From 0bfdf859fb26a0cc7f185007c882ff7cf0125c2d Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 9 Apr 2024 23:19:32 +0000 Subject: [PATCH] update docs --- 3-brief-examples.html | 31 +- FAQs.html | 39 +- _modules/index.html | 23 +- _modules/pybedtools.html | 34 +- _modules/pybedtools/bedtool.html | 508 +++++++++++++----- _modules/pybedtools/contrib/bigbed.html | 41 +- _modules/pybedtools/contrib/bigwig.html | 38 +- .../contrib/intersection_matrix.html | 33 +- .../contrib/long_range_interaction.html | 47 +- _modules/pybedtools/contrib/plotting.html | 84 ++- _modules/pybedtools/contrib/venn_maker.html | 34 +- _modules/pybedtools/filenames.html | 36 +- _modules/pybedtools/helpers.html | 76 ++- _modules/pybedtools/parallel.html | 28 +- .../pybedtools.contrib.plotting.Track.rst.txt | 3 + _sources/changes.rst.txt | 11 + _sources/topical-bam.rst.txt | 3 +- _static/alabaster.css | 23 +- _static/basic.css | 6 +- _static/documentation_options.js | 5 +- _static/pygments.css | 2 +- _static/searchtools.js | 26 +- _static/sphinx_highlight.js | 16 +- autodoc_source.html | 69 +-- ...ols.bedtool.BedTool.absolute_distance.html | 27 +- .../pybedtools.bedtool.BedTool.all_hits.html | 27 +- .../pybedtools.bedtool.BedTool.annotate.html | 29 +- .../pybedtools.bedtool.BedTool.any_hits.html | 27 +- ...tools.bedtool.BedTool.as_intervalfile.html | 27 +- autodocs/pybedtools.bedtool.BedTool.at.html | 27 +- ...pybedtools.bedtool.BedTool.bam_to_bed.html | 29 +- ...bedtools.bedtool.BedTool.bam_to_fastq.html | 29 +- autodocs/pybedtools.bedtool.BedTool.bed6.html | 29 +- ...bedtools.bedtool.BedTool.bedpe_to_bam.html | 29 +- .../pybedtools.bedtool.BedTool.bgzip.html | 27 +- autodocs/pybedtools.bedtool.BedTool.cat.html | 27 +- .../pybedtools.bedtool.BedTool.closest.html | 29 +- .../pybedtools.bedtool.BedTool.cluster.html | 29 +- ...ls.bedtool.BedTool.colormap_normalize.html | 27 +- ...pybedtools.bedtool.BedTool.complement.html | 29 +- .../pybedtools.bedtool.BedTool.count.html | 27 +- ...pybedtools.bedtool.BedTool.count_hits.html | 27 +- .../pybedtools.bedtool.BedTool.coverage.html | 29 +- autodocs/pybedtools.bedtool.BedTool.cut.html | 27 +- autodocs/pybedtools.bedtool.BedTool.each.html | 27 +- .../pybedtools.bedtool.BedTool.expand.html | 87 +-- ...ybedtools.bedtool.BedTool.field_count.html | 27 +- .../pybedtools.bedtool.BedTool.file_type.html | 27 +- .../pybedtools.bedtool.BedTool.filter.html | 27 +- .../pybedtools.bedtool.BedTool.flank.html | 29 +- ...tools.bedtool.BedTool.genome_coverage.html | 29 +- .../pybedtools.bedtool.BedTool.groupby.html | 201 +++---- autodocs/pybedtools.bedtool.BedTool.head.html | 27 +- autodocs/pybedtools.bedtool.BedTool.html | 29 +- autodocs/pybedtools.bedtool.BedTool.igv.html | 29 +- .../pybedtools.bedtool.BedTool.intersect.html | 29 +- .../pybedtools.bedtool.BedTool.introns.html | 27 +- .../pybedtools.bedtool.BedTool.jaccard.html | 29 +- .../pybedtools.bedtool.BedTool.liftover.html | 27 +- .../pybedtools.bedtool.BedTool.links.html | 29 +- autodocs/pybedtools.bedtool.BedTool.map.html | 29 +- ...pybedtools.bedtool.BedTool.mask_fasta.html | 29 +- .../pybedtools.bedtool.BedTool.merge.html | 29 +- .../pybedtools.bedtool.BedTool.moveto.html | 27 +- ...ls.bedtool.BedTool.multi_bam_coverage.html | 29 +- ...tools.bedtool.BedTool.multi_intersect.html | 29 +- ...ls.bedtool.BedTool.nucleotide_content.html | 29 +- .../pybedtools.bedtool.BedTool.overlap.html | 63 +-- ...ybedtools.bedtool.BedTool.pair_to_bed.html | 29 +- ...bedtools.bedtool.BedTool.pair_to_pair.html | 29 +- ...dtools.bedtool.BedTool.parallel_apply.html | 27 +- ...dtools.bedtool.BedTool.print_sequence.html | 27 +- .../pybedtools.bedtool.BedTool.random.html | 29 +- ...dtools.bedtool.BedTool.random_jaccard.html | 27 +- .../pybedtools.bedtool.BedTool.random_op.html | 27 +- ...edtools.bedtool.BedTool.random_subset.html | 27 +- ...ls.bedtool.BedTool.randomintersection.html | 27 +- ...bedtool.BedTool.randomintersection_bp.html | 27 +- ...ybedtools.bedtool.BedTool.randomstats.html | 27 +- ...ols.bedtool.BedTool.relative_distance.html | 27 +- .../pybedtools.bedtool.BedTool.reldist.html | 29 +- ...dtools.bedtool.BedTool.remove_invalid.html | 27 +- .../pybedtools.bedtool.BedTool.save_seqs.html | 27 +- .../pybedtools.bedtool.BedTool.saveas.html | 27 +- autodocs/pybedtools.bedtool.BedTool.seq.html | 27 +- .../pybedtools.bedtool.BedTool.sequence.html | 29 +- ...dtools.bedtool.BedTool.set_chromsizes.html | 27 +- .../pybedtools.bedtool.BedTool.shuffle.html | 29 +- autodocs/pybedtools.bedtool.BedTool.slop.html | 29 +- autodocs/pybedtools.bedtool.BedTool.sort.html | 29 +- .../pybedtools.bedtool.BedTool.split.html | 27 +- .../pybedtools.bedtool.BedTool.subtract.html | 29 +- .../pybedtools.bedtool.BedTool.tabix.html | 27 +- ...tools.bedtool.BedTool.tabix_intervals.html | 27 +- .../pybedtools.bedtool.BedTool.tag_bam.html | 29 +- .../pybedtools.bedtool.BedTool.to_bam.html | 27 +- ...dtools.bedtool.BedTool.total_coverage.html | 27 +- ...ols.bedtool.BedTool.truncate_to_chrom.html | 27 +- ...tools.bedtool.BedTool.union_bedgraphs.html | 29 +- .../pybedtools.bedtool.BedTool.window.html | 29 +- ...bedtools.bedtool.BedTool.window_maker.html | 353 ++++++------ ...pybedtools.bedtool.BedTool.with_attrs.html | 27 +- .../pybedtools.bedtool.example_bedtool.html | 27 +- autodocs/pybedtools.cbedtools.Interval.html | 29 +- ...s.cbedtools.create_interval_from_list.html | 27 +- ...pybedtools.contrib.IntersectionMatrix.html | 29 +- .../pybedtools.contrib.bigbed.bigbed.html | 27 +- ...bedtools.contrib.bigbed.bigbed_to_bed.html | 27 +- ...bedtools.contrib.bigwig.bam_to_bigwig.html | 27 +- ...ols.contrib.bigwig.bedgraph_to_bigwig.html | 27 +- ...bedtools.contrib.bigwig.wig_to_bigwig.html | 27 +- ...ge_interaction.cis_trans_interactions.html | 27 +- ...trib.long_range_interaction.tag_bedpe.html | 27 +- ...edtools.contrib.plotting.BedToolsDemo.html | 29 +- ...ntrib.plotting.ConfiguredBedToolsDemo.html | 29 +- .../pybedtools.contrib.plotting.Track.html | 288 +++++----- ...ools.contrib.plotting.TrackCollection.html | 29 +- ...tools.contrib.plotting.binary_heatmap.html | 27 +- ...tools.contrib.plotting.binary_summary.html | 27 +- ....contrib.venn_maker.cleaned_intersect.html | 27 +- autodocs/pybedtools.contrib.venn_maker.html | 25 +- ...edtools.contrib.venn_maker.venn_maker.html | 27 +- autodocs/pybedtools.debug_mode.html | 27 +- ...pybedtools.filenames.example_filename.html | 27 +- ...bedtools.filenames.list_example_files.html | 27 +- autodocs/pybedtools.helpers.chromsizes.html | 29 +- ...pybedtools.helpers.chromsizes_to_file.html | 27 +- autodocs/pybedtools.helpers.cleanup.html | 27 +- ...ools.helpers.get_chromsizes_from_ucsc.html | 27 +- autodocs/pybedtools.helpers.get_tempdir.html | 27 +- .../pybedtools.helpers.set_bedtools_path.html | 27 +- autodocs/pybedtools.helpers.set_tempdir.html | 27 +- .../pybedtools.parallel.parallel_apply.html | 27 +- changes.html | 106 ++-- create-a-bedtool-tutorial.html | 25 +- default-arguments.html | 27 +- each.html | 25 +- filtering.html | 27 +- flow-of-commands.html | 35 +- genindex.html | 23 +- history.html | 27 +- includeme.html | 23 +- index.html | 36 +- intersections.html | 25 +- intervals.html | 37 +- intro.html | 27 +- main.html | 51 +- objects.inv | Bin 4218 -> 4219 bytes piping.html | 27 +- py-modindex.html | 23 +- pybedtools-dev-history.html | 25 +- pybedtools.featurefuncs.TSS.html | 27 +- pybedtools.featurefuncs.add_color.html | 27 +- pybedtools.featurefuncs.bed2gff.html | 27 +- pybedtools.featurefuncs.bedgraph_scale.html | 27 +- pybedtools.featurefuncs.center.html | 27 +- pybedtools.featurefuncs.extend_fields.html | 27 +- pybedtools.featurefuncs.five_prime.html | 27 +- pybedtools.featurefuncs.gff2bed.html | 27 +- pybedtools.featurefuncs.greater_than.html | 27 +- pybedtools.featurefuncs.less_than.html | 27 +- pybedtools.featurefuncs.midpoint.html | 27 +- ...ols.featurefuncs.normalized_to_length.html | 27 +- pybedtools.featurefuncs.rename.html | 27 +- pybedtools.featurefuncs.three_prime.html | 27 +- save-results.html | 25 +- scripts.html | 25 +- search.html | 23 +- searchindex.js | 2 +- sh-comparison.html | 29 +- topical-bam-semantics.html | 25 +- topical-bam.html | 28 +- topical-comparisons.html | 25 +- topical-create-a-bedtool.html | 25 +- topical-design-principles.html | 39 +- topical-documentation-contents.html | 25 +- topical-genome.html | 33 +- topical-iterators.html | 29 +- topical-low-level-ops.html | 25 +- topical-random.html | 29 +- topical-saving.html | 33 +- topical-wrapping.html | 39 +- tutorial-contents.html | 25 +- 183 files changed, 3532 insertions(+), 2993 deletions(-) diff --git a/3-brief-examples.html b/3-brief-examples.html index 91cf10e8..43dbf3a4 100644 --- a/3-brief-examples.html +++ b/3-brief-examples.html @@ -1,16 +1,16 @@ - + - Three brief examples — pybedtools 0.9.1 documentation - - - + Three brief examples — pybedtools 0.10.0 documentation + + + - + @@ -18,8 +18,9 @@ + + - @@ -32,7 +33,7 @@
-

Three brief examples

+

Three brief examples

Here are three examples to show typical usage of pybedtools. More info can be found in the docstrings of pybedtools methods and in the Tutorial Contents.

@@ -56,7 +57,7 @@
-

Example 1: Save a BED file of intersections, with track line

+

Example 1: Save a BED file of intersections, with track line

This example saves a new BED file of intersections between your files mydata/snps.bed and mydata/exons.bed, adding a track line to the output:

>>> import pybedtools
@@ -66,7 +67,7 @@ 
Example 1: Save a BED file of intersections, with track line
-
Example 2: Intersections for a 3-way Venn diagram

+
Example 2: Intersections for a 3-way Venn diagram

 
This example gets values for a 3-way Venn diagram of overlaps.  This
 demonstrates operator overloading of BedTool objects.  It assumes that
 you have the files a.bed, b.bed, and c.bed in your current working
@@ -94,7 +95,7 @@ 
Example 2: Intersections for a 3-way Venn diagramR package.
-

Example 3: Count reads in introns and exons, in parallel

+

Example 3: Count reads in introns and exons, in parallel

This example shows how to count the number of reads in introns and exons in parallel. It is somewhat more involved, but illustrates several additional features of pybedtools such as:

@@ -190,18 +191,18 @@

Navigation

  • previous |
    • -
  • pybedtools 0.9.1 documentation »
    • +
  • pybedtools 0.10.0 documentation »
  • Three brief examples
    • - ©2010-2015, Ryan Dale. + ©2010-2015, Ryan Dale. | - Powered by Sphinx 7.1.2 - & Alabaster 0.7.13 + Powered by Sphinx 7.2.6 + & Alabaster 0.7.16 | - + - FAQs — pybedtools 0.9.1 documentation - - - + FAQs — pybedtools 0.10.0 documentation + + + - + @@ -18,8 +18,9 @@ + + - @@ -32,13 +33,13 @@
    -

    FAQs

    +

    FAQs

    Note

    More detailed answers to these questions can often be found on the Issues page.

    -

    “Does pybedtools have a simple reader/writer for BED files?”

    +

    “Does pybedtools have a simple reader/writer for BED files?”

    While pybedtools designed to work with BEDTools, the reading/writing/parsing function can be easily used for other things.

    Simply iterating over a BedTool object will parse each line into @@ -81,7 +82,7 @@

    “Does pybedtools have a simple reader/writer for BED files?”Saving the results for more on saving the results.

    -

    “Can I create a BedTool object from an existing list?”

    +

    “Can I create a BedTool object from an existing list?”

    Sure, the BedTool constructor will figure it out:

    items = [
     ('chr1', 100, 200),
@@ -93,7 +94,7 @@ 
    “Can I create a BedTool object from an existing list?”
-
    “I’m getting an empty BedTool”
    
+
    “I’m getting an empty BedTool”
    
 
    Check to make sure you’re not consuming a BedTool generator.  Note that
 BedTool.filter() and BedTool.each() will return a generator BedTool
 object. Keep in mind that checking the length of a generator BedTool will
@@ -111,21 +112,21 @@ 
    “I’m getting an empty BedTool”
-
    “I’m getting a MalformedBedLineError”
    
+
    “I’m getting a MalformedBedLineError”
    
 
    This error can be raised by BEDTools itself.  Typical reasons are that start
 > end, or the fields are not tab-delimited.
    
 
    You can try the pybedtools.remove_invalid() function to clean up your
 file, or manually edit the offending lines.
    -

    “I get a segfault when iterating over a BedTool object”

    +

    “I get a segfault when iterating over a BedTool object”

    Issue #88 which addresses this issue – in summary, Cython’s handling of iterators works unexpectedly. It’s best to call the next() method explicitly when doing complex manipulations on an iterating BedTool.

    -

    “Can I add extra information to FASTA headers when using BedTool.sequence()?”

    +

    “Can I add extra information to FASTA headers when using BedTool.sequence()?”

    Since BEDTools adds the feature name to the FASTA header, you can manipulate the feature name on the fly with a custom modifier function:

    def fields2name(f):
@@ -141,7 +142,7 @@ 
    “Can I add extra information to FASTA headers when using BedTool.sequence(
    -

    “Too many files open” error

    +

    “Too many files open” error

    Sometimes you may get the error:

    * Too many files open -- please submit a bug report so that this can be fixed
    @@ -291,18 +292,18 @@

    Navigation

  • previous |
    • -
  • pybedtools 0.9.1 documentation »
    • +
  • pybedtools 0.10.0 documentation »
  • FAQs
    • - ©2010-2015, Ryan Dale. + ©2010-2015, Ryan Dale. | - Powered by Sphinx 7.1.2 - & Alabaster 0.7.13 + Powered by Sphinx 7.2.6 + & Alabaster 0.7.16 | - + - Overview: module code — pybedtools 0.9.1 documentation - - - + Overview: module code — pybedtools 0.10.0 documentation + + + - + + + - @@ -111,18 +112,18 @@

    Navigation

  • modules |
    • -
  • pybedtools 0.9.1 documentation »
    • +
  • pybedtools 0.10.0 documentation »
  • Overview: module code
    • - ©2010-2015, Ryan Dale. + ©2010-2015, Ryan Dale. | - Powered by Sphinx 7.1.2 - & Alabaster 0.7.13 + Powered by Sphinx 7.2.6 + & Alabaster 0.7.16
    diff --git a/_modules/pybedtools.html b/_modules/pybedtools.html index 80381c33..830c4bc5 100644 --- a/_modules/pybedtools.html +++ b/_modules/pybedtools.html @@ -1,22 +1,23 @@ - + - pybedtools — pybedtools 0.9.1 documentation - - - + pybedtools — pybedtools 0.10.0 documentation + + + - + + + - @@ -34,8 +35,8 @@

    Source code for pybedtools

     import subprocess
 import tempfile
 import logging
-from six.moves import urllib
-from six.moves import copyreg
+import copyreg
+
 from .cbedtools import (
     Interval,
     IntervalFile,
@@ -70,7 +71,9 @@ 
    Source code for pybedtools
     example_files = ["a.bed.", "b.bed", "test.fa", "a.bam"]
 
 
-
    [docs]def debug_mode(x):
+
    
+[docs]
+def debug_mode(x):
     """
     Enable debug mode.
 
@@ -99,6 +102,7 @@ 
    Source code for pybedtools
             logger.info("Debug mode disabled")
    
 
 
+
 def check_for_bedtools(*args, **kwargs):
     """
     For backwards compatibility; please use helpers._check_for_bedtools()
@@ -159,7 +163,7 @@ 
    Source code for pybedtools
                     pass
 
     if isinstance(fn, str):
-        from six.moves import configparser
+        import configparser
 
         c = configparser.SafeConfigParser()
         c.read(fn)
@@ -245,7 +249,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • pybedtools 0.9.1 documentation »
    • 
+        
  • pybedtools 0.10.0 documentation »
    • 
           
  • Module code »
    • 
         
  • pybedtools
    •  
       
@@ -253,11 +257,11 @@ 
    Navigation
    
 
 
     
    
-      ©2010-2015, Ryan Dale.
+      ©2010-2015, Ryan Dale.
       
       |
-      Powered by Sphinx 7.1.2
-      & Alabaster 0.7.13
+      Powered by Sphinx 7.2.6
+      & Alabaster 0.7.16
       
     
    
 
diff --git a/_modules/pybedtools/bedtool.html b/_modules/pybedtools/bedtool.html
index bc3f71c1..229086bd 100644
--- a/_modules/pybedtools/bedtool.html
+++ b/_modules/pybedtools/bedtool.html
@@ -1,22 +1,23 @@
 
 
-
+
   
     
     
-    pybedtools.bedtool — pybedtools 0.9.1 documentation
-    
-    
-    
+    pybedtools.bedtool — pybedtools 0.10.0 documentation
+    
+    
+    
     
-    
+    
     
     
    
   
   
+
+  
   
-  
 
   
   
@@ -41,10 +42,10 @@ 
    Source code for pybedtools.bedtool
     import pprint
 from itertools import islice
 import multiprocessing
-import six
 import gzip
 import pysam
 from warnings import warn
+from pathlib import Path
 
 from .helpers import (
     get_tempdir,
@@ -84,7 +85,7 @@ 
    Source code for pybedtools.bedtool
         jaccard method doesn't return an interval file, rather, it returns a short
     summary of results.  Here, we simply parse it into a dict for convenience.
     """
-    if isinstance(s, six.string_types):
+    if isinstance(s, str):
         _s = open(s).read()
     elif hasattr(s, "next") or hasattr(s, "__next__"):
         _s = "".join([i for i in s])
@@ -109,11 +110,11 @@ 
    Source code for pybedtools.bedtool
         """
     if "detail" in kwargs:
         return BedTool(s)
-    if isinstance(s, six.string_types):
+    if isinstance(s, str):
         iterable = open(s)
     if hasattr(s, "next"):
         iterable = s
-    header = six.advance_iterator(iterable).split()
+    header = next(iterable).split()
     results = {}
     for h in header:
         results[h] = []
@@ -401,7 +402,7 @@ 
    Source code for pybedtools.bedtool
                 # keep the nonbam arg passed into the original _wraps() decorator
             # in scope.
             if nonbam is not None and nonbam != "ALL":
-                if isinstance(nonbam, six.string_types):
+                if isinstance(nonbam, str):
                     _nonbam = [nonbam]
                 else:
                     _nonbam = nonbam
@@ -464,10 +465,14 @@ 
    Source code for pybedtools.bedtool
         return decorator
 
 
-
    [docs]class BedTool(object):
+
    
+[docs]
+class BedTool(object):
     TEMPFILES = filenames.TEMPFILES
 
-
    [docs]    def __init__(self, fn=None, from_string=False, remote=False):
+
    
+[docs]
+    def __init__(self, fn=None, from_string=False, remote=False):
         """
         Wrapper around Aaron Quinlan's ``BEDtools`` suite of programs
         (https://github.com/arq5x/bedtools); also contains many useful
@@ -534,14 +539,12 @@ 
    Source code for pybedtools.bedtool
                     fn = fn.fn
 
             # from_string=False, so assume it's a filename
-            elif isinstance(fn, six.string_types):
+            elif isinstance(fn, str):
                 if remote:
                     self._isbam = True
                 else:
                     if not os.path.exists(fn):
                         msg = 'File "%s" does not exist' % fn
-                        if six.PY2:
-                            raise ValueError(msg)
                         raise FileNotFoundError(msg)
                     self._isbam = isBAM(fn)
 
@@ -618,6 +621,7 @@ 
    Source code for pybedtools.bedtool
             self._file_type = None
         self.history = History()
    
 
+
     @classmethod
     def from_dataframe(
         self,
@@ -649,7 +653,7 @@ 
    Source code for pybedtools.bedtool
             default_kwargs.update(kwargs)
         df.to_csv(outfile, **default_kwargs)
 
-        if isinstance(outfile, six.string_types):
+        if isinstance(outfile, str):
             fn = outfile
         else:
             try:
@@ -661,7 +665,9 @@ 
    Source code for pybedtools.bedtool
                     )
         return BedTool(fn)
 
-
    [docs]    def split(self, func, *args, **kwargs):
+
    
+[docs]
+    def split(self, func, *args, **kwargs):
         """
         Split each feature using a user-defined function.
 
@@ -681,7 +687,10 @@ 
    Source code for pybedtools.bedtool
     
         return BedTool(generator())
    
 
-
    [docs]    def truncate_to_chrom(self, genome):
+
+
    
+[docs]
+    def truncate_to_chrom(self, genome):
         """
         Ensure all features fall within chromosome limits.
 
@@ -701,7 +710,7 @@ 
    Source code for pybedtools.bedtool
             if isinstance(genome, dict):
             chromdict = genome
         else:
-            assert isinstance(genome, six.string_types)
+            assert isinstance(genome, str)
             chromdict = helpers.chromsizes(genome)
 
         tmp = self._tmp()
@@ -713,7 +722,10 @@ 
    Source code for pybedtools.bedtool
                     fout.write("\t".join([chrom, start, stop]) + "\n")
         return self.intersect(tmp)
    
 
-
    [docs]    def tabix_intervals(self, interval_or_string, check_coordinates=False):
+
+
    
+[docs]
+    def tabix_intervals(self, interval_or_string, check_coordinates=False):
         """
         Retrieve all intervals within coordinates from a "tabixed" BedTool.
 
@@ -772,6 +784,7 @@ 
    Source code for pybedtools.bedtool
             tbx.close()
         return x
    
 
+
     def tabix_contigs(self):
         """
         Returns a list of contigs from the tabix index.
@@ -785,7 +798,9 @@ 
    Source code for pybedtools.bedtool
             tbx = pysam.TabixFile(self.fn)
         return tbx.contigs
 
-
    [docs]    def tabix(self, in_place=True, force=False, is_sorted=False):
+
    
+[docs]
+    def tabix(self, in_place=True, force=False, is_sorted=False):
         """
         Prepare a BedTool for use with Tabix.
 
@@ -817,19 +832,22 @@ 
    Source code for pybedtools.bedtool
             pysam.tabix_index(fn, force=force, preset=self.file_type)
         return BedTool(fn)
    
 
+
     def _tabixed(self):
         """
         Verifies that we're working with a tabixed file: a string filename
         pointing to a BGZIPed file with a .tbi file in the same dir.
         """
         if (
-            isinstance(self.fn, six.string_types)
+            isinstance(self.fn, str)
             and isBGZIP(self.fn)
             and os.path.exists(self.fn + ".tbi")
         ):
             return True
 
-
    [docs]    def bgzip(self, in_place=True, force=False, is_sorted=False):
+
    
+[docs]
+    def bgzip(self, in_place=True, force=False, is_sorted=False):
         """
         Helper function for more control over "tabixed" BedTools.
 
@@ -851,7 +869,7 @@ 
    Source code for pybedtools.bedtool
                 force_arg = ""
 
         # It may already be BGZIPed...
-        if isinstance(self.fn, six.string_types) and not force:
+        if isinstance(self.fn, str) and not force:
             if isBGZIP(self.fn):
                 return self.fn
 
@@ -882,6 +900,7 @@ 
    Source code for pybedtools.bedtool
                 pysam.tabix_compress(fn, outfn, force=force)
             return outfn
    
 
+
     def delete_temporary_history(self, ask=True, raw_input_func=None):
         """
         Use at your own risk!  This method will delete temp files. You will be
@@ -961,7 +980,9 @@ 
    Source code for pybedtools.bedtool
             decorated.__doc__ = method.__doc__
         return decorated
 
-
    [docs]    def filter(self, func, *args, **kwargs):
+
    
+[docs]
+    def filter(self, func, *args, **kwargs):
         """
         Filter features by user-defined function.
 
@@ -984,7 +1005,10 @@ 
    Source code for pybedtools.bedtool
             """
         return BedTool((f for f in self if func(f, *args, **kwargs)))
    
 
-
    [docs]    def field_count(self, n=10):
+
+
    
+[docs]
+    def field_count(self, n=10):
         """
         Number of fields in each line of this BedTool (checks `n` lines)
 
@@ -1008,7 +1032,10 @@ 
    Source code for pybedtools.bedtool
             assert len(fields) == 1, fields
         return list(fields)[0]
    
 
-
    [docs]    def each(self, func, *args, **kwargs):
+
+
    
+[docs]
+    def each(self, func, *args, **kwargs):
         """
         Modify each feature with a user-defined function.
 
@@ -1046,7 +1073,10 @@ 
    Source code for pybedtools.bedtool
     
         return BedTool(_generator())
    
 
-
    [docs]    def introns(self, gene="gene", exon="exon"):
+
+
    
+[docs]
+    def introns(self, gene="gene", exon="exon"):
         """
         Create intron features (requires specific input format).
 
@@ -1117,6 +1147,7 @@ 
    Source code for pybedtools.bedtool
                             )
         return BedTool(fh.name)
    
 
+
     def features(self):
         """
         Returns an iterable of features
@@ -1135,7 +1166,7 @@ 
    Source code for pybedtools.bedtool
             >>> print(a.file_type)
         bed
         """
-        if not isinstance(self.fn, six.string_types):
+        if not isinstance(self.fn, str):
             raise ValueError(
                 "Checking file_type not supported for "
                 "non-file BedTools. Use .saveas() to "
@@ -1145,13 +1176,15 @@ 
    Source code for pybedtools.bedtool
                 self._file_type = "bam"
         else:
             try:
-                self._file_type = six.advance_iterator(iter(self)).file_type
+                self._file_type = next(iter(self)).file_type
             except StopIteration:
                 self._file_type = "empty"
 
         return self._file_type
 
-
    [docs]    def cut(self, indexes, stream=False):
+
    
+[docs]
+    def cut(self, indexes, stream=False):
         """
         Analagous to unix `cut`.
 
@@ -1181,6 +1214,7 @@ 
    Source code for pybedtools.bedtool
                         print("\t".join(map(str, [f[attr] for attr in indexes])), file=fh)
             return BedTool(fh.name)
    
 
+
     @classmethod
     def _tmp(self):
         """
@@ -1208,7 +1242,7 @@ 
    Source code for pybedtools.bedtool
                 return BAM(self.fn)
 
         # Plain ol' filename
-        if isinstance(self.fn, six.string_types):
+        if isinstance(self.fn, str):
             if not os.path.exists(self.fn):
                 raise BedToolsFileError("{0} does not exist".format(self.fn))
             if isGZIP(self.fn):
@@ -1223,13 +1257,13 @@ 
    Source code for pybedtools.bedtool
     
     @property
     def intervals(self):
-        if isinstance(self.fn, six.string_types):
+        if isinstance(self.fn, str):
             return IntervalFile(self.fn)
         else:
             raise ValueError("Please convert to a file-based BedTool using saveas")
 
     def __repr__(self):
-        if isinstance(self.fn, six.string_types):
+        if isinstance(self.fn, str):
             if os.path.exists(self.fn) or self.remote:
                 return "<BedTool(%s)>" % self.fn
             else:
@@ -1255,11 +1289,11 @@ 
    Source code for pybedtools.bedtool
             return self.count()
 
     def __eq__(self, other):
-        if isinstance(other, six.string_types):
+        if isinstance(other, str):
             other_str = other
         elif isinstance(other, BedTool):
-            if not isinstance(self.fn, six.string_types) or not isinstance(
-                other.fn, six.string_types
+            if not isinstance(self.fn, str) or not isinstance(
+                other.fn, str
             ):
                 raise NotImplementedError(
                     "Testing equality only supported for"
@@ -1307,7 +1341,9 @@ 
    Source code for pybedtools.bedtool
                     result = pybedtools.BedTool("", from_string=True)
         return result
 
-
    [docs]    def head(self, n=10, as_string=False):
+
    
+[docs]
+    def head(self, n=10, as_string=False):
         """
         Prints the first *n* lines or returns them if as_string is True
 
@@ -1321,7 +1357,7 @@ 
    Source code for pybedtools.bedtool
             <BLANKLINE>
 
         """
-        if not isinstance(self.fn, six.string_types):
+        if not isinstance(self.fn, str):
             raise NotImplementedError(
                 "head() not supported for non file-based BedTools"
             )
@@ -1342,7 +1378,10 @@ 
    Source code for pybedtools.bedtool
                             break
                     print(line, end=" ")
    
 
-
    [docs]    def set_chromsizes(self, chromsizes):
+
+
    
+[docs]
+    def set_chromsizes(self, chromsizes):
         """
         Prepare BedTool for operations that require chromosome coords.
 
@@ -1360,7 +1399,7 @@ 
    Source code for pybedtools.bedtool
                 (0, 249250621)
 
         """
-        if isinstance(chromsizes, six.string_types):
+        if isinstance(chromsizes, str):
             self.chromsizes = pybedtools.chromsizes(chromsizes)
         elif isinstance(chromsizes, dict):
             self.chromsizes = chromsizes
@@ -1371,6 +1410,7 @@ 
    Source code for pybedtools.bedtool
                 )
         return self
    
 
+
     def _collapse(
         self,
         iterable,
@@ -1424,7 +1464,7 @@ 
    Source code for pybedtools.bedtool
     
         # If we're just working with filename-based BedTool objects, just copy
         # the files directly
-        if isinstance(iterable, BedTool) and isinstance(iterable.fn, six.string_types):
+        if isinstance(iterable, BedTool) and isinstance(iterable.fn, str):
             with out_open_func(fn, "wt") as out_:
                 if sys.version_info > (3,0):
                     in_ = in_open_func(iterable.fn, "rt", errors="ignore")
@@ -1495,7 +1535,7 @@ 
    Source code for pybedtools.bedtool
                     instream1 = instream1.fn
 
             # Filename? No pipe, just provide the file
-            if isinstance(instream1, six.string_types):
+            if isinstance(instream1, str):
                 kwargs[inarg1] = instream1
                 stdin = None
 
@@ -1525,7 +1565,7 @@ 
    Source code for pybedtools.bedtool
                     instream2 = instream2.fn
 
             # Filename
-            if isinstance(instream2, six.string_types):
+            if isinstance(instream2, str):
                 kwargs[inarg2] = instream2
 
             # If it's a list of strings, then we need to figure out if it's
@@ -1542,7 +1582,7 @@ 
    Source code for pybedtools.bedtool
                 # left to the user.
             #
             elif isinstance(instream2, (list, tuple)) and isinstance(
-                instream2[0], six.string_types
+                instream2[0], str
             ):
                 try:
                     _ = create_interval_from_list(instream2[0].split("\t"))
@@ -1658,13 +1698,13 @@ 
    Source code for pybedtools.bedtool
     
         if not os.path.exists(kwargs["g"]):
             msg = 'Genome file "%s" does not exist' % (kwargs["g"])
-            if six.PY2:
-                raise ValueError(msg)
             raise FileNotFoundError(msg)
 
         return kwargs
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     def remove_invalid(self):
         """
         Remove invalid features that may break BEDTools programs.
@@ -1681,7 +1721,7 @@ 
    Source code for pybedtools.bedtool
     
         # If it's a file-based BedTool -- which is likely, if we're trying to
         # remove invalid features -- then we need to parse it line by line.
-        if isinstance(self.fn, six.string_types):
+        if isinstance(self.fn, str):
             i = IntervalIterator(open(self.fn, "r"))
         else:
             tmp = self.saveas()
@@ -1707,7 +1747,10 @@ 
    Source code for pybedtools.bedtool
     
         return BedTool(_generator())
    
 
-
    [docs]    def all_hits(self, interval, same_strand=False, overlap=0.0):
+
+
    
+[docs]
+    def all_hits(self, interval, same_strand=False, overlap=0.0):
         """
         Return all intervals that overlap `interval`.
 
@@ -1728,14 +1771,17 @@ 
    Source code for pybedtools.bedtool
             if not isinstance(interval, Interval):
             raise ValueError("Need an Interval instance")
         fn = self.fn
-        if not isinstance(fn, six.string_types):
+        if not isinstance(fn, str):
             fn = self.saveas().fn
         if self._isbam:
             fn = self.bam_to_bed().fn
         interval_file = pybedtools.IntervalFile(fn)
         return interval_file.all_hits(interval, same_strand, overlap)
    
 
-
    [docs]    def any_hits(self, interval, same_strand=False, overlap=0.0):
+
+
    
+[docs]
+    def any_hits(self, interval, same_strand=False, overlap=0.0):
         """
         Return whether or not any intervals overlap `interval`.
 
@@ -1756,14 +1802,17 @@ 
    Source code for pybedtools.bedtool
             if not isinstance(interval, Interval):
             raise ValueError("Need an Interval instance")
         fn = self.fn
-        if not isinstance(fn, six.string_types):
+        if not isinstance(fn, str):
             fn = self.saveas().fn
         if self._isbam:
             fn = self.bam_to_bed().fn
         interval_file = pybedtools.IntervalFile(fn)
         return interval_file.any_hits(interval, same_strand, overlap)
    
 
-
    [docs]    def count_hits(self, interval, same_strand=False, overlap=0.0):
+
+
    
+[docs]
+    def count_hits(self, interval, same_strand=False, overlap=0.0):
         """
         Return the number of intervals that overlap `interval`.
 
@@ -1784,14 +1833,17 @@ 
    Source code for pybedtools.bedtool
             if not isinstance(interval, Interval):
             raise ValueError("Need an Interval instance")
         fn = self.fn
-        if not isinstance(fn, six.string_types):
+        if not isinstance(fn, str):
             fn = self.saveas().fn
         if self._isbam:
             fn = self.bam_to_bed().fn
         interval_file = pybedtools.IntervalFile(fn)
         return interval_file.count_hits(interval, same_strand, overlap)
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="bed12ToBed6", implicit="i", bam=None, other=None)
     def bed6(self, **kwargs):
         """
@@ -1799,16 +1851,20 @@ 
    Source code for pybedtools.bedtool
             """
         pass
    
 
+
     # Alias for backward compatibility
     bed12tobed6 = bed6
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="bamToBed", implicit="i", other=None, nonbam="ALL", bam="i")
     def bam_to_bed(self, **kwargs):
         """
         Wraps `bedtools bamtobed`.
         """
    
 
+
     # Alias for backward compatibility
     bamtobed = bam_to_bed
 
@@ -1819,7 +1875,9 @@ 
    Source code for pybedtools.bedtool
             self.to_bam (which needs to do something different for SAM files...)
         """
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     def to_bam(self, **kwargs):
         """
         Wraps `bedtools bedtobam`
@@ -1883,10 +1941,13 @@ 
    Source code for pybedtools.bedtool
                 new_bedtool._isbam = True
             return new_bedtool
    
 
+
     # Alias for backward compatibility
     bedtobam = to_bam
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="intersectBed", implicit="a", other="b", bam="abam",
             nonbam="bed", arg_order=["a", "abam"])
     def intersect(self):
@@ -1894,7 +1955,10 @@ 
    Source code for pybedtools.bedtool
             Wraps `bedtools intersect`.
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(
         prog="fastaFromBed",
         implicit="bed",
@@ -1931,10 +1995,13 @@ 
    Source code for pybedtools.bedtool
     
         '''
    
 
+
     # Alias for backwards compatibility
     getfasta = sequence
 
-
    [docs]    @staticmethod
+
    
+[docs]
+    @staticmethod
     def seq(loc, fasta):
         """
         Return just the sequence from a region string or a single location
@@ -1944,7 +2011,7 @@ 
    Source code for pybedtools.bedtool
             >>> BedTool.seq(('chr1', 1, 10), fn)
         'GATGAGTCT'
         """
-        if isinstance(loc, six.string_types):
+        if isinstance(loc, str):
             chrom, start_end = loc.split(":")
             start, end = list(map(int, start_end.split("-")))
             start -= 1
@@ -1955,7 +2022,10 @@ 
    Source code for pybedtools.bedtool
             lseq = loc.sequence(fi=fasta)
         return "".join([l.rstrip() for l in open(lseq.seqfn, "r") if l[0] != ">"])
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(
         prog="nucBed", implicit="bed", other="fi", check_stderr=_check_sequence_stderr
     )
@@ -1967,10 +2037,13 @@ 
    Source code for pybedtools.bedtool
             information about the nucleotide content
         """
    
 
+
     # Alias for backwards compatibility
     nuc = nucleotide_content
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="multiBamCov", implicit="bed")
     def multi_bam_coverage(self):
         """
@@ -1979,10 +2052,13 @@ 
    Source code for pybedtools.bedtool
             Pass a list of sorted and indexed BAM files as `bams`
         """
    
 
+
     # Alias for backwards compatibility
     multicov = multi_bam_coverage
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="subtractBed", implicit="a", other="b", bam=None)
     def subtract(self):
         """
@@ -2012,13 +2088,17 @@ 
    Source code for pybedtools.bedtool
             stream = call_bedtools(cmds, tmp, stdin=stdin)
         return BedTool(stream)
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="slopBed", implicit="i", other=None, bam=None, uses_genome=True)
     def slop(self):
         """
         Wraps `bedtools slop`.
         """
    
 
+
     @_log_to_history
     @_wraps(prog="shiftBed", implicit="i", other=None, bam=None, uses_genome=True)
     def shift(self):
@@ -2064,7 +2144,9 @@ 
    Source code for pybedtools.bedtool
     
         """
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="mergeBed", implicit="i", other=None, bam=None)
     def merge(self):
         """
@@ -2086,7 +2168,10 @@ 
    Source code for pybedtools.bedtool
     
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="closestBed", implicit="a", other="b", bam=None)
     def closest(self):
         """
@@ -2105,7 +2190,10 @@ 
    Source code for pybedtools.bedtool
     
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="windowBed", implicit="a", other="b", bam="abam", nonbam="bed")
     def window(self):
         """
@@ -2127,7 +2215,10 @@ 
    Source code for pybedtools.bedtool
                 <BLANKLINE>
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="shuffleBed", implicit="i", other=None, bam=None, uses_genome=True)
     def shuffle(self):
         """
@@ -2146,7 +2237,10 @@ 
    Source code for pybedtools.bedtool
             <BLANKLINE>
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="sortBed", implicit="i", uses_genome=True, genome_if=["g", "genome"])
     def sort(self):
         """
@@ -2173,7 +2267,10 @@ 
    Source code for pybedtools.bedtool
             <BLANKLINE>
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="annotateBed", implicit="i")
     def annotate(self):
         """
@@ -2192,7 +2289,10 @@ 
    Source code for pybedtools.bedtool
             <BLANKLINE>
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="flankBed", implicit="i", uses_genome=True)
     def flank(self):
         """
@@ -2222,7 +2322,10 @@ 
    Source code for pybedtools.bedtool
             stream = call_bedtools(cmds, tmp, stdin=stdin)
         return BedTool(stream)
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(
         prog="genomeCoverageBed",
         implicit="i",
@@ -2270,10 +2373,13 @@ 
    Source code for pybedtools.bedtool
             >>> df = b.to_dataframe(names=['chrom', 'depth', 'n', 'chromsize', 'fraction'])
         """
    
 
+
     # Alias for backwards compatibility
     genomecov = genome_coverage
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="coverageBed", implicit="a", other="b", bam="abam", nonbam="ALL")
     def coverage(self):
         """
@@ -2292,7 +2398,10 @@ 
    Source code for pybedtools.bedtool
             chr1	800	901	feature6	0	+	1	1	101	0.0099010
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(
         prog="maskFastaFromBed",
         implicit="bed",
@@ -2322,10 +2431,13 @@ 
    Source code for pybedtools.bedtool
             ...     os.unlink('masked.fa.example.fai')
         """
    
 
+
     # Alias for backwards compatibility
     maskfasta = mask_fasta
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="complementBed", implicit="i", uses_genome=True)
     def complement(self):
         """
@@ -2341,7 +2453,10 @@ 
    Source code for pybedtools.bedtool
             chr3	0	198022430
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="getOverlap", implicit="i")
     def overlap(self):
         """
@@ -2359,28 +2474,37 @@ 
    Source code for pybedtools.bedtool
             <BLANKLINE>
         """
    
 
+
     # TODO: needs test files and doctests written
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="pairToBed", implicit="a", other="b", bam="abam", nonbam="bedpe")
     def pair_to_bed(self):
         """
         Wraps `bedtools pairtobed`.
         """
    
 
+
     # Alias for backwards compatibility
     pairtobed = pair_to_bed
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="pairToPair", implicit="a", other="b")
     def pair_to_pair(self):
         """
         Wraps `bedtools pairtopair`.
         """
    
 
+
     # Alias for backwards compatibility
     pairtopair = pair_to_pair
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="groupBy", implicit="i")
     def groupby(self):
         """
@@ -2407,7 +2531,10 @@ 
    Source code for pybedtools.bedtool
     
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="tagBam", implicit="i", bam="i")
     def tag_bam(self):
         """
@@ -2417,17 +2544,23 @@ 
    Source code for pybedtools.bedtool
     
         """
    
 
+
     # Alias for backwards compatibility
     tag = tag_bam
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="mapBed", implicit="a", other="b")
     def map(self):
         """
         Wraps  `bedtools map`; See also :meth:`BedTool.each`.
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="multiIntersectBed", uses_genome=True, genome_if=["empty"])
     def multi_intersect(self):
         """
@@ -2451,10 +2584,13 @@ 
    Source code for pybedtools.bedtool
     
         """
    
 
+
     # Alias for backwards compatibility
     multiinter = multi_intersect
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="randomBed", uses_genome=True)
     def random(self):
         """
@@ -2467,24 +2603,33 @@ 
    Source code for pybedtools.bedtool
             >>> y = x.random(l=100, n=10, genome='hg19')
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps("bedpeToBam", implicit="i", uses_genome=True, force_bam=True)
     def bedpe_to_bam(self):
         """
         Wraps `bedtools bedpetobam`.
         """
    
 
+
     # Alias for backwards compatibility
     bedpetobam = bedpe_to_bam
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="clusterBed", implicit="i")
     def cluster(self):
         """
         Wraps  `bedtools cluster`.
         """
    
 
-
    [docs]    @_log_to_history
+
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="unionBedGraphs")
     def union_bedgraphs(self):
         """
@@ -2494,27 +2639,36 @@ 
    Source code for pybedtools.bedtool
             not in true BED format, which may break downstream analysis.
         """
    
 
+
     # Alias for backwards compatibility
     unionbedg = union_bedgraphs
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="windowMaker", uses_genome=True, genome_none_if=["b"], other="b", arg_order=["w"])
     def window_maker(self):
         """
         Wraps `bedtools makewindows`.
         """
    
 
+
     # Alias for backwards compatibility
     makewindows = window_maker
 
-
    [docs]    @_log_to_history
+
    
+[docs]
+    @_log_to_history
     @_wraps(prog="expandCols", implicit="i")
     def expand(self):
         """
         Wraps `bedtools expand`
         """
    
 
-