[med-svn] [Git][med-team/python-bx][master] 4 commits: d/rules: use dh_numpy3 to inject a dependency on the appropriate numpy ABI.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Feb 27 17:35:24 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / python-bx
Commits:
f8f9a340 by Michael R. Crusoe at 2024-02-27T16:05:20+01:00
d/rules: use dh_numpy3 to inject a dependency on the appropriate numpy ABI.
- - - - -
08e1f20c by Michael R. Crusoe at 2024-02-27T16:15:44+01:00
mark the fix_BIN_OFFSETS_MAX patch as being forwarded upstream.
- - - - -
03a2ae6a by Michael R. Crusoe at 2024-02-27T16:16:04+01:00
d/control: switch to pyproject based building.
- - - - -
ad9cf2d2 by Michael R. Crusoe at 2024-02-27T16:49:48+01:00
d/patches/pytest8: add pytest 8.x compatability.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_BIN_OFFSETS_MAX
- + debian/patches/pytest8
- debian/patches/series
- debian/patches/shebang.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-bx (0.11.0-2) UNRELEASED; urgency=medium
+
+ * d/rules: use dh_numpy3 to inject a dependency on the appropriate
+ numpy ABI.
+ * mark the fix_BIN_OFFSETS_MAX patch as being forwarded upstream.
+ * d/control: switch to pyproject based building.
+ * d/patches/pytest8: add pytest 8.x compatability.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 27 Feb 2024 16:05:18 +0100
+
python-bx (0.11.0-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
zlib1g-dev,
python3-setuptools,
+ pybuild-plugin-pyproject,
python3-all-dev:any,
python3-lzo,
python3-pytest <!nocheck>,
=====================================
debian/patches/fix_BIN_OFFSETS_MAX
=====================================
@@ -1,8 +1,9 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: fix error for 32bit systems
---- a/lib/bx/interval_index_file.py
-+++ b/lib/bx/interval_index_file.py
-@@ -123,7 +123,7 @@ for i in range(BIN_LEVELS - 2):
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: fix off by one error on 32 bit systems
+Forwarded: https://github.com/bxlab/bx-python/pull/54
+--- python-bx.orig/lib/bx/interval_index_file.py
++++ python-bx/lib/bx/interval_index_file.py
+@@ -124,7 +124,7 @@
BIN_OFFSETS_MAX.insert(0, (BIN_OFFSETS_MAX[0] << BIN_NEXT_SHIFT))
# The maximum size for the top bin is actually bigger than the signed integers
# we use to store positions in the file, so we'll change it to prevent confusion
@@ -11,7 +12,7 @@ Subject: fix error for 32bit systems
# Constants for the minimum and maximum size of the overall interval
MIN = 0
-@@ -136,12 +136,14 @@ def offsets_for_max_size(max_size):
+@@ -137,12 +137,14 @@
"""
Return the subset of offsets needed to contain intervals over (0,max_size)
"""
=====================================
debian/patches/pytest8
=====================================
@@ -0,0 +1,70 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Add pytest 8.x compatability
+Forwarded: https://github.com/bxlab/bx-python/pull/92
+
+nose-style module setup function renamed to the pytest way.
+--- python-bx.orig/lib/bx/binned_array_tests.py
++++ python-bx/lib/bx/binned_array_tests.py
+@@ -16,18 +16,17 @@
+ FileBinnedArray,
+ )
+
++import pytest
++
+ # Bigger values take longer, but excercise more bins
+ CHUNK_SIZE_RANDOM = 945
+ CHUNK_SIZE_ZEROS = 897
+ # CHUNK_SIZE_RANDOM=9456
+ # CHUNK_SIZE_ZEROS=8972
+
+-source = target = None
+-
+
+-def setup():
+- global source
+- global target
++ at pytest.fixture(scope="module")
++def source_target():
+ source = []
+ for _ in range(13):
+ if random() < 0.5:
+@@ -43,7 +42,8 @@
+ return source, target
+
+
+-def test_simple():
++def test_simple(source_target):
++ source, target = source_target
+ # Verify
+ for i in range(len(source)):
+ assert source[i] == target[i], "No match, index: %d, source: %f, target: %f, len( source ): %d" % (
+@@ -66,7 +66,8 @@
+ )
+
+
+-def test_file():
++def test_file(source_target):
++ source, target = source_target
+ # With a file (zlib)
+ target.to_file(open("/tmp/foo", "wb"))
+ target2 = FileBinnedArray(open("/tmp/foo", "rb"))
+@@ -87,7 +88,8 @@
+ )
+
+
+-def test_file_lzo():
++def test_file_lzo(source_target):
++ source, target = source_target
+ # With a file (lzo)
+ target.to_file(open("/tmp/foo3", "wb"), comp_type="lzo")
+ target3 = FileBinnedArray(open("/tmp/foo3", "rb"))
+@@ -109,7 +111,8 @@
+ )
+
+
+-def test_binned_array_writer():
++def test_binned_array_writer(source_target):
++ source, target = source_target
+ # Test with ba writer
+ o = open("/tmp/foo4", "wb")
+ w = BinnedArrayWriter(o, 128, comp_type="lzo")
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
+pytest8
shebang.patch
fix_BIN_OFFSETS_MAX
=====================================
debian/patches/shebang.patch
=====================================
@@ -2,808 +2,808 @@ Author: Nilesh Patra
Last-Update: 2022-02-18 12:18:53 +0530
Description: Fix shebang line to point to python3
---- a/lib/bx/intervals/operations/subtract.py
-+++ b/lib/bx/intervals/operations/subtract.py
+--- python-bx.orig/lib/bx/intervals/operations/subtract.py
++++ python-bx/lib/bx/intervals/operations/subtract.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Subtract one set of genomic intervals from another (base-by-base or whole
intervals). The returned GenomicIntervals will be in the order
---- a/lib/bx/pwm/bed_score_aligned_pwm.py
-+++ b/lib/bx/pwm/bed_score_aligned_pwm.py
+--- python-bx.orig/lib/bx/pwm/bed_score_aligned_pwm.py
++++ python-bx/lib/bx/pwm/bed_score_aligned_pwm.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/python3
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
---- a/lib/bx/pwm/bed_score_aligned_string.py
-+++ b/lib/bx/pwm/bed_score_aligned_string.py
+--- python-bx.orig/lib/bx/pwm/bed_score_aligned_string.py
++++ python-bx/lib/bx/pwm/bed_score_aligned_string.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/python3
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
---- a/lib/bx/pwm/maf_select_motifs.py
-+++ b/lib/bx/pwm/maf_select_motifs.py
+--- python-bx.orig/lib/bx/pwm/maf_select_motifs.py
++++ python-bx/lib/bx/pwm/maf_select_motifs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/python3
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
---- a/lib/bx/pwm/position_weight_matrix.py
-+++ b/lib/bx/pwm/position_weight_matrix.py
+--- python-bx.orig/lib/bx/pwm/position_weight_matrix.py
++++ python-bx/lib/bx/pwm/position_weight_matrix.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import math
import sys
---- a/lib/bx/pwm/pwm_score_motifs.py
-+++ b/lib/bx/pwm/pwm_score_motifs.py
+--- python-bx.orig/lib/bx/pwm/pwm_score_motifs.py
++++ python-bx/lib/bx/pwm/pwm_score_motifs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/python3
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
---- a/lib/bx/pwm/pwm_score_positions.py
-+++ b/lib/bx/pwm/pwm_score_positions.py
+--- python-bx.orig/lib/bx/pwm/pwm_score_positions.py
++++ python-bx/lib/bx/pwm/pwm_score_positions.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2.4
+#!/usr/bin/python3
"""
Returns all positions of a maf with any pwm score > threshold
The positions are projected onto human coordinates
---- a/scripts/aggregate_scores_in_intervals.py
-+++ b/scripts/aggregate_scores_in_intervals.py
+--- python-bx.orig/scripts/aggregate_scores_in_intervals.py
++++ python-bx/scripts/aggregate_scores_in_intervals.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Given a list of intervals in BED format (`interval_file`) and a set of scores
---- a/scripts/align_print_template.py
-+++ b/scripts/align_print_template.py
+--- python-bx.orig/scripts/align_print_template.py
++++ python-bx/scripts/align_print_template.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read an alignment from stdin and for each block print the result of
---- a/scripts/axt_extract_ranges.py
-+++ b/scripts/axt_extract_ranges.py
+--- python-bx.orig/scripts/axt_extract_ranges.py
++++ python-bx/scripts/axt_extract_ranges.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Reads a list of intervals and an axt. Produces a new axt containing the
---- a/scripts/axt_to_fasta.py
-+++ b/scripts/axt_to_fasta.py
+--- python-bx.orig/scripts/axt_to_fasta.py
++++ python-bx/scripts/axt_to_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert AXT file to FASTA file. Reads an AXT file from standard
input and writes a FASTA file to standard out.
---- a/scripts/axt_to_lav.py
-+++ b/scripts/axt_to_lav.py
+--- python-bx.orig/scripts/axt_to_lav.py
++++ python-bx/scripts/axt_to_lav.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert AXT file to LAV file. Reads an AXT file from standard
---- a/scripts/axt_to_maf.py
-+++ b/scripts/axt_to_maf.py
+--- python-bx.orig/scripts/axt_to_maf.py
++++ python-bx/scripts/axt_to_maf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert AXT file to MAF file. Reads an AXT file from standard
---- a/scripts/bed_bigwig_profile.py
-+++ b/scripts/bed_bigwig_profile.py
+--- python-bx.orig/scripts/bed_bigwig_profile.py
++++ python-bx/scripts/bed_bigwig_profile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Create a site profile vector showing the average signal accumulated from a
---- a/scripts/bed_build_windows.py
-+++ b/scripts/bed_build_windows.py
+--- python-bx.orig/scripts/bed_build_windows.py
++++ python-bx/scripts/bed_build_windows.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Build windows of length `window_size` over the sequences defined by
---- a/scripts/bed_complement.py
-+++ b/scripts/bed_complement.py
+--- python-bx.orig/scripts/bed_complement.py
++++ python-bx/scripts/bed_complement.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Complement the regions of a bed file. Requires a file that maps source names
---- a/scripts/bed_count_by_interval.py
-+++ b/scripts/bed_count_by_interval.py
+--- python-bx.orig/scripts/bed_count_by_interval.py
++++ python-bx/scripts/bed_count_by_interval.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.
---- a/scripts/bed_count_overlapping.py
-+++ b/scripts/bed_count_overlapping.py
+--- python-bx.orig/scripts/bed_count_overlapping.py
++++ python-bx/scripts/bed_count_overlapping.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.
---- a/scripts/bed_coverage.py
-+++ b/scripts/bed_coverage.py
+--- python-bx.orig/scripts/bed_coverage.py
++++ python-bx/scripts/bed_coverage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Print number of bases covered by all intervals in a bed file (bases covered by
---- a/scripts/bed_coverage_by_interval.py
-+++ b/scripts/bed_coverage_by_interval.py
+--- python-bx.orig/scripts/bed_coverage_by_interval.py
++++ python-bx/scripts/bed_coverage_by_interval.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each interval in `bed1` print the fraction of bases covered by `bed2`.
---- a/scripts/bed_diff_basewise_summary.py
-+++ b/scripts/bed_diff_basewise_summary.py
+--- python-bx.orig/scripts/bed_diff_basewise_summary.py
++++ python-bx/scripts/bed_diff_basewise_summary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Given two bed files print the number of bases covered 1) by both, 2) only by
---- a/scripts/bed_extend_to.py
-+++ b/scripts/bed_extend_to.py
+--- python-bx.orig/scripts/bed_extend_to.py
++++ python-bx/scripts/bed_extend_to.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read BED file and extend each record to the specified minimum length. If chromosome
---- a/scripts/bed_intersect.py
-+++ b/scripts/bed_intersect.py
+--- python-bx.orig/scripts/bed_intersect.py
++++ python-bx/scripts/bed_intersect.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Find regions of first bed file that overlap regions in a second bed file. The
---- a/scripts/bed_intersect_basewise.py
-+++ b/scripts/bed_intersect_basewise.py
+--- python-bx.orig/scripts/bed_intersect_basewise.py
++++ python-bx/scripts/bed_intersect_basewise.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Find regions of first bed file that overlap regions in a second bed file. This
---- a/scripts/bed_merge_overlapping.py
-+++ b/scripts/bed_merge_overlapping.py
+--- python-bx.orig/scripts/bed_merge_overlapping.py
++++ python-bx/scripts/bed_merge_overlapping.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Merge any overlapping regions of bed files. Bed files can be provided on the
---- a/scripts/bed_rand_intersect.py
-+++ b/scripts/bed_rand_intersect.py
+--- python-bx.orig/scripts/bed_rand_intersect.py
++++ python-bx/scripts/bed_rand_intersect.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
From a set of regions and two sets of intervals inside those regions
---- a/scripts/bed_subtract_basewise.py
-+++ b/scripts/bed_subtract_basewise.py
+--- python-bx.orig/scripts/bed_subtract_basewise.py
++++ python-bx/scripts/bed_subtract_basewise.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Find continuous regions that are covered by the first bed file (`bed_file_1`)
---- a/scripts/bnMapper.py
-+++ b/scripts/bnMapper.py
+--- python-bx.orig/scripts/bnMapper.py
++++ python-bx/scripts/bnMapper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""Map features from the target species to the query species of a chain alignment file.
This is intended for mapping relatively short features such as Chip-Seq
---- a/scripts/div_snp_table_chr.py
-+++ b/scripts/div_snp_table_chr.py
+--- python-bx.orig/scripts/div_snp_table_chr.py
++++ python-bx/scripts/div_snp_table_chr.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
FIXME!
---- a/scripts/find_in_sorted_file.py
-+++ b/scripts/find_in_sorted_file.py
+--- python-bx.orig/scripts/find_in_sorted_file.py
++++ python-bx/scripts/find_in_sorted_file.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Extract ranges of scores from a sorted file in which each line contains a
---- a/scripts/get_scores_in_intervals.py
-+++ b/scripts/get_scores_in_intervals.py
+--- python-bx.orig/scripts/get_scores_in_intervals.py
++++ python-bx/scripts/get_scores_in_intervals.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read scores in "wiggle" format from `score_file` and intervals in "bed" format
---- a/scripts/int_seqs_to_char_strings.py
-+++ b/scripts/int_seqs_to_char_strings.py
+--- python-bx.orig/scripts/int_seqs_to_char_strings.py
++++ python-bx/scripts/int_seqs_to_char_strings.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Translate lists of space separated integers (magnitude less than 62) and print
---- a/scripts/interval_count_intersections.py
-+++ b/scripts/interval_count_intersections.py
+--- python-bx.orig/scripts/interval_count_intersections.py
++++ python-bx/scripts/interval_count_intersections.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read two lists of intervals (with chromosomes) and count the number of entries
---- a/scripts/interval_join.py
-+++ b/scripts/interval_join.py
+--- python-bx.orig/scripts/interval_join.py
++++ python-bx/scripts/interval_join.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Match up intersecting intervals from two files. This performs a "full join",
---- a/scripts/lav_to_axt.py
-+++ b/scripts/lav_to_axt.py
+--- python-bx.orig/scripts/lav_to_axt.py
++++ python-bx/scripts/lav_to_axt.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert LAV file to AXT file. Reads a LAV file from standard
input and writes a AXT file to standard out; some statistics are written
---- a/scripts/lav_to_maf.py
-+++ b/scripts/lav_to_maf.py
+--- python-bx.orig/scripts/lav_to_maf.py
++++ python-bx/scripts/lav_to_maf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert LAV file to MAF file. Reads a LAV file from standard
input and writes a MAF file to standard out; some statistics are written to
---- a/scripts/line_select.py
-+++ b/scripts/line_select.py
+--- python-bx.orig/scripts/line_select.py
++++ python-bx/scripts/line_select.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a file containing a 0 or 1 on each line (`feature_file`), output
---- a/scripts/lzop_build_offset_table.py
-+++ b/scripts/lzop_build_offset_table.py
+--- python-bx.orig/scripts/lzop_build_offset_table.py
++++ python-bx/scripts/lzop_build_offset_table.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a compressed file as created by 'lzop' from stdin and write a table to
---- a/scripts/mMK_bitset.py
-+++ b/scripts/mMK_bitset.py
+--- python-bx.orig/scripts/mMK_bitset.py
++++ python-bx/scripts/mMK_bitset.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
from optparse import OptionParser
---- a/scripts/maf_build_index.py
-+++ b/scripts/maf_build_index.py
+--- python-bx.orig/scripts/maf_build_index.py
++++ python-bx/scripts/maf_build_index.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Build an index file for a set of MAF alignment blocks.
---- a/scripts/maf_chop.py
-+++ b/scripts/maf_chop.py
+--- python-bx.orig/scripts/maf_chop.py
++++ python-bx/scripts/maf_chop.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Chops alignments in a MAF file to piece of a specified length. A random set of
---- a/scripts/maf_chunk.py
-+++ b/scripts/maf_chunk.py
+--- python-bx.orig/scripts/maf_chunk.py
++++ python-bx/scripts/maf_chunk.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from stdin and break into several new mafs containing no more than
---- a/scripts/maf_col_counts.py
-+++ b/scripts/maf_col_counts.py
+--- python-bx.orig/scripts/maf_col_counts.py
++++ python-bx/scripts/maf_col_counts.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For every column that occurs in a multiple alignment print the column
---- a/scripts/maf_col_counts_all.py
-+++ b/scripts/maf_col_counts_all.py
+--- python-bx.orig/scripts/maf_col_counts_all.py
++++ python-bx/scripts/maf_col_counts_all.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For every column that occurs in a multiple alignment print the column
---- a/scripts/maf_count.py
-+++ b/scripts/maf_count.py
+--- python-bx.orig/scripts/maf_count.py
++++ python-bx/scripts/maf_count.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from standard input and print counts of alignments, bases, or
---- a/scripts/maf_covered_ranges.py
-+++ b/scripts/maf_covered_ranges.py
+--- python-bx.orig/scripts/maf_covered_ranges.py
++++ python-bx/scripts/maf_covered_ranges.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
usage: %prog species1,species2,... nrequired < maf
---- a/scripts/maf_covered_regions.py
-+++ b/scripts/maf_covered_regions.py
+--- python-bx.orig/scripts/maf_covered_regions.py
++++ python-bx/scripts/maf_covered_regions.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a maf file and print the regions covered to a set of bed files (one for
---- a/scripts/maf_div_sites.py
-+++ b/scripts/maf_div_sites.py
+--- python-bx.orig/scripts/maf_div_sites.py
++++ python-bx/scripts/maf_div_sites.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Create a bed file listing all the divergent sites between two specific species
in a maf.
---- a/scripts/maf_drop_overlapping.py
-+++ b/scripts/maf_drop_overlapping.py
+--- python-bx.orig/scripts/maf_drop_overlapping.py
++++ python-bx/scripts/maf_drop_overlapping.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Remove any blocks from a maf that overlap any of a set of intervals.
---- a/scripts/maf_extract_chrom_ranges.py
-+++ b/scripts/maf_extract_chrom_ranges.py
+--- python-bx.orig/scripts/maf_extract_chrom_ranges.py
++++ python-bx/scripts/maf_extract_chrom_ranges.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Reads a list of intervals and a maf. Produces a new maf containing the
---- a/scripts/maf_extract_ranges.py
-+++ b/scripts/maf_extract_ranges.py
+--- python-bx.orig/scripts/maf_extract_ranges.py
++++ python-bx/scripts/maf_extract_ranges.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Reads a list of intervals (start, stop) and a maf. Produces a new maf
---- a/scripts/maf_extract_ranges_indexed.py
-+++ b/scripts/maf_extract_ranges_indexed.py
+--- python-bx.orig/scripts/maf_extract_ranges_indexed.py
++++ python-bx/scripts/maf_extract_ranges_indexed.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Reads a list of intervals and a maf. Produces a new maf containing the
---- a/scripts/maf_filter.py
-+++ b/scripts/maf_filter.py
+--- python-bx.orig/scripts/maf_filter.py
++++ python-bx/scripts/maf_filter.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Filter each block in a maf file. Can filter blocks for a minimum number of
---- a/scripts/maf_filter_max_wc.py
-+++ b/scripts/maf_filter_max_wc.py
+--- python-bx.orig/scripts/maf_filter_max_wc.py
++++ python-bx/scripts/maf_filter_max_wc.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Filter maf blocks for presence of wildcard columns. Blocks must meet the
---- a/scripts/maf_gap_frequency.py
-+++ b/scripts/maf_gap_frequency.py
+--- python-bx.orig/scripts/maf_gap_frequency.py
++++ python-bx/scripts/maf_gap_frequency.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from standard input and print the fraction of gap columns in
---- a/scripts/maf_gc_content.py
-+++ b/scripts/maf_gc_content.py
+--- python-bx.orig/scripts/maf_gc_content.py
++++ python-bx/scripts/maf_gc_content.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from standard input and print average GC content of each alignment
---- a/scripts/maf_interval_alignibility.py
-+++ b/scripts/maf_interval_alignibility.py
+--- python-bx.orig/scripts/maf_interval_alignibility.py
++++ python-bx/scripts/maf_interval_alignibility.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
WARNING: bz2/bz2t support and file cache support are new and not as well
---- a/scripts/maf_limit_to_species.py
-+++ b/scripts/maf_limit_to_species.py
+--- python-bx.orig/scripts/maf_limit_to_species.py
++++ python-bx/scripts/maf_limit_to_species.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a maf file from stdin and write out a new maf with only blocks having all
---- a/scripts/maf_mapping_word_frequency.py
-+++ b/scripts/maf_mapping_word_frequency.py
+--- python-bx.orig/scripts/maf_mapping_word_frequency.py
++++ python-bx/scripts/maf_mapping_word_frequency.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
---- a/scripts/maf_mask_cpg.py
-+++ b/scripts/maf_mask_cpg.py
+--- python-bx.orig/scripts/maf_mask_cpg.py
++++ python-bx/scripts/maf_mask_cpg.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Mask out potential CpG sites from a maf. Restricted or inclusive definition
---- a/scripts/maf_mean_length_ungapped_piece.py
-+++ b/scripts/maf_mean_length_ungapped_piece.py
+--- python-bx.orig/scripts/maf_mean_length_ungapped_piece.py
++++ python-bx/scripts/maf_mean_length_ungapped_piece.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from standard input and determine the mean length of ungapped pieces
---- a/scripts/maf_percent_columns_matching.py
-+++ b/scripts/maf_percent_columns_matching.py
+--- python-bx.orig/scripts/maf_percent_columns_matching.py
++++ python-bx/scripts/maf_percent_columns_matching.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a PAIRWISE maf from stdin and print the fraction of columns whose bases
---- a/scripts/maf_percent_identity.py
-+++ b/scripts/maf_percent_identity.py
+--- python-bx.orig/scripts/maf_percent_identity.py
++++ python-bx/scripts/maf_percent_identity.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a PAIRWISE maf from stdin and print the percent identity of each
---- a/scripts/maf_print_chroms.py
-+++ b/scripts/maf_print_chroms.py
+--- python-bx.orig/scripts/maf_print_chroms.py
++++ python-bx/scripts/maf_print_chroms.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a maf from stdin and print the chromosome number for each alignment. It
---- a/scripts/maf_print_scores.py
-+++ b/scripts/maf_print_scores.py
+--- python-bx.orig/scripts/maf_print_scores.py
++++ python-bx/scripts/maf_print_scores.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from standard input and print the score of each block. It can
---- a/scripts/maf_randomize.py
-+++ b/scripts/maf_randomize.py
+--- python-bx.orig/scripts/maf_randomize.py
++++ python-bx/scripts/maf_randomize.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Randomize the order of blocks in a MAF file. If `sample_size` is specified,
---- a/scripts/maf_region_coverage_by_src.py
-+++ b/scripts/maf_region_coverage_by_src.py
+--- python-bx.orig/scripts/maf_region_coverage_by_src.py
++++ python-bx/scripts/maf_region_coverage_by_src.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Reads a list of intervals and a set of indexed mafs. For each interval print
---- a/scripts/maf_select.py
-+++ b/scripts/maf_select.py
+--- python-bx.orig/scripts/maf_select.py
++++ python-bx/scripts/maf_select.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a feature file containing a 0 or 1 on each line, output
---- a/scripts/maf_shuffle_columns.py
-+++ b/scripts/maf_shuffle_columns.py
+--- python-bx.orig/scripts/maf_shuffle_columns.py
++++ python-bx/scripts/maf_shuffle_columns.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Randomly shuffle the columns of each block of a maf file. Note that this does
---- a/scripts/maf_species_in_all_files.py
-+++ b/scripts/maf_species_in_all_files.py
+--- python-bx.orig/scripts/maf_species_in_all_files.py
++++ python-bx/scripts/maf_species_in_all_files.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Takes a list of maf filenames on the command line and prints a comma separated
---- a/scripts/maf_split_by_src.py
-+++ b/scripts/maf_split_by_src.py
+--- python-bx.orig/scripts/maf_split_by_src.py
++++ python-bx/scripts/maf_split_by_src.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF from stdin and break into several mafs based on the source of
---- a/scripts/maf_thread_for_species.py
-+++ b/scripts/maf_thread_for_species.py
+--- python-bx.orig/scripts/maf_thread_for_species.py
++++ python-bx/scripts/maf_thread_for_species.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a maf file from stdin and write out a new maf with only blocks having all of
---- a/scripts/maf_tile.py
-+++ b/scripts/maf_tile.py
+--- python-bx.orig/scripts/maf_tile.py
++++ python-bx/scripts/maf_tile.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
'Tile' the blocks of a maf file over each of a set of intervals. The
---- a/scripts/maf_tile_2.py
-+++ b/scripts/maf_tile_2.py
+--- python-bx.orig/scripts/maf_tile_2.py
++++ python-bx/scripts/maf_tile_2.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
'Tile' the blocks of a maf file over each of a set of intervals. The
---- a/scripts/maf_tile_2bit.py
-+++ b/scripts/maf_tile_2bit.py
+--- python-bx.orig/scripts/maf_tile_2bit.py
++++ python-bx/scripts/maf_tile_2bit.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
'Tile' the blocks of a maf file over each of a set of intervals. The
---- a/scripts/maf_to_axt.py
-+++ b/scripts/maf_to_axt.py
+--- python-bx.orig/scripts/maf_to_axt.py
++++ python-bx/scripts/maf_to_axt.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Application to convert MAF file to AXT file, projecting to any two species.
Reads a MAF file from standard input and writes an AXT file to standard out;
---- a/scripts/maf_to_concat_fasta.py
-+++ b/scripts/maf_to_concat_fasta.py
+--- python-bx.orig/scripts/maf_to_concat_fasta.py
++++ python-bx/scripts/maf_to_concat_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a maf and print the text as a fasta file, concatenating blocks. A
---- a/scripts/maf_to_fasta.py
-+++ b/scripts/maf_to_fasta.py
+--- python-bx.orig/scripts/maf_to_fasta.py
++++ python-bx/scripts/maf_to_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python.
+#!/usr/bin/python3
"""
Read a maf and print the text as a fasta file.
---- a/scripts/maf_to_int_seqs.py
-+++ b/scripts/maf_to_int_seqs.py
+--- python-bx.orig/scripts/maf_to_int_seqs.py
++++ python-bx/scripts/maf_to_int_seqs.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each block in a maf file (read from stdin) write a sequence of ints
---- a/scripts/maf_translate_chars.py
-+++ b/scripts/maf_translate_chars.py
+--- python-bx.orig/scripts/maf_translate_chars.py
++++ python-bx/scripts/maf_translate_chars.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Translate a maf file containing gap ambiguity characters as produced by
---- a/scripts/maf_truncate.py
-+++ b/scripts/maf_truncate.py
+--- python-bx.orig/scripts/maf_truncate.py
++++ python-bx/scripts/maf_truncate.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Pass through blocks from a maf file until a certain number of columns
---- a/scripts/maf_word_frequency.py
-+++ b/scripts/maf_word_frequency.py
+--- python-bx.orig/scripts/maf_word_frequency.py
++++ python-bx/scripts/maf_word_frequency.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a MAF and print counts and frequencies of all n-mers
---- a/scripts/mask_quality.py
-+++ b/scripts/mask_quality.py
+--- python-bx.orig/scripts/mask_quality.py
++++ python-bx/scripts/mask_quality.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Masks an AXT or MAF file based on quality (from a binned_array) and
---- a/scripts/nib_chrom_intervals_to_fasta.py
-+++ b/scripts/nib_chrom_intervals_to_fasta.py
+--- python-bx.orig/scripts/nib_chrom_intervals_to_fasta.py
++++ python-bx/scripts/nib_chrom_intervals_to_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a set of ranges and a nib file, print portions of nib overlapping
---- a/scripts/nib_intervals_to_fasta.py
-+++ b/scripts/nib_intervals_to_fasta.py
+--- python-bx.orig/scripts/nib_intervals_to_fasta.py
++++ python-bx/scripts/nib_intervals_to_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a set of ranges and a nib file, print portions of nib overlapping
---- a/scripts/nib_length.py
-+++ b/scripts/nib_length.py
+--- python-bx.orig/scripts/nib_length.py
++++ python-bx/scripts/nib_length.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Print the number of bases in a nib file.
---- a/scripts/one_field_per_line.py
-+++ b/scripts/one_field_per_line.py
+--- python-bx.orig/scripts/one_field_per_line.py
++++ python-bx/scripts/one_field_per_line.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a file from stdin, split each line and write fields one per line to
---- a/scripts/out_to_chain.py
-+++ b/scripts/out_to_chain.py
+--- python-bx.orig/scripts/out_to_chain.py
++++ python-bx/scripts/out_to_chain.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import logging
import sys
---- a/scripts/prefix_lines.py
-+++ b/scripts/prefix_lines.py
+--- python-bx.orig/scripts/prefix_lines.py
++++ python-bx/scripts/prefix_lines.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Simple script to add a prefix to every line in a file.
---- a/scripts/pretty_table.py
-+++ b/scripts/pretty_table.py
+--- python-bx.orig/scripts/pretty_table.py
++++ python-bx/scripts/pretty_table.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read some whitespace separated data from stdin and pretty print it so that
---- a/scripts/qv_to_bqv.py
-+++ b/scripts/qv_to_bqv.py
+--- python-bx.orig/scripts/qv_to_bqv.py
++++ python-bx/scripts/qv_to_bqv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Convert a qual (qv) file to several BinnedArray files for fast seek.
---- a/scripts/random_lines.py
-+++ b/scripts/random_lines.py
+--- python-bx.orig/scripts/random_lines.py
++++ python-bx/scripts/random_lines.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Script to select random lines from a file. Reads entire file into
---- a/scripts/table_add_column.py
-+++ b/scripts/table_add_column.py
+--- python-bx.orig/scripts/table_add_column.py
++++ python-bx/scripts/table_add_column.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Tool for adding a column to a table. Expressions for the column are similar
---- a/scripts/table_filter.py
-+++ b/scripts/table_filter.py
+--- python-bx.orig/scripts/table_filter.py
++++ python-bx/scripts/table_filter.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Tool for filtering a tabular data file. Fields are separated by tabs, the
---- a/scripts/tfloc_summary.py
-+++ b/scripts/tfloc_summary.py
+--- python-bx.orig/scripts/tfloc_summary.py
++++ python-bx/scripts/tfloc_summary.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read TFLOC output from stdin and write out a summary in which the nth line
---- a/scripts/ucsc_gene_table_to_intervals.py
-+++ b/scripts/ucsc_gene_table_to_intervals.py
+--- python-bx.orig/scripts/ucsc_gene_table_to_intervals.py
++++ python-bx/scripts/ucsc_gene_table_to_intervals.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a table dump in the UCSC gene table format and print a tab separated
---- a/scripts/wiggle_to_array_tree.py
-+++ b/scripts/wiggle_to_array_tree.py
+--- python-bx.orig/scripts/wiggle_to_array_tree.py
++++ python-bx/scripts/wiggle_to_array_tree.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read data in UCSC wiggle format and write it to an "array tree" file.
---- a/scripts/wiggle_to_binned_array.py
-+++ b/scripts/wiggle_to_binned_array.py
+--- python-bx.orig/scripts/wiggle_to_binned_array.py
++++ python-bx/scripts/wiggle_to_binned_array.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Convert wiggle data to a binned array. This assumes the input data is on a
---- a/scripts/wiggle_to_chr_binned_array.py
-+++ b/scripts/wiggle_to_chr_binned_array.py
+--- python-bx.orig/scripts/wiggle_to_chr_binned_array.py
++++ python-bx/scripts/wiggle_to_chr_binned_array.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Writes compressed data from a wiggle file by chromosome.
---- a/scripts/wiggle_to_simple.py
-+++ b/scripts/wiggle_to_simple.py
+--- python-bx.orig/scripts/wiggle_to_simple.py
++++ python-bx/scripts/wiggle_to_simple.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Read a wiggle track and print out a series of lines containing
---- a/lib/bx/pwm/pwm_score_maf.py
-+++ b/lib/bx/pwm/pwm_score_maf.py
+--- python-bx.orig/lib/bx/pwm/pwm_score_maf.py
++++ python-bx/lib/bx/pwm/pwm_score_maf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python2.4
+#!/usr/bin/python3
=====================================
debian/rules
=====================================
@@ -24,3 +24,4 @@ override_dh_auto_clean:
override_dh_python3:
dh_python3 --shebang=/usr/bin/python3
+ dh_numpy3
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/54f7a6e26b5de7af1864501656d54ea5273669bf...ad9cf2d25fc899d03f67a3690b52042fa9d7a8ac
--
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/54f7a6e26b5de7af1864501656d54ea5273669bf...ad9cf2d25fc899d03f67a3690b52042fa9d7a8ac
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