[med-svn] [Git][med-team/python-bx][master] 3 commits: B-D on python3-pytest-cython
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Feb 18 07:01:17 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / python-bx
Commits:
0c79fd8d by Nilesh Patra at 2022-02-18T06:34:52+00:00
B-D on python3-pytest-cython
- - - - -
4a28bc53 by Nilesh Patra at 2022-02-18T12:25:43+05:30
Re-diff, Re-enable shebang.patch
- - - - -
32037317 by Nilesh Patra at 2022-02-18T12:25:43+05:30
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_BIN_OFFSETS_MAX
- debian/patches/series
- debian/patches/shebang.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,16 @@
-python-bx (0.8.13-1) UNRELEASED; urgency=medium
+python-bx (0.8.13-1) unstable; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
* Build-Depends: s/nose/pytest/
- -- Andreas Tille <tille at debian.org> Thu, 17 Feb 2022 20:35:53 +0100
+ [ Nilesh Patra ]
+ * B-D on python3-pytest-cython
+ * Re-diff, Re-enable shebang.patch
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 18 Feb 2022 12:05:03 +0530
python-bx (0.8.9-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-all-dev:any,
python3-lzo,
python3-pytest <!nocheck>,
+ python3-pytest-cython <!nocheck>,
python3-numpy <!nocheck>,
python3-six,
cython3
=====================================
debian/patches/fix_BIN_OFFSETS_MAX
=====================================
@@ -2,7 +2,7 @@ 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):
+@@ -123,7 +123,7 @@
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 +11,7 @@ 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):
+@@ -136,12 +136,14 @@
"""
Return the subset of offsets needed to contain intervals over (0,max_size)
"""
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,2 @@
-#shebang.patch
+shebang.patch
fix_BIN_OFFSETS_MAX
=====================================
debian/patches/shebang.patch
=====================================
@@ -1,130 +1,808 @@
-Index: python-bx/scripts/bed_build_windows.py
-===================================================================
---- python-bx.orig/scripts/bed_build_windows.py
-+++ python-bx/scripts/bed_build_windows.py
+--- a/lib/bx/intervals/operations/subtract.py
++++ b/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
+@@ -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
@@ -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
+@@ -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
+@@ -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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.4
++#!/usr/bin/python3
"""
- Build windows of length `window_size` over the sequences defined by
-Index: python-bx/scripts/bed_complement.py
-===================================================================
---- python-bx.orig/scripts/bed_complement.py
-+++ python-bx/scripts/bed_complement.py
+ 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
@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
-Index: python-bx/scripts/bed_count_by_interval.py
-===================================================================
---- python-bx.orig/scripts/bed_count_by_interval.py
-+++ python-bx/scripts/bed_count_by_interval.py
+--- a/scripts/bed_count_by_interval.py
++++ b/scripts/bed_count_by_interval.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.
-Index: python-bx/scripts/bed_count_overlapping.py
-===================================================================
---- python-bx.orig/scripts/bed_count_overlapping.py
-+++ python-bx/scripts/bed_count_overlapping.py
+--- a/scripts/bed_count_overlapping.py
++++ b/scripts/bed_count_overlapping.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/usr/bin/env python
+#!/usr/bin/python3
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.
-Index: python-bx/scripts/bed_rand_intersect.py
-===================================================================
---- python-bx.orig/scripts/bed_rand_intersect.py
-+++ python-bx/scripts/bed_rand_intersect.py
+--- a/scripts/bed_coverage.py
++++ b/scripts/bed_coverage.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
+#!/usr/bin/python3
"""
From a set of regions and two sets of intervals inside those regions
-Index: python-bx/scripts/div_snp_table_chr.py
-===================================================================
---- python-bx.orig/scripts/div_snp_table_chr.py
-+++ python-bx/scripts/div_snp_table_chr.py
+--- a/scripts/bed_subtract_basewise.py
++++ b/scripts/bed_subtract_basewise.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
+#!/usr/bin/python3
"""
FIXME!
-Index: python-bx/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
+--- a/scripts/find_in_sorted_file.py
++++ b/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
+@@ -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
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Translate lists of space separated integers (magnitude less than 62) and print
-Index: python-bx/scripts/interval_join.py
-===================================================================
---- python-bx.orig/scripts/interval_join.py
-+++ python-bx/scripts/interval_join.py
+--- a/scripts/interval_count_intersections.py
++++ b/scripts/interval_count_intersections.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
+#!/usr/bin/python3
"""
Match up intersecting intervals from two files. This performs a "full join",
-Index: python-bx/scripts/lzop_build_offset_table.py
-===================================================================
---- python-bx.orig/scripts/lzop_build_offset_table.py
-+++ python-bx/scripts/lzop_build_offset_table.py
+--- a/scripts/lav_to_axt.py
++++ b/scripts/lav_to_axt.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -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
+@@ -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
+@@ -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
-Index: python-bx/scripts/mMK_bitset.py
-===================================================================
---- python-bx.orig/scripts/mMK_bitset.py
-+++ python-bx/scripts/mMK_bitset.py
+--- a/scripts/mMK_bitset.py
++++ b/scripts/mMK_bitset.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/usr/bin/env python
+#!/usr/bin/python3
- from __future__ import print_function
from optparse import OptionParser
-Index: python-bx/scripts/maf_div_sites.py
-===================================================================
---- python-bx.orig/scripts/maf_div_sites.py
-+++ python-bx/scripts/maf_div_sites.py
+
+--- a/scripts/maf_build_index.py
++++ b/scripts/maf_build_index.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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.
-Index: python-bx/scripts/maf_interval_alignibility.py
-===================================================================
---- python-bx.orig/scripts/maf_interval_alignibility.py
-+++ python-bx/scripts/maf_interval_alignibility.py
+--- a/scripts/maf_drop_overlapping.py
++++ b/scripts/maf_drop_overlapping.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
-Index: python-bx/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
+--- a/scripts/maf_limit_to_species.py
++++ b/scripts/maf_limit_to_species.py
@@ -1,4 +1,4 @@
--#!/usr/bin/env python2.4
+-#!/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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ """
+
+--- a/scripts/maf_mask_cpg.py
++++ b/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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python2.4
++#!/usr/bin/python3
+
+ import sys
+
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301
--
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/8dbb13d4a54da0ddc7475177cba1c06118755cff...3203731742944fb8a351d0b1cf67359d4f3f5301
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