[med-svn] [Git][med-team/q2-demux][master] 6 commits: routine-update: New upstream version
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jul 19 16:33:00 BST 2022
Andreas Tille pushed to branch master at Debian Med / q2-demux
Commits:
25333aed by Andreas Tille at 2022-07-19T17:22:39+02:00
routine-update: New upstream version
- - - - -
8b9773ff by Andreas Tille at 2022-07-19T17:22:40+02:00
New upstream version 2022.2.0+dfsg
- - - - -
c3436817 by Andreas Tille at 2022-07-19T17:22:40+02:00
Update upstream source from tag 'upstream/2022.2.0+dfsg'
Update to upstream version '2022.2.0+dfsg'
with Debian dir b06f73d29b0949a0c4034fa56315660071a98680
- - - - -
fe06c5d6 by Andreas Tille at 2022-07-19T17:22:40+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
acfdeca1 by Andreas Tille at 2022-07-19T17:30:02+02:00
Adjust versioned (Build-)Depends
- - - - -
2138646f by Andreas Tille at 2022-07-19T17:32:03+02:00
Upload to unstable
- - - - -
29 changed files:
- LICENSE
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- q2_demux/__init__.py
- q2_demux/_demux.py
- q2_demux/_ecc.py
- q2_demux/_filter.py
- q2_demux/_format.py
- q2_demux/_subsample.py
- q2_demux/_summarize/__init__.py
- q2_demux/_summarize/_visualizer.py
- q2_demux/_summarize/assets/src/box.js
- q2_demux/_summarize/assets/src/brush.js
- q2_demux/_summarize/assets/src/main.js
- q2_demux/_summarize/assets/src/plot.js
- q2_demux/_summarize/assets/webpack.config.js
- q2_demux/_transformer.py
- q2_demux/_type.py
- q2_demux/_version.py
- q2_demux/plugin_setup.py
- q2_demux/tests/__init__.py
- q2_demux/tests/test_demux.py
- q2_demux/tests/test_ecc.py
- q2_demux/tests/test_filter.py
- q2_demux/tests/test_format.py
- q2_demux/tests/test_subsample.py
- q2_demux/tests/test_transformer.py
- setup.py
Changes:
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2021, QIIME 2 development team.
+Copyright (c) 2016-2022, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
ci/recipe/meta.yaml
=====================================
@@ -11,10 +11,15 @@ build:
script: make install
requirements:
+ build:
+ # nodejs is only necessary in the build phase - our build script needs it
+ # in order to render out transpiled js assets for various visualizations.
+ # once rendered, node is no longer necessary. don't set this in host reqs.
+ - nodejs
+
host:
- python {{ python }}
- setuptools
- - nodejs
run:
- python {{ python }}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-demux (2022.2.0+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.1 (routine-update)
+ * Adjust versioned (Build-)Depends
+
+ -- Andreas Tille <tille at debian.org> Tue, 19 Jul 2022 17:30:17 +0200
+
q2-demux (2021.8.0+dfsg-2) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -18,10 +18,10 @@ Build-Depends: debhelper-compat (= 13),
python3-skbio,
python3-psutil,
python3-seaborn,
- qiime (>= 2021.8.0),
- q2-types (>= 2021.8.0),
- q2templates (>= 2021.8.0)
-Standards-Version: 4.6.0
+ qiime (>= 2022.2.0),
+ q2-types (>= 2022.2.0),
+ q2templates (>= 2022.2.0)
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/q2-demux
Vcs-Git: https://salsa.debian.org/med-team/q2-demux.git
Homepage: https://qiime2.org/
@@ -40,9 +40,9 @@ Depends: ${shlibs:Depends},
python3-yaml,
python3-psutil,
python3-ipywidgets,
- qiime (>= 2021.8.0),
- q2-types (>= 2021.8.0),
- q2templates (>= 2021.8.0),
+ qiime (>= 2022.2.0),
+ q2-types (>= 2022.2.0),
+ q2templates (>= 2022.2.0),
node-d3
Description: QIIME 2 plugin for demultiplexing of sequence reads
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
=====================================
q2_demux/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_demux.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -296,10 +296,10 @@ def emp_single(seqs: BarcodeSequenceFastqIterator,
ec_details = ECDetails(ec_details_fmt)
for i, (barcode_record, sequence_record) in enumerate(seqs, start=1):
- barcode_read = barcode_record[1]
+ raw_barcode_read = barcode_record[1][:barcode_len]
if rev_comp_barcodes:
- barcode_read = str(skbio.DNA(barcode_read).reverse_complement())
- raw_barcode_read = barcode_read[:barcode_len]
+ barcode_as_DNA = skbio.DNA(raw_barcode_read)
+ raw_barcode_read = str(barcode_as_DNA.reverse_complement())
if golay_error_correction:
# A three bit filter is implicitly used by the decoder. See Hamady
@@ -398,10 +398,10 @@ def emp_paired(seqs: BarcodePairedSequenceFastqIterator,
for i, record in enumerate(seqs, start=1):
barcode_record, forward_record, reverse_record = record
- barcode_read = barcode_record[1]
+ raw_barcode_read = barcode_record[1][:barcode_len]
if rev_comp_barcodes:
- barcode_read = str(skbio.DNA(barcode_read).reverse_complement())
- raw_barcode_read = barcode_read[:barcode_len]
+ barcode_as_DNA = skbio.DNA(raw_barcode_read)
+ raw_barcode_read = str(barcode_as_DNA.reverse_complement())
if golay_error_correction:
# A three bit filter is implicitly used by the decoder. See Hamady
=====================================
q2_demux/_ecc.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_filter.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_subsample.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_summarize/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_summarize/_visualizer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_summarize/assets/src/box.js
=====================================
@@ -1,5 +1,5 @@
// ----------------------------------------------------------------------------
-// Copyright (c) 2016-2021, QIIME 2 development team.
+// Copyright (c) 2016-2022, QIIME 2 development team.
//
// Distributed under the terms of the Modified BSD License.
//
=====================================
q2_demux/_summarize/assets/src/brush.js
=====================================
@@ -1,5 +1,5 @@
// ----------------------------------------------------------------------------
-// Copyright (c) 2016-2021, QIIME 2 development team.
+// Copyright (c) 2016-2022, QIIME 2 development team.
//
// Distributed under the terms of the Modified BSD License.
//
=====================================
q2_demux/_summarize/assets/src/main.js
=====================================
@@ -1,5 +1,5 @@
// ----------------------------------------------------------------------------
-// Copyright (c) 2016-2021, QIIME 2 development team.
+// Copyright (c) 2016-2022, QIIME 2 development team.
//
// Distributed under the terms of the Modified BSD License.
//
=====================================
q2_demux/_summarize/assets/src/plot.js
=====================================
@@ -1,5 +1,5 @@
// ----------------------------------------------------------------------------
-// Copyright (c) 2016-2021, QIIME 2 development team.
+// Copyright (c) 2016-2022, QIIME 2 development team.
//
// Distributed under the terms of the Modified BSD License.
//
=====================================
q2_demux/_summarize/assets/webpack.config.js
=====================================
@@ -1,5 +1,5 @@
// ----------------------------------------------------------------------------
-// Copyright (c) 2016-2021, QIIME 2 development team.
+// Copyright (c) 2016-2022, QIIME 2 development team.
//
// Distributed under the terms of the Modified BSD License.
//
=====================================
q2_demux/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 2021.8.0)"
- git_full = "698ef5d055238d7e40ddd73cdddfd574cf10b9a3"
- git_date = "2021-09-09 18:35:30 +0000"
+ git_refnames = " (tag: 2022.2.0)"
+ git_full = "1ae11e79bdf2199c230c59d8425476f84e941c48"
+ git_date = "2022-02-18 19:08:10 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_demux/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/test_demux.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -523,8 +523,27 @@ class EmpSingleTests(unittest.TestCase, EmpTestingUtils):
('@s9/2 abc/2', 'CGGCG', '+', 'PPPP'),
('@s10/2 abc/2', 'CGGCG', '+', 'PPPP'),
('@s11/2 abc/2', 'GGAAG', '+', 'PPPP')]
+ self._barcode_trimming(barcodes, False)
+
+ def test_barcode_trimming_rev_comp_barcodes(self):
+ # NOTE: the 5th nucleotide in these barcodes should be trimmed off
+ barcodes = [('@s1/2 abc/2', 'TTTTG', '+', 'YYYY'),
+ ('@s2/2 abc/2', 'TTAAG', '+', 'PPPP'),
+ ('@s3/2 abc/2', 'GGTTG', '+', 'PPPP'),
+ ('@s4/2 abc/2', 'TTAAG', '+', 'PPPP'),
+ ('@s5/2 abc/2', 'GGTTG', '+', 'PPPP'),
+ ('@s6/2 abc/2', 'TTTTN', '+', 'PPPP'),
+ ('@s7/2 abc/2', 'GCCGG', '+', 'PPPP'),
+ ('@s8/2 abc/2', 'TTCCG', '+', 'PPPP'),
+ ('@s9/2 abc/2', 'GCCGG', '+', 'PPPP'),
+ ('@s10/2 abc/2', 'GCCGG', '+', 'PPPP'),
+ ('@s11/2 abc/2', 'TTCCG', '+', 'PPPP')]
+ self._barcode_trimming(barcodes, True)
+
+ def _barcode_trimming(self, barcodes, rev_comp_barcodes):
bsi = BarcodeSequenceFastqIterator(barcodes, self.sequences)
actual, ecc = emp_single(bsi, self.barcode_map,
+ rev_comp_barcodes=rev_comp_barcodes,
golay_error_correction=False)
output_fastq = list(actual.sequences.iter_views(FastqGzFormat))
# five per-sample files were written
@@ -889,6 +908,26 @@ class EmpPairedTests(unittest.TestCase, EmpTestingUtils):
barcodes, self.forward, self.reverse)
self.check_valid(bpsi, self.barcode_map, golay_error_correction=False)
+ def test_barcode_trimming_rev_comp(self):
+ # these barcodes are longer then the ones in the mapping file.
+ # only the first barcode_length bases should be used when
+ # when reverse complementing
+ barcodes = [('@s1/2 abc/2', 'TTTTT', '+', 'YYYY'),
+ ('@s2/2 abc/2', 'TTAAT', '+', 'PPPP'),
+ ('@s3/2 abc/2', 'GGTTT', '+', 'PPPP'),
+ ('@s4/2 abc/2', 'TTAAT', '+', 'PPPP'),
+ ('@s5/2 abc/2', 'GGTTT', '+', 'PPPP'),
+ ('@s6/2 abc/2', 'TTTTT', '+', 'PPPP'),
+ ('@s7/2 abc/2', 'GCCGT', '+', 'PPPP'),
+ ('@s8/2 abc/2', 'TTCCT', '+', 'PPPP'),
+ ('@s9/2 abc/2', 'GCCGT', '+', 'PPPP'),
+ ('@s10/2 abc/2', 'GCCGT', '+', 'PPPP'),
+ ('@s11/2 abc/2', 'TTCCT', '+', 'PPPP')]
+ bpsi = BarcodePairedSequenceFastqIterator(
+ barcodes, self.forward, self.reverse)
+ self.check_valid(bpsi, self.barcode_map, golay_error_correction=False,
+ rev_comp_barcodes=True)
+
class SummarizeTests(TestPluginBase):
package = 'q2_demux.tests'
=====================================
q2_demux/tests/test_ecc.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/test_filter.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/test_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/test_subsample.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_demux/tests/test_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2021, QIIME 2 development team.
+# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/compare/dc28402168941a01a765c2ee6fcaf5a6b8d09d3c...2138646f23bda7df450b68ab55630e7318b0f374
--
View it on GitLab: https://salsa.debian.org/med-team/q2-demux/-/compare/dc28402168941a01a765c2ee6fcaf5a6b8d09d3c...2138646f23bda7df450b68ab55630e7318b0f374
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