species:
-        species = {}
+        species = set()
        try:
            for i, m in enumerate( maf.Reader( open( input_filename, 'r' ) ) ):
                for c in m.components:
                    spec, chrom = maf.src_split( c.src )
                    if not spec or not chrom:
                        spec = chrom = c.src
-                    species[spec] = ""
-            species = species.keys()
+                    species.add(spec)
        except:
-            print >>sys.stderr, "Invalid MAF file specified"
+            print("Invalid MAF file specified", file=sys.stderr)
            return

    if "?" in species:
-        print >>sys.stderr, "Invalid dbkey specified"
+        print("Invalid dbkey specified", file=sys.stderr)
        return

-    for i in range( 0, len( species ) ):
-        spec = species[i]
+    for i, spec in enumerate( species ):
        if i == 0:
            out_files[spec] = open( output_filename, 'w' )
            primary_spec = spec
@@ -48,7 +47,7 @@ def __main__():
            out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_bed_%s' % ( output_id, spec, spec ) ), 'wb+' )
    num_species = len( species )

-    print "Restricted to species:", ",".join( species )
+    print("Restricted to species:", ",".join( species ))

    file_in = open( input_filename, 'r' )
    maf_reader = maf.Reader( file_in )
@@ -78,7 +77,7 @@ def __main__():
    for file_out in out_files.keys():
        out_files[file_out].close()

-    print "#FILE1_DBKEY\t%s" % ( primary_spec )
+    print("#FILE1_DBKEY\t%s" % ( primary_spec ))

 if __name__ == "__main__":
    __main__()
@@ -1,5 +1,5 @@
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    output_data = out_data.items()[0][1]
+    output_data = next(iter(out_data.values()))
    new_stdout = ""
    split_stdout = stdout.split("\n")
    for line in split_stdout:
@@ -5,6 +5,8 @@ Read a maf and output a single block fasta file, concatenating blocks
 usage %prog species1,species2 maf_file out_file
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 from bx.align import maf
@@ -27,9 +29,9 @@ def __main__():
        maf_utilities.tool_fail( "Error opening file for output: %s" % e )

    if species:
-        print "Restricted to species: %s" % ', '.join( species )
+        print("Restricted to species: %s" % ', '.join( species ))
    else:
-        print "Not restricted to species."
+        print("Not restricted to species.")

    if not species:
        try:
@@ -1,9 +1,10 @@
 #!/usr/bin/env python
-
 """
 Read a maf and output a multiple block fasta file.
 """
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys

 from bx.align import maf
@@ -34,9 +35,9 @@ def __main__():
        maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )

    if species:
-        print "Restricted to species: %s" % ', '.join( species )
+        print("Restricted to species: %s" % ', '.join( species ))
    else:
-        print "Not restricted to species."
+        print("Not restricted to species.")

    for block_num, block in enumerate( maf_reader ):
        if species:
@@ -1,23 +1,25 @@
 # Dan Blankenberg
+from __future__ import print_function
+
 import sys
 from optparse import OptionParser

 import bx.align.maf
-
 import galaxy_utils.sequence.vcf
+from six import Iterator

 UNKNOWN_NUCLEOTIDE = '*'


-class PopulationVCFParser( object ):
+class PopulationVCFParser( Iterator ):
    def __init__( self, reader, name ):
        self.reader = reader
        self.name = name
        self.counter = 0

-    def next( self ):
+    def __next__( self ):
        rval = []
-        vc = self.reader.next()
+        vc = next(self.reader)
        for i, allele in enumerate( vc.alt ):
            rval.append( ( '%s_%i.%i' % ( self.name, i + 1, self.counter + 1 ), allele ) )
        self.counter += 1
@@ -25,17 +27,17 @@ class PopulationVCFParser( object ):

    def __iter__( self ):
        while True:
-            yield self.next()
+            yield next(self)


-class SampleVCFParser( object ):
+class SampleVCFParser( Iterator ):
    def __init__( self, reader ):
        self.reader = reader
        self.counter = 0

-    def next( self ):
+    def __next__( self ):
        rval = []
-        vc = self.reader.next()
+        vc = next(self.reader)
        alleles = [ vc.ref ] + vc.alt

        if 'GT' in vc.format:
@@ -55,7 +57,7 @@ class SampleVCFParser( object ):

    def __iter__( self ):
        while True:
-            yield self.next()
+            yield next(self)


 def main():
@@ -69,7 +71,7 @@ def main():

    if len( args ) < 3:
        if options.galaxy:
-            print >>sys.stderr, "It appears that you forgot to specify an input VCF file, click 'Add new VCF...' to add at least input.\n"
+            print("It appears that you forgot to specify an input VCF file, click 'Add new VCF...' to add at least input.\n", file=sys.stderr)
        parser.error( "Need to specify an output file, a dbkey and at least one input file" )

    if not ( options.population ^ options.sample ):
@@ -154,7 +156,7 @@ def main():
    maf_writer.close()

    if non_spec_skipped:
-        print 'Skipped %i non-specification compliant indels.' % non_spec_skipped
+        print('Skipped %i non-specification compliant indels.' % non_spec_skipped)

 if __name__ == "__main__":
    main()
@@ -86,7 +86,7 @@ def __main__():
    # check SHRiMP output: count number of lines
    num_hits = 0
    if shrimp_outfile:
-        for i, line in enumerate(file(shrimp_outfile)):
+        for i, line in enumerate(open(shrimp_outfile)):
            line = line.rstrip('\r\n')
            if not line or line.startswith('#'):
                continue
@@ -99,7 +99,7 @@ def __main__():
    if num_hits == 0:   # no hits generated
        err_msg = ''
        if shrimp_log:
-            for i, line in enumerate(file(shrimp_log)):
+            for i, line in enumerate(open(shrimp_log)):
                if line.startswith('error'):            # deal with memory error:
                    err_msg += line                     # error: realloc failed: Cannot allocate memory
                if re.search('Reads Matched', line):    # deal with zero hits
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 TODO
 1. decrease memory usage
@@ -42,8 +41,8 @@ SHRiMP output:
 >7:2:1147:982/1 chr3    +   36586562    36586595    2   35  36  2900    3G16G13
 >7:2:1147:982/1 chr3    +   95338194    95338225    4   35  36  2700    9T7C14
 >7:2:587:93/1   chr3    +   14913541    14913577    1   35  36  2960    19--16
-
 """
+from __future__ import print_function

 import os
 import os.path
@@ -86,7 +85,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
    seq = ''
    title = None

-    for i, line in enumerate(file(ref_file)):
+    for i, line in enumerate(open(ref_file)):
        line = line.rstrip()
        if not line or line.startswith('#'):
            continue
@@ -109,7 +108,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe

    # find hits: one end and/or the other
    hits = {}
-    for i, line in enumerate(file(result_file)):
+    for i, line in enumerate(open(result_file)):
        line = line.rstrip()
        if not line or line.startswith('#'):
            continue
@@ -145,7 +144,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
    score = ''
    for num_score_file in range(len(all_score_file)):
        score_file = all_score_file[num_score_file]
-        for i, line in enumerate(file(score_file)):
+        for i, line in enumerate(open(score_file)):
            line = line.rstrip()
            if not line or line.startswith('#'):
                continue
@@ -375,7 +374,7 @@ def generate_sub_table(result_file, ref_file, score_files, table_outfile, hit_pe
        os.remove(temp_table_name)

    if invalid_editstring_char:
-        print 'Skip ', invalid_editstring_char, ' invalid characters in editstrings'
+        print('Skip ', invalid_editstring_char, ' invalid characters in editstrings')

    return True

@@ -592,7 +591,7 @@ def __main__():
    # check SHRiMP output: count number of lines
    num_hits = 0
    if shrimp_outfile:
-        for i, line in enumerate(file(shrimp_outfile)):
+        for i, line in enumerate(open(shrimp_outfile)):
            line = line.rstrip('\r\n')
            if not line or line.startswith('#'):
                continue
@@ -605,7 +604,7 @@ def __main__():
    if num_hits == 0:   # no hits generated
        err_msg = ''
        if shrimp_log:
-            for i, line in enumerate(file(shrimp_log)):
+            for i, line in enumerate(open(shrimp_log)):
                if line.startswith('error'):            # deal with memory error:
                    err_msg += line                     # error: realloc failed: Cannot allocate memory
                if re.search('Reads Matched', line):    # deal with zero hits
@@ -1,10 +1,12 @@
 #!/usr/bin/env python

-import sys
-import string
 import optparse
-import tempfile
 import sqlite3
+import string
+import sys
+import tempfile
+
+import six


 def stop_err( msg ):
@@ -28,13 +30,13 @@ def solid2sanger( quality_string, min_qual=0 ):
    return sanger


-def Translator(frm='', to='', delete='', keep=None):
-    allchars = string.maketrans('', '')
+def Translator(frm='', to='', delete=''):
    if len(to) == 1:
        to = to * len(frm)
-    trans = string.maketrans(frm, to)
-    if keep is not None:
-        delete = allchars.translate(allchars, keep.translate(allchars, delete))
+    if six.PY2:
+        trans = string.maketrans(frm, to)
+    else:
+        trans = str.maketrans(frm, to)

    def callable(s):
        return s.translate(trans, delete)
@@ -41,13 +41,13 @@ def __main__():
    # common temp file setup
    tmpf = tempfile.NamedTemporaryFile()  # forward reads
    tmpqf = tempfile.NamedTemporaryFile()
-    tmpqf = replaceNeg1(file(options.input2, 'r'), tmpqf)
+    tmpqf = replaceNeg1(open(options.input2, 'r'), tmpqf)
    # if paired-end data (have reverse input files)
    if options.input3 != "None" and options.input4 != "None":
        tmpr = tempfile.NamedTemporaryFile()  # reverse reads
        # replace the -1 in the qualities file
        tmpqr = tempfile.NamedTemporaryFile()
-        tmpqr = replaceNeg1(file(options.input4, 'r'), tmpqr)
+        tmpqr = replaceNeg1(open(options.input4, 'r'), tmpqr)
        cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, tmpr.name, options.input1, tmpqf.name, options.input3, tmpqr.name)
        try:
            os.system(cmd1)
@@ -19,6 +19,9 @@ usage: %prog [options]
 # removed output of all simulation results on request (not working)
 #   -r, --sim_results=r: Output all tabular simulation results (number of polymorphisms times number of detection thresholds)
 #   -o, --output=o: Base name for summary output for each run
+from __future__ import print_function
+
+import itertools
 import os
 import random
 import sys
@@ -101,7 +104,7 @@ def __main__():
 #    else:
 #        out_name_template = tempfile.NamedTemporaryFile().name + '_%s'
    out_name_template = tempfile.NamedTemporaryFile().name + '_%s'
-    print 'out_name_template:', out_name_template
+    print('out_name_template:', out_name_template)

    # set up output files
    outputs = {}
@@ -120,24 +123,24 @@ def __main__():
            sim_count = 0
            while sim_count < num_sims:
                # randomly pick heteroplasmic base index
-                hbase = random.choice( range( 0, seq_len ) )
+                hbase = random.randrange( seq_len )
                # hbase = seq_len/2#random.randrange( 0, seq_len )
                # create 2D quasispecies list
-                qspec = map( lambda x: [], [0] * seq_len )
+                qspec = [[] for _ in range(seq_len)]
                # simulate read indices and assign to quasispecies
                i = 0
                while i < ( avg_coverage * ( seq_len / read_len ) ):  # number of reads (approximates coverage)
-                    start = random.choice( range( 0, seq_len ) )
+                    start = random.randrange( seq_len )
                    if random.random() < 0.5:  # positive sense read
                        end = start + read_len  # assign read end
                        if end > seq_len:  # overshooting origin
-                            read = range( start, seq_len ) + range( 0, ( end - seq_len ) )
+                            read = itertools.chain(range( start, seq_len ), range( 0, end - seq_len ))
                        else:  # regular read
                            read = range( start, end )
                    else:  # negative sense read
                        end = start - read_len  # assign read end
                        if end < -1:  # overshooting origin
-                            read = range( start, -1, -1) + range( ( seq_len - 1 ), ( seq_len + end ), -1 )
+                            read = itertools.chain(range( start, -1, -1 ), range( seq_len - 1, seq_len + end, -1))
                        else:  # regular read
                            read = range( start, end, -1 )
                    # assign read to quasispecies list by index
@@ -37,6 +37,7 @@ b) a file where each line has the following:
 where SNP is one of  the SNPs and the "list" is a comma separated list of SNPs
 that exceed the rsquare threshold with the first SNP.
 """
+from __future__ import print_function

 from getopt import getopt, GetoptError
 from sys import argv, exit, stderr
@@ -90,7 +91,7 @@ def read_inputfile(filename, samples):
 def annotate_locus(input, minorallelefrequency, snpsfile):
    locus = {}
    for k, v in input.items():
-        genotypes = [x for x in v.values()]
+        genotypes = v.values()
        alleles = [y for x in genotypes for y in x]
        alleleset = list(set(alleles))
        alleleset = list(set(alleles) - set(["N", "X"]))
@@ -124,7 +125,7 @@ def annotate_locus(input, minorallelefrequency, snpsfile):

            locus[k] = genotypevec, minorfreq
        elif len(alleleset) > 2:
-            print >> snpsfile, k
+            print(k, file=snpsfile)
    return locus


@@ -187,7 +188,7 @@ def main(inputfile, snpsfile, neigborhoodfile,
         rsquare, minorallelefrequency, samples):
    # read the input file
    input = read_inputfile(inputfile, samples)
-    print >> stderr, "Read %d locations" % len(input)
+    print("Read %d locations" % len(input), file=stderr)

    # open the snpsfile to print
    file = open(snpsfile, "w")
@@ -195,17 +196,17 @@ def main(inputfile, snpsfile, neigborhoodfile,
    # annotate the inputs, remove the abnormal loci (which do not have 2 alleles
    # and add the major and minor allele to each loci
    loci = annotate_locus(input, minorallelefrequency, file)
-    print >> stderr, "Read %d interesting locations" % len(loci)
+    print("Read %d interesting locations" % len(loci), file=stderr)

    # print all the interesting loci as candidate snps
    for k in loci.keys():
-        print >> file, k
+        print(k, file=file)
    file.close()
-    print >> stderr, "Finished creating the snpsfile"
+    print("Finished creating the snpsfile", file=stderr)

    # calculate the LD values and store it if it exceeds the threshold
    lds = calculateLD(loci, rsquare)
-    print >> stderr, "Calculated all the LD values"
+    print("Calculated all the LD values", file=stderr)

    # create a list of SNPs
    snps = {}
@@ -236,9 +237,9 @@ def main(inputfile, snpsfile, neigborhoodfile,
    for k, v in snps.items():
        ldv = ldvals[k]
        if debug_flag is True:
-            print >> file, "%s\t%s\t%s" % (k, ",".join(v), ",".join(ldv))
+            print("%s\t%s\t%s" % (k, ",".join(v), ",".join(ldv)), file=file)
        else:
-            print >> file, "%s\t%s" % (k, ",".join(v))
+            print("%s\t%s" % (k, ",".join(v)), file=file)

    file.close()

@@ -256,24 +257,24 @@ def read_list(filename):

 def usage():
    f = stderr
-    print >> f, "usage:"
-    print >> f, "pagetag [options] input.txt snps.txt neighborhood.txt"
-    print >> f, "where input.txt is the prettybase file"
-    print >> f, "where snps.txt is the first output file with the snps"
-    print >> f, "where neighborhood.txt is the output neighborhood file"
-    print >> f, "where the options are:"
-    print >> f, "-h,--help : print usage and quit"
-    print >> f, "-d,--debug: print debug information"
-    print >> f, "-r,--rsquare: the rsquare threshold (default : 0.64)"
-    print >> f, "-f,--freq : the minimum MAF required (default: 0.0)"
-    print >> f, "-s,--sample : a list of samples to be clustered"
+    print("usage:", file=f)
+    print("pagetag [options] input.txt snps.txt neighborhood.txt", file=f)
+    print("where input.txt is the prettybase file", file=f)
+    print("where snps.txt is the first output file with the snps", file=f)
+    print("where neighborhood.txt is the output neighborhood file", file=f)
+    print("where the options are:", file=f)
+    print("-h,--help : print usage and quit", file=f)
+    print("-d,--debug: print debug information", file=f)
+    print("-r,--rsquare: the rsquare threshold (default : 0.64)", file=f)
+    print("-f,--freq : the minimum MAF required (default: 0.0)", file=f)
+    print("-s,--sample : a list of samples to be clustered", file=f)

 if __name__ == "__main__":
    try:
        opts, args = getopt(argv[1:], "hds:r:f:",
                            ["help", "debug", "rsquare=", "freq=", "sample="])
    except GetoptError as err:
-        print str(err)
+        print(str(err))
        usage()
        exit(2)

@@ -297,11 +298,11 @@ if __name__ == "__main__":
            assert False, "unhandled option"

    if rsquare < 0.00 or rsquare > 1.00:
-        print >> stderr, "input value of rsquare should be in [0.00, 1.00]"
+        print("input value of rsquare should be in [0.00, 1.00]", file=stderr)
        exit(3)

    if minorallelefrequency < 0.0 or minorallelefrequency > 0.5:
-        print >> stderr, "input value of MAF should be (0.00,0.50]"
+        print("input value of MAF should be (0.00,0.50]", file=stderr)
        exit(4)

    if len(args) != 3:
@@ -21,6 +21,7 @@ d) Mark that SNP and all the snps connected to it as "visited". This should be
 done for each population.
 e) Continue steps b-e until all SNPs, in all populations have been visited.
 """
+from __future__ import print_function

 import heapq
 import os
@@ -82,7 +83,7 @@ class graph:
            ms = [x for x in n.edges]
            for m in ms:
                if n not in m.edges:
-                    print >> stderr, "check : %s - %s" % (n, m)
+                    print("check : %s - %s" % (n, m), file=stderr)


 def construct_graph(ldfile, snpfile):
@@ -98,7 +99,7 @@ def construct_graph(ldfile, snpfile):
        g.add_node(n)

    file.close()
-    print >> stderr, "Added %d nodes to a graph" % len(g.nodes)
+    print("Added %d nodes to a graph" % len(g.nodes), file=stderr)

    # now add all the edges
    file = open(ldfile, "r")
@@ -117,7 +118,7 @@ def construct_graph(ldfile, snpfile):
                g.add_edges(n1, n2)

    file.close()
-    print >> stderr, "Added all edges to the graph"
+    print("Added all edges to the graph", file=stderr)

    return g

@@ -137,7 +138,7 @@ def check_output(g, tagsnps):

    if set(allsnps) != set(mysnps):
        diff = list(set(allsnps) - set(mysnps))
-        print >> stderr, "%s are not covered" % ",".join(diff)
+        print("%s are not covered" % ",".join(diff), file=stderr)


 def main(ldfile, snpsfile, required, excluded):
@@ -165,7 +166,7 @@ def main(ldfile, snpsfile, required, excluded):
        neighbors[t.name] = list(set(ns))

    # find the tag SNPs for this graph
-    data = [x for x in g.nodes.values()]
+    data = g.nodes.values()[:]
    heapq.heapify(data)

    while data:
@@ -189,9 +190,9 @@ def main(ldfile, snpsfile, required, excluded):

    for s in tagsnps:
        if len(neighbors[s.name]) > 0:
-            print "%s\t%s" % (s, ",".join(neighbors[s.name]))
+            print("%s\t%s" % (s, ",".join(neighbors[s.name])))
            continue
-        print s
+        print(s)

    if debug_flag is True:
        check_output(g, tagsnps)
@@ -211,22 +212,22 @@ def read_list(filename):

 def usage():
    f = stderr
-    print >> f, "usage:"
-    print >> f, "senatag [options] neighborhood.txt inputsnps.txt"
-    print >> f, "where inputsnps.txt is a file of snps from one population"
-    print >> f, "where neighborhood.txt is neighborhood details for the pop."
-    print >> f, "where the options are:"
-    print >> f, "-h,--help : print usage and quit"
-    print >> f, "-d,--debug: print debug information"
-    print >> f, "-e,--excluded : file with names of SNPs that cannot be TagSNPs"
-    print >> f, "-r,--required : file with names of SNPs that should be TagSNPs"
+    print("usage:", file=f)
+    print("senatag [options] neighborhood.txt inputsnps.txt", file=f)
+    print("where inputsnps.txt is a file of snps from one population", file=f)
+    print("where neighborhood.txt is neighborhood details for the pop.", file=f)
+    print("where the options are:", file=f)
+    print("-h,--help : print usage and quit", file=f)
+    print("-d,--debug: print debug information", file=f)
+    print("-e,--excluded : file with names of SNPs that cannot be TagSNPs", file=f)
+    print("-r,--required : file with names of SNPs that should be TagSNPs", file=f)

 if __name__ == "__main__":
    try:
        opts, args = getopt(argv[1:], "hdr:e:",
                            ["help", "debug", "required=", "excluded="])
    except GetoptError as err:
-        print str(err)
+        print(str(err))
        usage()
        exit(2)

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 # Guruprasad Ananda
 # MAQ mapper for SOLiD colourspace-reads
+from __future__ import print_function

 import os
 import subprocess
@@ -101,7 +102,7 @@ def __main__():
            cmdpileup = "maq pileup -m %s -q %s %s %s > %s" % (max_mismatch, min_mapqual, ref_bfa.name, tmpcsmap.name, tmppileup.name)
            os.system(cmdpileup)
            tmppileup.seek(0)
-            print >> out_f2, "#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count"
+            print("#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count", file=out_f2)
            for line in open(tmppileup.name):
                elems = line.strip().split()
                ref_nt = elems[2].capitalize()
@@ -127,8 +128,8 @@ def __main__():
                        else:
                            c += 1
                    except ValueError as we:
-                        print >>sys.stderr, we
-                print >> out_f2, "%s\t%s\t%s\t%s\t%s\t%s" % ("\t".join(elems[:4]), coverage - ref_nt_count, a, t, g, c)
+                        print(we, file=sys.stderr)
+                print("%s\t%s\t%s\t%s\t%s\t%s" % ("\t".join(elems[:4]), coverage - ref_nt_count, a, t, g, c), file=out_f2)
        except Exception as er2:
            stop_err("Encountered error while mapping: %s" % (str(er2)))

@@ -177,7 +178,7 @@ def __main__():
            cmdpileup = "maq pileup -m %s -q %s %s %s > %s" % (max_mismatch, min_mapqual, ref_bfa.name, tmpcsmap.name, tmppileup.name)
            os.system(cmdpileup)
            tmppileup.seek(0)
-            print >> out_f2, "#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count"
+            print("#chr\tposition\tref_nt\tcoverage\tSNP_count\tA_count\tT_count\tG_count\tC_count", file=out_f2)
            for line in open(tmppileup.name):
                elems = line.strip().split()
                ref_nt = elems[2].capitalize()
@@ -204,7 +205,7 @@ def __main__():
                            c += 1
                    except:
                        pass
-                print >> out_f2, "%s\t%s\t%s\t%s\t%s\t%s" % ("\t".join(elems[:4]), coverage - ref_nt_count, a, t, g, c)
+                print("%s\t%s\t%s\t%s\t%s\t%s" % ("\t".join(elems[:4]), coverage - ref_nt_count, a, t, g, c), file=out_f2)
        except Exception as er2:
            stop_err("Encountered error while mapping: %s" % (str(er2)))

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 # Guruprasad Ananda
+from __future__ import print_function

 import sys
 import tempfile
@@ -46,7 +47,7 @@ def __main__():
            if not readlen:
                readlen = len(elems)
            if len(elems) != readlen:
-                print "Note: Reads in the input dataset are of variable lengths."
+                print("Note: Reads in the input dataset are of variable lengths.")
            j += 1
        except ValueError:
            invalid_lines += 1
@@ -54,8 +55,8 @@ def __main__():
            break

    position_dict = {}
-    print >>fout, "column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW"
-    for k, line in enumerate(file( infile_name )):
+    print("column\tcount\tmin\tmax\tsum\tmean\tQ1\tmed\tQ3\tIQR\tlW\trW", file=fout)
+    for k, line in enumerate(open( infile_name )):
        line = line.strip()
        if not(line) or line.startswith("#") or line.startswith(">"):
            continue
@@ -123,16 +124,16 @@ def __main__():
            left_whisker = max(q1 - 1.5 * iqr, lowest)
            right_whisker = min(q3 + 1.5 * iqr, highest)

-            print >>fout, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (pos + 1, total, lowest, highest, qsum, mean, q1, median, q3, iqr, left_whisker, right_whisker)
+            print("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (pos + 1, total, lowest, highest, qsum, mean, q1, median, q3, iqr, left_whisker, right_whisker), file=fout)
        except:
            invalid_positions += 1
            nullvals = ['NA'] * 11
-            print >>fout, "%s\t%s" % (pos + 1, '\t'.join(nullvals))
+            print("%s\t%s" % (pos + 1, '\t'.join(nullvals)), file=fout)

    if invalid_lines:
-        print "Skipped %d reads as invalid." % invalid_lines
+        print("Skipped %d reads as invalid." % invalid_lines)
    if invalid_positions:
-        print "Skipped stats computation for %d read positions." % invalid_positions
+        print("Skipped stats computation for %d read positions." % invalid_positions)

 if __name__ == "__main__":
    __main__()
@@ -1,9 +1,10 @@
 #!/usr/bin/env python
-
 """
 Classes encapsulating decypher tool.
 James E Johnson - University of Minnesota
 """
+from __future__ import print_function
+
 import os
 import subprocess
 import sys
@@ -23,7 +24,7 @@ def __main__():
    for _ in ('Roadmaps', 'Sequences'):
        os.symlink(os.path.join(working_dir, _), _)
    cmdline = 'velvetg . %s' % (inputs)
-    print "Command to be executed: %s" % cmdline
+    print("Command to be executed: %s" % cmdline)
    try:
        proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
        returncode = proc.wait()
@@ -161,7 +161,7 @@ def __main__():
                    all_index_cmds += " -R"

                if options.indexContigOptions:
-                    index_contig_options = map( int, options.indexContigOptions.split( ',' ) )
+                    index_contig_options = [ int(_) for _ in options.indexContigOptions.split( ',' ) ]
                    if index_contig_options[0] >= 0:
                        all_index_cmds += ' -s "%s"' % index_contig_options[0]
                    if index_contig_options[1] >= 0:
@@ -1,12 +1,11 @@
 #!/usr/bin/env python
 # This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
 # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
-
-from __future__ import division
+from __future__ import division, print_function

 import re
 import sys
-from ast import parse, Module, walk
+from ast import Module, parse, walk

 AST_NODE_TYPE_WHITELIST = [
    'Expr', 'Load', 'Str', 'Num', 'BoolOp', 'Compare', 'And', 'Eq', 'NotEq',
@@ -240,7 +239,7 @@ for i, line in enumerate( open( in_fname ) ):
 ''' % ( assign, wrap, cond_text )
 valid_filter = True
 try:
-    exec code
+    exec(code)
 except Exception as e:
    out.close()
    if str( e ).startswith( 'invalid syntax' ):
@@ -252,12 +251,12 @@ except Exception as e:
 if valid_filter:
    out.close()
    valid_lines = total_lines - skipped_lines
-    print 'Filtering with %s, ' % cond_text
+    print('Filtering with %s, ' % cond_text)
    if valid_lines > 0:
-        print 'kept %4.2f%% of %d valid lines (%d total lines).' % ( 100.0 * lines_kept / valid_lines, valid_lines, total_lines )
+        print('kept %4.2f%% of %d valid lines (%d total lines).' % ( 100.0 * lines_kept / valid_lines, valid_lines, total_lines ))
    else:
-        print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text
+        print('Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % cond_text)
    if invalid_lines:
-        print 'Skipped %d invalid line(s) starting at line #%d: "%s"' % ( invalid_lines, first_invalid_line, invalid_line )
+        print('Skipped %d invalid line(s) starting at line #%d: "%s"' % ( invalid_lines, first_invalid_line, invalid_line ))
    if skipped_lines:
-        print 'Skipped %i comment (starting with #) or blank line(s)' % skipped_lines
+        print('Skipped %i comment (starting with #) or blank line(s)' % skipped_lines)
@@ -4,8 +4,10 @@
 """
 This tool provides the SQL "group by" functionality.
 """
-import commands
+from __future__ import print_function
+
 import random
+import subprocess
 import sys
 import tempfile
 from itertools import groupby
@@ -88,10 +90,10 @@ def main():
    except Exception as exc:
        stop_err( 'Initialization error -> %s' % str(exc) )

-    error_code, stdout = commands.getstatusoutput(command_line)
-
-    if error_code != 0:
-        stop_err( "Sorting input dataset resulted in error: %s: %s" % ( error_code, stdout ))
+    try:
+        subprocess.check_output(command_line, stderr=subprocess.STDOUT, shell=True)
+    except subprocess.CalledProcessError as e:
+        stop_err( "Sorting input dataset resulted in error: %s: %s" % ( e.returncode, e.output ))

    fout = open(sys.argv[1], "w")

@@ -139,7 +141,7 @@ def main():
            else:
                # some kind of numpy fn
                try:
-                    data = map(float, data)
+                    data = [float(_) for _ in data]
                except ValueError:
                    sys.stderr.write( "Operation %s expected number values but got %s instead.\n" % (op, data) )
                    sys.exit( 1 )
@@ -168,7 +170,7 @@ def main():

        msg += op + "[c" + cols[i] + "] "

-    print msg
+    print(msg)
    fout.close()
    tmpfile.close()

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+from __future__ import print_function

 import re
 import sys
@@ -116,7 +117,7 @@ def main():
        outfile.close()

        if skipped_lines:
-            print "Skipped %d invalid lines beginning with line #%d.  See tool tips for data requirements." % ( skipped_lines, first_invalid_line )
+            print("Skipped %d invalid lines beginning with line #%d.  See tool tips for data requirements." % ( skipped_lines, first_invalid_line ))

 if __name__ == "__main__":
    main()
@@ -1,10 +1,11 @@
 # post processing, add sequence and additional annoation info if available
-from urllib import urlencode
+from six.moves.urllib.parse import urlencode
+
 from galaxy.datatypes.images import create_applet_tag_peek


 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    primary_data = out_data.items()[0][1]
+    primary_data = next(iter(out_data.values()))

    # default params for LAJ type
    params = {