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|
Description: Use 2to3 to port to Python3
Bug-Debian: https://bugs.debian.org/936199
Author: Andreas Tille <tille@debian.org>
Last-Update: 2023-06-23
Forwarded: not-needed
Reviewed-By: Étienne Mollier <emollier@debian.org>
--- bedtools.orig/docs/conf.py
+++ bedtools/docs/conf.py
@@ -43,8 +43,8 @@
master_doc = 'index'
# General information about the project.
-project = u'bedtools'
-copyright = u'2009 - 2023, Aaron R. Quinlan'
+project = 'bedtools'
+copyright = '2009 - 2023, Aaron R. Quinlan'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -186,8 +186,8 @@
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'bedtools.tex', u'Bedtools Documentation',
- u'Quinlan lab @ Univ. of Utah', 'manual'),
+ ('index', 'bedtools.tex', 'Bedtools Documentation',
+ 'Quinlan lab @ Univ. of Utah', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
@@ -219,7 +219,7 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1)
+ ('index', 'bedtools', 'Bedtools Documentation', ['UU'], 1)
]
# Example configuration for intersphinx: refer to the Python standard library.
--- bedtools.orig/test/fisher/README.md
+++ bedtools/test/fisher/README.md
@@ -2,7 +2,7 @@
==============
Fisher is now based on the count of interval overlaps, subject to `-f`.
-We can compare the output of fisher on simulated data by running `python sim.py`
+We can compare the output of fisher on simulated data by running `python3 sim.py`
which will show the output from `bedtools fisher` and then running `bash shuf.sh`
which will repeatedly run
--- bedtools.orig/test/fisher/cmp.sh
+++ bedtools/test/fisher/cmp.sh
@@ -3,7 +3,7 @@
echo "fisher,shuffled"
for i in $(seq 1000); do
- fisher=$(python ./sim.py | tail -1 | cut -f 2)
+ fisher=$(python3 ./sim.py | tail -1 | cut -f 2)
shuffle=$(bash shuf.sh)
echo "$fisher,$shuffle"
done
--- bedtools.orig/test/fisher/sim.py
+++ bedtools/test/fisher/sim.py
@@ -25,7 +25,7 @@
fh.write("chr1\t%i\t%i\n" % (s, e))
fh.flush()
-print >> open('tgg.genome', 'w'), ("chr1\t%i" % genome_size)
+print(("chr1\t%i" % genome_size), file=open('tgg.genome', 'w'))
# NOTE: add -m here to make merged output
-print check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip()
+print(check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip())
--- bedtools.orig/test/bigchroms/test-bigchroms.sh
+++ bedtools/test/bigchroms/test-bigchroms.sh
@@ -28,7 +28,7 @@
rm obs
if [[ "$BT_NO_BIG_FILES" != "" ]]; then
-python make-big-chrom.py
+python3 make-big-chrom.py
echo -e " bigchroms.t03...big get fasta \c"
$BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
--- bedtools.orig/scripts/makeBashScripts.py
+++ bedtools/scripts/makeBashScripts.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
# encoding: utf-8
"""
makeBashScripts.py
@@ -58,4 +58,4 @@
script.close()
if __name__ == "__main__":
- main()
\ No newline at end of file
+ main()
--- bedtools.orig/test/genomecov/test-genomecov.sh
+++ bedtools/test/genomecov/test-genomecov.sh
@@ -288,7 +288,7 @@
check obs exp
rm obs exp
-python mk-deep.py > deep.sam
+python3 mk-deep.py > deep.sam
echo -e " genomecov.t18...\c"
echo "c1 1 1000000" > exp
$BT genomecov -d -ibam deep.sam | head -1 > obs
--- bedtools.orig/tutorial/bedtools.html
+++ bedtools/tutorial/bedtools.html
@@ -495,7 +495,7 @@
<p>Now let’s make a 20x20 matrix of the Jaccard statistic. This will allow the data to play nicely with R.</p>
<pre><code>awk 'NF==3' pairwise.dnase.shortnames.txt \
| awk '$1 ~ /^f/ && $2 ~ /^f/' \
-| python make-matrix.py \
+| python3 make-matrix.py \
> dnase.shortnames.distance.matrix</code></pre>
<p>Let’s also make a file of labels for each dataset so that we can label each dataset in our R plot.</p>
<pre><code>cut -f 1 dnase.shortnames.distance.matrix | cut -f 1 -d "-" | cut -f 1 -d "_" > labels.txt</code></pre>
--- bedtools.orig/tutorial/bedtools.md
+++ bedtools/tutorial/bedtools.md
@@ -606,7 +606,7 @@
awk 'NF==3' pairwise.dnase.shortnames.txt \
| awk '$1 ~ /^f/ && $2 ~ /^f/' \
- | python make-matrix.py \
+ | python3 make-matrix.py \
> dnase.shortnames.distance.matrix
Let's also make a file of labels for each dataset so that we can label each dataset in our R plot.
|
