New Upstream Snapshot - nanolyse
Ready changes
Summary
Merged new upstream version: 1.2.0+git20230116.1.837fcb4 (was: 1.2.0).
Resulting package
Built on 2023-01-20T02:35 (took 5m8s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots nanolyse
Lintian Result
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 87edd53..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,5 +0,0 @@
-NanoLyse.egg-info/
-README.rst
-nanolyse/__pycache__/
-dist/
-.remote-sync.json
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 3abb749..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-language: python
-
-python:
- - "3.6"
- - "3.7"
- - "3.8"
-
-before_install:
- - cp README.md README.rst
-
-install:
- - pip install -e .
-
-script: python -c "import nanolyse"
-
-notifications:
- email: false
- webhooks:
- urls:
- - https://webhooks.gitter.im/e/4b1c45cea6826ce475c2
diff --git a/MANIFEST.in b/MANIFEST.in
index 97c726f..3d59c81 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,2 +1,3 @@
include reference/lambda.fasta.gz
+include reference/DNA_CS.fasta
include README.md
diff --git a/NanoLyse.egg-info/PKG-INFO b/NanoLyse.egg-info/PKG-INFO
new file mode 100644
index 0000000..d5fcd06
--- /dev/null
+++ b/NanoLyse.egg-info/PKG-INFO
@@ -0,0 +1,73 @@
+Metadata-Version: 2.1
+Name: NanoLyse
+Version: 1.2.1
+Summary: Removing reads mapping to the lambda genome
+Home-page: https://github.com/wdecoster/nanolyse
+Author: Wouter De Coster
+Author-email: decosterwouter@gmail.com
+License: GPLv3
+Keywords: nanopore sequencing processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# NanoLyse
+
+**Please be aware that NanoLyse will no longer receive any updates, as its functionality is included in [chopper](https://github.com/wdecoster/chopper) (which should be lots faster, too).**
+
+Remove reads mapping to the lambda phage genome from a fastq file.
+This script uses Heng Li's [minimap2](https://github.com/lh3/minimap2) and his [mappy](https://pypi.python.org/pypi/mappy) Python binding.
+
+[](https://twitter.com/wouter_decoster)
+[](http://bioconda.github.io/recipes/nanolyse/README.html)
+
+## INSTALLATION
+
+`pip install NanoLyse`
+
+### USAGE
+
+```text
+Reads fastq from stdin and writes to stdout.
+
+NanoLyse [-h] [-v] [-r REFERENCE]
+
+ Remove reads mapping to the lambda genome.
+ Reads fastq from stdin and writes to stdout.
+
+ Example usage:
+ zcat reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz
+
+
+optional arguments:
+ -h, --help show this help message and exit
+ -v, --version Print version and exit.
+ -r REFERENCE, --reference REFERENCE
+ Specify a reference fasta file against which to filter.
+```
+
+### WARNING
+
+If (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.
+
+### EXAMPLES
+
+`gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz`
+In combination with [NanoFilt](https://github.com/wdecoster/nanofilt):
+`gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz`
+Using a different genome to filter on (rather than lambda phage):
+`gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz`
+
+I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanolyse/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
+
+## CITATION
+
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
diff --git a/NanoLyse.egg-info/SOURCES.txt b/NanoLyse.egg-info/SOURCES.txt
new file mode 100644
index 0000000..c0a030e
--- /dev/null
+++ b/NanoLyse.egg-info/SOURCES.txt
@@ -0,0 +1,15 @@
+LICENSE
+MANIFEST.in
+README.md
+setup.py
+NanoLyse.egg-info/PKG-INFO
+NanoLyse.egg-info/SOURCES.txt
+NanoLyse.egg-info/dependency_links.txt
+NanoLyse.egg-info/entry_points.txt
+NanoLyse.egg-info/requires.txt
+NanoLyse.egg-info/top_level.txt
+nanolyse/NanoLyse.py
+nanolyse/__init__.py
+nanolyse/version.py
+reference/DNA_CS.fasta
+reference/lambda.fasta.gz
\ No newline at end of file
diff --git a/NanoLyse.egg-info/dependency_links.txt b/NanoLyse.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/NanoLyse.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/NanoLyse.egg-info/entry_points.txt b/NanoLyse.egg-info/entry_points.txt
new file mode 100644
index 0000000..221c2a9
--- /dev/null
+++ b/NanoLyse.egg-info/entry_points.txt
@@ -0,0 +1,2 @@
+[console_scripts]
+NanoLyse = nanolyse.NanoLyse:main
diff --git a/NanoLyse.egg-info/requires.txt b/NanoLyse.egg-info/requires.txt
new file mode 100644
index 0000000..2313100
--- /dev/null
+++ b/NanoLyse.egg-info/requires.txt
@@ -0,0 +1,2 @@
+biopython
+mappy>=2.2
diff --git a/NanoLyse.egg-info/top_level.txt b/NanoLyse.egg-info/top_level.txt
new file mode 100644
index 0000000..0841fc0
--- /dev/null
+++ b/NanoLyse.egg-info/top_level.txt
@@ -0,0 +1,2 @@
+nanolyse
+reference
diff --git a/PKG-INFO b/PKG-INFO
new file mode 100644
index 0000000..d5fcd06
--- /dev/null
+++ b/PKG-INFO
@@ -0,0 +1,73 @@
+Metadata-Version: 2.1
+Name: NanoLyse
+Version: 1.2.1
+Summary: Removing reads mapping to the lambda genome
+Home-page: https://github.com/wdecoster/nanolyse
+Author: Wouter De Coster
+Author-email: decosterwouter@gmail.com
+License: GPLv3
+Keywords: nanopore sequencing processing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# NanoLyse
+
+**Please be aware that NanoLyse will no longer receive any updates, as its functionality is included in [chopper](https://github.com/wdecoster/chopper) (which should be lots faster, too).**
+
+Remove reads mapping to the lambda phage genome from a fastq file.
+This script uses Heng Li's [minimap2](https://github.com/lh3/minimap2) and his [mappy](https://pypi.python.org/pypi/mappy) Python binding.
+
+[](https://twitter.com/wouter_decoster)
+[](http://bioconda.github.io/recipes/nanolyse/README.html)
+
+## INSTALLATION
+
+`pip install NanoLyse`
+
+### USAGE
+
+```text
+Reads fastq from stdin and writes to stdout.
+
+NanoLyse [-h] [-v] [-r REFERENCE]
+
+ Remove reads mapping to the lambda genome.
+ Reads fastq from stdin and writes to stdout.
+
+ Example usage:
+ zcat reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz
+
+
+optional arguments:
+ -h, --help show this help message and exit
+ -v, --version Print version and exit.
+ -r REFERENCE, --reference REFERENCE
+ Specify a reference fasta file against which to filter.
+```
+
+### WARNING
+
+If (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.
+
+### EXAMPLES
+
+`gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz`
+In combination with [NanoFilt](https://github.com/wdecoster/nanofilt):
+`gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz`
+Using a different genome to filter on (rather than lambda phage):
+`gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz`
+
+I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanolyse/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
+
+## CITATION
+
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
diff --git a/README.md b/README.md
index b054314..01ef67b 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,20 @@
# NanoLyse
+
+**Please be aware that NanoLyse will no longer receive any updates, as its functionality is included in [chopper](https://github.com/wdecoster/chopper) (which should be lots faster, too).**
+
Remove reads mapping to the lambda phage genome from a fastq file.
This script uses Heng Li's [minimap2](https://github.com/lh3/minimap2) and his [mappy](https://pypi.python.org/pypi/mappy) Python binding.
[](https://twitter.com/wouter_decoster)
-[](https://travis-ci.org/wdecoster/nanolyse)
[](http://bioconda.github.io/recipes/nanolyse/README.html)
+## INSTALLATION
-### INSTALLATION
`pip install NanoLyse`
### USAGE
-```
+
+```text
Reads fastq from stdin and writes to stdout.
NanoLyse [-h] [-v] [-r REFERENCE]
@@ -30,27 +33,20 @@ optional arguments:
Specify a reference fasta file against which to filter.
```
-
### WARNING
+
If (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.
### EXAMPLES
+
`gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz`
In combination with [NanoFilt](https://github.com/wdecoster/nanofilt):
`gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz`
Using a different genome to filter on (rather than lambda phage):
`gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz`
-
-
-
-
-
-
-
-
I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanolyse/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
-
## CITATION
+
If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
diff --git a/debian/changelog b/debian/changelog
index 8bc4ea7..be0c517 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+nanolyse (1.2.0+git20230116.1.837fcb4-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Fri, 20 Jan 2023 02:31:41 -0000
+
nanolyse (1.2.0-4) unstable; urgency=medium
* Fix watch file
diff --git a/debian/patches/path_to_reference.patch b/debian/patches/path_to_reference.patch
index da7b07f..d7697ef 100644
--- a/debian/patches/path_to_reference.patch
+++ b/debian/patches/path_to_reference.patch
@@ -2,9 +2,11 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 13 May 2020 10:53:01 +0200
Description: Fixed path to reference in Debian package
---- a/nanolyse/NanoLyse.py
-+++ b/nanolyse/NanoLyse.py
-@@ -87,7 +87,7 @@ def getIndex(reference):
+Index: nanolyse.git/nanolyse/NanoLyse.py
+===================================================================
+--- nanolyse.git.orig/nanolyse/NanoLyse.py
++++ nanolyse.git/nanolyse/NanoLyse.py
+@@ -99,7 +99,7 @@ def getIndex(reference):
reffas = reference
else:
parent_directory = path.dirname(path.abspath(path.dirname(__file__)))
diff --git a/nanolyse/NanoLyse.py b/nanolyse/NanoLyse.py
index 7f0a6da..f1913cd 100644
--- a/nanolyse/NanoLyse.py
+++ b/nanolyse/NanoLyse.py
@@ -144,7 +144,13 @@ def filter_summary(summary_file, output, read_ids_file):
with open(output, 'wb') as summary_out, open(summary_file, 'rb') as summary_in:
header = next(summary_in)
summary_out.write(header)
- index = header.split(b'\t').index(b'read_id')
+ try:
+ index = header.split(b'\t').index(b'read_id')
+ except ValueError:
+ sys.stderr.write("ERROR: Filtering your FASTQ went okay.\n")
+ sys.stderr.write("But something unexpected happened with the summary file.\n")
+ sys.stderr.write("Header which NanoLyse was trying to parse: {}\n".format(header))
+ raise
for line in summary_in:
i += 1
if not line.split(b'\t')[index] in lambda_identifiers:
diff --git a/nanolyse/version.py b/nanolyse/version.py
index c68196d..a955fda 100644
--- a/nanolyse/version.py
+++ b/nanolyse/version.py
@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.2.1"
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..8bfd5a1
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,4 @@
+[egg_info]
+tag_build =
+tag_date = 0
+
diff --git a/setup.py b/setup.py
index feb4b16..2f553f3 100644
--- a/setup.py
+++ b/setup.py
@@ -1,42 +1,44 @@
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
+
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
-exec(open('nanolyse/version.py').read())
+exec(open("nanolyse/version.py").read())
setup(
- name='NanoLyse',
+ name="NanoLyse",
version=__version__,
- description='Removing reads mapping to the lambda genome',
+ description="Removing reads mapping to the lambda genome",
long_description=open(path.join(here, "README.md")).read(),
long_description_content_type="text/markdown",
- url='https://github.com/wdecoster/nanolyse',
- author='Wouter De Coster',
- author_email='decosterwouter@gmail.com',
- license='GPLv3',
+ url="https://github.com/wdecoster/nanolyse",
+ author="Wouter De Coster",
+ author_email="decosterwouter@gmail.com",
+ license="GPLv3",
classifiers=[
- 'Development Status :: 4 - Beta',
- 'Intended Audience :: Science/Research',
- 'Topic :: Scientific/Engineering :: Bio-Informatics',
- 'License :: OSI Approved :: MIT License',
- 'Programming Language :: Python :: 3',
- 'Programming Language :: Python :: 3.3',
- 'Programming Language :: Python :: 3.4',
- 'Programming Language :: Python :: 3.5',
+ "Development Status :: 4 - Beta",
+ "Intended Audience :: Science/Research",
+ "Topic :: Scientific/Engineering :: Bio-Informatics",
+ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.3",
+ "Programming Language :: Python :: 3.4",
+ "Programming Language :: Python :: 3.5",
],
- keywords='nanopore sequencing processing',
- packages=find_packages() + ['reference'],
- python_requires='>=3',
- install_requires=[
- 'mappy>=2.2',
- 'biopython'],
- package_data={'nanolyse': []},
- package_dir={'nanolyse': 'nanolyse'},
+ keywords="nanopore sequencing processing",
+ packages=find_packages() + ["reference"],
+ python_requires=">=3.6",
+ install_requires=["mappy>=2.2", "biopython"],
+ package_data={"nanolyse": []},
+ package_dir={"nanolyse": "nanolyse"},
include_package_data=True,
entry_points={
- 'console_scripts': ['NanoLyse=nanolyse.NanoLyse:main', ]}
+ "console_scripts": [
+ "NanoLyse=nanolyse.NanoLyse:main",
+ ]
+ },
)
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.1.egg-info/PKG-INFO -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.1.egg-info/dependency_links.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.1.egg-info/entry_points.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.1.egg-info/requires.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.1.egg-info/top_level.txt
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.0.egg-info/PKG-INFO -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.0.egg-info/dependency_links.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.0.egg-info/entry_points.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.0.egg-info/requires.txt -rw-r--r-- root/root /usr/lib/python3/dist-packages/NanoLyse-1.2.0.egg-info/top_level.txt
No differences were encountered in the control files