[med-svn] [Git][med-team/poretools][master] 5 commits: Fix circular import, "poretools times" output
Nilesh Patra
gitlab at salsa.debian.org
Wed Jun 3 11:14:00 BST 2020
Nilesh Patra pushed to branch master at Debian Med / poretools
Commits:
59a74018 by Nilesh Patra at 2020-06-03T15:18:30+05:30
Fix circular import, "poretools times" output
- - - - -
a7c6533e by Nilesh Patra at 2020-06-03T15:19:04+05:30
Add autopkgtests
- - - - -
0e0fcf6b by Nilesh Patra at 2020-06-03T09:56:54+00:00
Fix with cme
- - - - -
73fc01b0 by Nilesh Patra at 2020-06-03T10:00:09+00:00
Update upstream/metadata
- - - - -
58e4e4c0 by Nilesh Patra at 2020-06-03T15:40:45+05:30
Remove un-needed override
- - - - -
6 changed files:
- debian/control
- debian/patches/python3.patch
- − debian/source/lintian-overrides
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/control
=====================================
@@ -11,10 +11,11 @@ Build-Depends: debhelper-compat (= 12),
python3-matplotlib,
python3-seaborn,
python3-pandas
-Standards-Version: 4.4.0
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/poretools
Vcs-Git: https://salsa.debian.org/med-team/poretools.git
Homepage: https://poretools.readthedocs.org
+Rules-Requires-Root: no
Package: poretools
Architecture: all
=====================================
debian/patches/python3.patch
=====================================
@@ -6,10 +6,8 @@ Author: Steve Langasek <steve.langasek at ubuntu.com>
Last-Modified: 2019-08-15
Bug-Debian: https://bugs.debian.org/934845
-Index: poretools-0.6.0+dfsg/setup.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/setup.py
-+++ poretools-0.6.0+dfsg/setup.py
+--- a/setup.py
++++ b/setup.py
@@ -3,7 +3,7 @@
version_py = os.path.join(os.path.dirname(__file__), 'poretools', 'version.py')
@@ -19,23 +17,18 @@ Index: poretools-0.6.0+dfsg/setup.py
long_description = """
``poretools`` is a toolset for working with nanopore sequencing data'
"""
-Index: poretools-0.6.0+dfsg/poretools/__init__.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/__init__.py
-+++ poretools-0.6.0+dfsg/poretools/__init__.py
-@@ -1,5 +1,5 @@
+--- a/poretools/__init__.py
++++ b/poretools/__init__.py
+@@ -1,5 +1,4 @@
import os
import sys
-import scripts
-from Fast5File import *
-from version import __version__
+from . import scripts
-+from .Fast5File import *
+from .version import __version__
-Index: poretools-0.6.0+dfsg/poretools/Fast5File.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/Fast5File.py
-+++ poretools-0.6.0+dfsg/poretools/Fast5File.py
+--- a/poretools/Fast5File.py
++++ b/poretools/Fast5File.py
@@ -11,8 +11,8 @@
@@ -282,10 +275,8 @@ Index: poretools-0.6.0+dfsg/poretools/Fast5File.py
+ except Exception as e:
self.keyinfo = None
logger.warning("Cannot find keyinfo. Exiting.\n")
-Index: poretools-0.6.0+dfsg/poretools/formats.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/formats.py
-+++ poretools-0.6.0+dfsg/poretools/formats.py
+--- a/poretools/formats.py
++++ b/poretools/formats.py
@@ -19,7 +19,7 @@
phred = ord(score) - 33
error_count += 10.0 ** (-phred / 10.0)
@@ -295,10 +286,8 @@ Index: poretools-0.6.0+dfsg/poretools/formats.py
return 0.0
-Index: poretools-0.6.0+dfsg/poretools/times.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/times.py
-+++ poretools-0.6.0+dfsg/poretools/times.py
+--- a/poretools/times.py
++++ b/poretools/times.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -318,15 +307,17 @@ Index: poretools-0.6.0+dfsg/poretools/times.py
for fast5 in Fast5File.Fast5FileSet(args.files):
if fast5.is_open:
-@@ -29,7 +29,7 @@
+@@ -29,8 +29,8 @@
read_length = 0
lt = localtime(start_time)
- print "\t".join([fast5.get_channel_number(),
-+ print("\t".join([fast5.get_channel_number(),
- fast5.filename,
+- fast5.filename,
++ print("\t".join([str(fast5.get_channel_number()),
++ str(fast5.filename),
str(read_length),
str(fast5.get_exp_start_time()),
+ str(start_time), \
@@ -39,5 +39,5 @@
strftime('%Y-%m-%dT%H:%M:%S%z', lt),
strftime('%d', lt),
@@ -334,10 +325,8 @@ Index: poretools-0.6.0+dfsg/poretools/times.py
- strftime('%M', lt)])
+ strftime('%M', lt)]))
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/events.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/events.py
-+++ poretools-0.6.0+dfsg/poretools/events.py
+--- a/poretools/events.py
++++ b/poretools/events.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -367,10 +356,8 @@ Index: poretools-0.6.0+dfsg/poretools/events.py
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/qualdist.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/qualdist.py
-+++ poretools-0.6.0+dfsg/poretools/qualdist.py
+--- a/poretools/qualdist.py
++++ b/poretools/qualdist.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -386,10 +373,8 @@ Index: poretools-0.6.0+dfsg/poretools/qualdist.py
\ No newline at end of file
+ print ('\t'.join(str(s) for s in [chr(q+33), q, qual_count[q],
+ total_nucs, float(qual_count[q]) / float(total_nucs)]))
-Index: poretools-0.6.0+dfsg/poretools/metadata.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/metadata.py
-+++ poretools-0.6.0+dfsg/poretools/metadata.py
+--- a/poretools/metadata.py
++++ b/poretools/metadata.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -419,10 +404,8 @@ Index: poretools-0.6.0+dfsg/poretools/metadata.py
+ print("%s\t%s\t%s" % (asic_id, asic_temp, heatsink_temp))
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/fastq.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/fastq.py
-+++ poretools-0.6.0+dfsg/poretools/fastq.py
+--- a/poretools/fastq.py
++++ b/poretools/fastq.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -438,10 +421,8 @@ Index: poretools-0.6.0+dfsg/poretools/fastq.py
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/occupancy.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/occupancy.py
-+++ poretools-0.6.0+dfsg/poretools/occupancy.py
+--- a/poretools/occupancy.py
++++ b/poretools/occupancy.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -481,10 +462,8 @@ Index: poretools-0.6.0+dfsg/poretools/occupancy.py
fast5.close()
if args.plot_type == 'read_count':
-Index: poretools-0.6.0+dfsg/poretools/index.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/index.py
-+++ poretools-0.6.0+dfsg/poretools/index.py
+--- a/poretools/index.py
++++ b/poretools/index.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -514,10 +493,8 @@ Index: poretools-0.6.0+dfsg/poretools/index.py
+ asic_id, asic_temp, heatsink_temp,channel_number,exp_start_time,exp_start_time_string,start_time,start_time_string,duration,fast5_version))
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/readstats.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/readstats.py
-+++ poretools-0.6.0+dfsg/poretools/readstats.py
+--- a/poretools/readstats.py
++++ b/poretools/readstats.py
@@ -1,8 +1,8 @@
-import Fast5File
+from . import Fast5File
@@ -537,10 +514,8 @@ Index: poretools-0.6.0+dfsg/poretools/readstats.py
+ print("%s\t%s\t%s\t%s\t%s" % (start_time, channel_number, read_number, template_len, complement_len))
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/winner.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/winner.py
-+++ poretools-0.6.0+dfsg/poretools/winner.py
+--- a/poretools/winner.py
++++ b/poretools/winner.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -554,10 +529,8 @@ Index: poretools-0.6.0+dfsg/poretools/winner.py
- print longest_read
+ print(longest_read)
-Index: poretools-0.6.0+dfsg/poretools/stats.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/stats.py
-+++ poretools-0.6.0+dfsg/poretools/stats.py
+--- a/poretools/stats.py
++++ b/poretools/stats.py
@@ -1,5 +1,5 @@
-import statistics as stat
-import Fast5File
@@ -635,10 +608,8 @@ Index: poretools-0.6.0+dfsg/poretools/stats.py
+ print("N75\t%d" % (nxvalues[75]))
else:
logger.warning("No valid sequences observed.\n")
-Index: poretools-0.6.0+dfsg/poretools/nucdist.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/nucdist.py
-+++ poretools-0.6.0+dfsg/poretools/nucdist.py
+--- a/poretools/nucdist.py
++++ b/poretools/nucdist.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -654,10 +625,8 @@ Index: poretools-0.6.0+dfsg/poretools/nucdist.py
\ No newline at end of file
+ print ('\t'.join(str(s) for s in [n, nuc_count[n],
+ total_nucs, float(nuc_count[n]) / float(total_nucs)]))
-Index: poretools-0.6.0+dfsg/poretools/tabular.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/tabular.py
-+++ poretools-0.6.0+dfsg/poretools/tabular.py
+--- a/poretools/tabular.py
++++ b/poretools/tabular.py
@@ -1,8 +1,8 @@
-import Fast5File
+from . import Fast5File
@@ -678,10 +647,8 @@ Index: poretools-0.6.0+dfsg/poretools/tabular.py
\ No newline at end of file
+ print ('\t'.join([str(len(fq.seq)), fq.name, fq.seq, fq.qual]))
+ fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/fasta.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/fasta.py
-+++ poretools-0.6.0+dfsg/poretools/fasta.py
+--- a/poretools/fasta.py
++++ b/poretools/fasta.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
@@ -697,10 +664,8 @@ Index: poretools-0.6.0+dfsg/poretools/fasta.py
fast5.close()
-Index: poretools-0.6.0+dfsg/poretools/statistics.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/statistics.py
-+++ poretools-0.6.0+dfsg/poretools/statistics.py
+--- a/poretools/statistics.py
++++ b/poretools/statistics.py
@@ -27,25 +27,25 @@
return None
@@ -741,10 +706,8 @@ Index: poretools-0.6.0+dfsg/poretools/statistics.py
else:
return None
-Index: poretools-0.6.0+dfsg/poretools/poretools_main.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/poretools_main.py
-+++ poretools-0.6.0+dfsg/poretools/poretools_main.py
+--- a/poretools/poretools_main.py
++++ b/poretools/poretools_main.py
@@ -13,43 +13,43 @@
def run_subtool(parser, args):
@@ -835,10 +798,8 @@ Index: poretools-0.6.0+dfsg/poretools/poretools_main.py
if e.errno != 32: # ignore SIGPIPE
raise
-Index: poretools-0.6.0+dfsg/poretools/combine.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/combine.py
-+++ poretools-0.6.0+dfsg/poretools/combine.py
+--- a/poretools/combine.py
++++ b/poretools/combine.py
@@ -1,6 +1,6 @@
import tarfile
import sys
@@ -847,10 +808,8 @@ Index: poretools-0.6.0+dfsg/poretools/combine.py
#logging
import logging
-Index: poretools-0.6.0+dfsg/poretools/hist.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/hist.py
-+++ poretools-0.6.0+dfsg/poretools/hist.py
+--- a/poretools/hist.py
++++ b/poretools/hist.py
@@ -6,7 +6,7 @@
from matplotlib import pyplot as plt
@@ -860,30 +819,24 @@ Index: poretools-0.6.0+dfsg/poretools/hist.py
import logging
logger = logging.getLogger('poretools')
-Index: poretools-0.6.0+dfsg/poretools/organise.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/organise.py
-+++ poretools-0.6.0+dfsg/poretools/organise.py
+--- a/poretools/organise.py
++++ b/poretools/organise.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
import sys
import os
from os import makedirs
-Index: poretools-0.6.0+dfsg/poretools/qual_v_pos.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/qual_v_pos.py
-+++ poretools-0.6.0+dfsg/poretools/qual_v_pos.py
+--- a/poretools/qual_v_pos.py
++++ b/poretools/qual_v_pos.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
from collections import defaultdict
import pandas
import matplotlib.pyplot as plt
-Index: poretools-0.6.0+dfsg/poretools/squiggle.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/squiggle.py
-+++ poretools-0.6.0+dfsg/poretools/squiggle.py
+--- a/poretools/squiggle.py
++++ b/poretools/squiggle.py
@@ -10,7 +10,7 @@
import logging
logger = logging.getLogger('poretools')
@@ -902,10 +855,8 @@ Index: poretools-0.6.0+dfsg/poretools/squiggle.py
for fast5 in fast5_set:
# only create a squiggle plot for multiple reads if saving to file.
if args.saveas is None:
-Index: poretools-0.6.0+dfsg/poretools/yield_plot.py
-===================================================================
---- poretools-0.6.0+dfsg.orig/poretools/yield_plot.py
-+++ poretools-0.6.0+dfsg/poretools/yield_plot.py
+--- a/poretools/yield_plot.py
++++ b/poretools/yield_plot.py
@@ -1,4 +1,4 @@
-import Fast5File
+from . import Fast5File
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# It does. It's just that the options are listed one-per-line.
-debian-watch-file-should-mangle-version line 9
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,123 @@
+#!/bin/bash
+set -e
+
+pkg=poretools
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/${pkg}/data -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+mv data test_data
+echo 'Test 1'
+echo 'poretools fastq --min-length 5000 test_data/'
+poretools fastq --min-length 5000 test_data/
+echo 'PASS'
+echo
+
+echo 'Test 2'
+echo 'poretools yield_plot \
+ --plot-type basepairs \
+ --saveas foo.pdf \
+ test_data/'
+
+poretools yield_plot \
+ --plot-type basepairs \
+ --saveas foo.pdf \
+ test_data/
+
+echo 'poretools yield_plot \
+ --plot-type basepairs \
+ --saveas foo.png \
+ --theme-bw \'
+
+poretools yield_plot \
+ --plot-type basepairs \
+ --saveas foo.png \
+ --theme-bw \
+ test_data/
+echo 'PASS'
+echo
+
+echo 'Test 3'
+echo 'poretools winner test_data/'
+poretools winner test_data/
+
+echo 'poretools winner --type all test_data/'
+poretools winner --type all test_data/
+
+echo 'poretools winner --type 2D test_data/'
+poretools winner --type 2D test_data/
+
+echo 'poretools winner --type fwd,rev test_data/'
+poretools winner --type fwd,rev test_data/
+
+echo 'poretools winner --type best test_data/'
+poretools winner --type best test_data/
+echo 'PASS'
+echo
+
+echo 'Test 4'
+echo 'poretools stats test_data/'
+poretools stats test_data/
+echo 'PASS'
+echo
+
+echo 'Test 5'
+echo 'poretools hist --num-bins 20 --max-length 10000 test_data/ --saveas pdf'
+poretools hist --num-bins 20 --max-length 10000 test_data/ --saveas pdf
+echo 'PASS'
+echo
+
+echo 'Test 6'
+echo 'poretools nucdist test_data/'
+poretools nucdist test_data/
+echo 'PASS'
+echo
+
+echo 'Test 7'
+echo 'poretools qualdist test_data/'
+poretools qualdist test_data/
+echo 'PASS'
+echo
+
+echo 'Test 8'
+echo 'poretools qualpos test_data/'
+poretools qualpos test_data/
+echo 'PASS'
+echo
+
+echo 'Test 9'
+echo 'poretools tabular test_data/2016_3_4_3507_1_ch120_read418_strand.fast5'
+poretools tabular test_data/2016_3_4_3507_1_ch120_read418_strand.fast5
+echo 'PASS'
+echo
+
+echo 'Test 10'
+echo 'poretools events test_data/ | head -5'
+poretools events test_data/ | head -5
+echo 'PASS'
+echo
+
+echo 'Test 11'
+echo 'poretools events --pre-basecalled test_data/ | head -5'
+poretools events --pre-basecalled test_data/ | head -5
+echo 'PASS'
+echo
+
+echo 'Test 12'
+echo 'poretools times test_data/'
+poretools times test_data/
+echo 'PASS'
+echo
+
+echo 'Test 13'
+echo 'poretools index test_data | head -5'
+poretools index test_data | head -5
+echo 'PASS'
+echo
=====================================
debian/upstream/metadata
=====================================
@@ -20,3 +20,10 @@ Registry:
Entry: NA
- Name: conda:bioconda
Entry: poretools
+Archive:
+Bug-Database: https://github.com/arq5x/poretools/issues
+Bug-Submit: https://github.com/arq5x/poretools/issues/new
+Changelog: https://github.com/arq5x/poretools/tags
+Repository: https://github.com/arq5x/poretools.git
+Repository-Browse: https://github.com/arq5x/poretools
+
View it on GitLab: https://salsa.debian.org/med-team/poretools/-/compare/fe9b3dddc1938d867df8dd7749ccec82d64b2686...58e4e4c052cee506944a7ed5402e53fafc5668fd
--
View it on GitLab: https://salsa.debian.org/med-team/poretools/-/compare/fe9b3dddc1938d867df8dd7749ccec82d64b2686...58e4e4c052cee506944a7ed5402e53fafc5668fd
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