automatic import of python-abstar

3 files changed, 342 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..d0be04d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/abstar-0.6.1.tar.gz
diff --git a/python-abstar.spec b/python-abstar.spec
new file mode 100644
index 0000000..042bbc0
--- /dev/null
+++ b/python-abstar.spec
@@ -0,0 +1,340 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-abstar
+Version:	0.6.1
+Release:	1
+Summary:	VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
+License:	MIT License
+URL:		https://www.github.com/briney/abstar
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/cc/f7/9513bb778b9745b6ae0c07434e87a3bcd3a6380dc5fedd7d96d83b05dcb5/abstar-0.6.1.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-biopython
+Requires:	python3-celery
+Requires:	python3-dask[complete]
+Requires:	python3-matplotlib
+Requires:	python3-numpy
+Requires:	python3-pandas
+Requires:	python3-parasail
+Requires:	python3-pyarrow
+Requires:	python3-pymongo
+Requires:	python3-pytest
+
+%description
+![](https://img.shields.io/pypi/v/abstar.svg?colorB=blue)
+[![Build Status](https://travis-ci.com/briney/abstar.svg?branch=master)](https://app.travis-ci.com/github/briney/abstar)
+[![Documentation Status](https://readthedocs.org/projects/abstar/badge/?version=latest)](https://abstar.readthedocs.io/en/latest/?badge=latest)
+![](https://img.shields.io/pypi/pyversions/abstar.svg)
+![](https://img.shields.io/badge/license-MIT-blue.svg)
+
+# abstar  
+  
+VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.  
+  
+  - Source code: [github.com/briney/abstar](https://github.com/briney/abstar)  
+  - Documentation: [abstar.readthedocs.org](http://abstar.readthedocs.org)  
+  - Download: [pypi.python.org/pypi/abstar](https://pypi.python.org/pypi/abstar)  
+  - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)  
+  
+### install  
+`pip install abstar`  
+  
+### use  
+
+To run abstar on a single FASTA or FASTQ file:  
+`abstar -i <input-file> -o <output-directory> -t <temp-directory>`
+
+To iteratively run abstar on all files in an input directory:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory>`
+  
+To run abstar using the included test data as input:  
+`abstar -o <output-directory> -t <temp-directory> --use-test-data`  
+  
+When using the abstar test data, note that although the test data file contains 1,000 sequences, one of the test sequences is not a valid antibody recombination. Only 999 sequences should be processed successfully.  
+
+When using BaseSpace as the input data source, you can optionally provide all of the required directories:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory> -b`  
+  
+Or you can simply provide a single project directory, and all required directories will be created in the project directory:  
+`abstar -p <project_directory> -b`  
+  
+  
+### additional options  
+`-l LOG_LOCATION, --log LOG_LOCATION` Change the log directory location. Default is the parent directory of `<output_directory>`.  
+  
+`-m, --merge` Input directory should contain paired FASTQ (or gzipped FASTQ) files. Paired files will be merged with PANDAseq prior to processing with abstar. Note that when using the BaseSpace option (`-b, --basespace`), this option is implied.  
+  
+`-b, --basespace` Download a sequencing run from BaseSpace, which is Illumina's cloud storage environment. Since Illumina sequencers produce paired-end reads, `--merge` is implied.  
+  
+`-u N, --uaid N` Sequences contain a unique antibody ID (UAID, or molecular barcode) of length N. The uaid will be parsed from the beginning of each input sequence and added to the JSON output. Negative values result in the UAID being parsed from the end of the sequence.  
+  
+`-s SPECIES, --species SPECIES` Select the species from which the input sequences are derived. Supported options are 'human', 'mouse', and 'macaque'. Default is 'human'.  
+   
+`-c, --cluster` Runs abstar in distributed mode on a Celery cluster.  
+  
+`-h, --help` Prints detailed information about all runtime options.
+  
+`-D --debug` Much more verbose logging.  
+  
+
+### api  
+Most core abstar functions are available through a public API, making it easier to run abstar as a component of integrated analysis pipelines. See the abstar [documentation](http://abstar.readthedocs.org) for more detail about the API.  
+  
+  
+### helper scripts  
+A few helper scripts are included with abstar:  
+`batch_mongoimport` automates the import of multiple JSON output files into a MongoDB database.  
+`build_abstar_germline_db` creates abstar germline databases from IMGT-gapped FASTA files of V, D and J gene segments.  
+`make_basespace_credfile` makes a credentials file for BaseSpace, which is required if downloading sequences from BaseSpace with abstar. Developer credentials are required, and the process for obtaining them is explained [here](https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader)  
+  
+
+### testing  
+To run the test suite, clone or download the repository and run `pytest ./` from the top-level directory.  
+  
+### requirements  
+Python 3.8+   
+abutils  
+biopython  
+celery  
+nwalign3  
+pymongo  
+pytest  
+scikit-bio  
+
+All of the above dependencies can be installed with pip, and will be installed automatically when installing abstar with pip.  
+If you're new to Python, a great way to get started is to install the [Anaconda Python distribution](https://www.continuum.io/downloads), which includes pip as well as a ton of useful scientific Python packages.
+  
+sequence merging requires [PANDAseq](https://github.com/neufeld/pandaseq)  
+batch_mongoimport requires [MongoDB](http://www.mongodb.org/)  
+BaseSpace downloading requires the [BaseSpace Python SDK](https://github.com/basespace/basespace-python-sdk)  
+
+
+%package -n python3-abstar
+Summary:	VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
+Provides:	python-abstar
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-abstar
+![](https://img.shields.io/pypi/v/abstar.svg?colorB=blue)
+[![Build Status](https://travis-ci.com/briney/abstar.svg?branch=master)](https://app.travis-ci.com/github/briney/abstar)
+[![Documentation Status](https://readthedocs.org/projects/abstar/badge/?version=latest)](https://abstar.readthedocs.io/en/latest/?badge=latest)
+![](https://img.shields.io/pypi/pyversions/abstar.svg)
+![](https://img.shields.io/badge/license-MIT-blue.svg)
+
+# abstar  
+  
+VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.  
+  
+  - Source code: [github.com/briney/abstar](https://github.com/briney/abstar)  
+  - Documentation: [abstar.readthedocs.org](http://abstar.readthedocs.org)  
+  - Download: [pypi.python.org/pypi/abstar](https://pypi.python.org/pypi/abstar)  
+  - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)  
+  
+### install  
+`pip install abstar`  
+  
+### use  
+
+To run abstar on a single FASTA or FASTQ file:  
+`abstar -i <input-file> -o <output-directory> -t <temp-directory>`
+
+To iteratively run abstar on all files in an input directory:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory>`
+  
+To run abstar using the included test data as input:  
+`abstar -o <output-directory> -t <temp-directory> --use-test-data`  
+  
+When using the abstar test data, note that although the test data file contains 1,000 sequences, one of the test sequences is not a valid antibody recombination. Only 999 sequences should be processed successfully.  
+
+When using BaseSpace as the input data source, you can optionally provide all of the required directories:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory> -b`  
+  
+Or you can simply provide a single project directory, and all required directories will be created in the project directory:  
+`abstar -p <project_directory> -b`  
+  
+  
+### additional options  
+`-l LOG_LOCATION, --log LOG_LOCATION` Change the log directory location. Default is the parent directory of `<output_directory>`.  
+  
+`-m, --merge` Input directory should contain paired FASTQ (or gzipped FASTQ) files. Paired files will be merged with PANDAseq prior to processing with abstar. Note that when using the BaseSpace option (`-b, --basespace`), this option is implied.  
+  
+`-b, --basespace` Download a sequencing run from BaseSpace, which is Illumina's cloud storage environment. Since Illumina sequencers produce paired-end reads, `--merge` is implied.  
+  
+`-u N, --uaid N` Sequences contain a unique antibody ID (UAID, or molecular barcode) of length N. The uaid will be parsed from the beginning of each input sequence and added to the JSON output. Negative values result in the UAID being parsed from the end of the sequence.  
+  
+`-s SPECIES, --species SPECIES` Select the species from which the input sequences are derived. Supported options are 'human', 'mouse', and 'macaque'. Default is 'human'.  
+   
+`-c, --cluster` Runs abstar in distributed mode on a Celery cluster.  
+  
+`-h, --help` Prints detailed information about all runtime options.
+  
+`-D --debug` Much more verbose logging.  
+  
+
+### api  
+Most core abstar functions are available through a public API, making it easier to run abstar as a component of integrated analysis pipelines. See the abstar [documentation](http://abstar.readthedocs.org) for more detail about the API.  
+  
+  
+### helper scripts  
+A few helper scripts are included with abstar:  
+`batch_mongoimport` automates the import of multiple JSON output files into a MongoDB database.  
+`build_abstar_germline_db` creates abstar germline databases from IMGT-gapped FASTA files of V, D and J gene segments.  
+`make_basespace_credfile` makes a credentials file for BaseSpace, which is required if downloading sequences from BaseSpace with abstar. Developer credentials are required, and the process for obtaining them is explained [here](https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader)  
+  
+
+### testing  
+To run the test suite, clone or download the repository and run `pytest ./` from the top-level directory.  
+  
+### requirements  
+Python 3.8+   
+abutils  
+biopython  
+celery  
+nwalign3  
+pymongo  
+pytest  
+scikit-bio  
+
+All of the above dependencies can be installed with pip, and will be installed automatically when installing abstar with pip.  
+If you're new to Python, a great way to get started is to install the [Anaconda Python distribution](https://www.continuum.io/downloads), which includes pip as well as a ton of useful scientific Python packages.
+  
+sequence merging requires [PANDAseq](https://github.com/neufeld/pandaseq)  
+batch_mongoimport requires [MongoDB](http://www.mongodb.org/)  
+BaseSpace downloading requires the [BaseSpace Python SDK](https://github.com/basespace/basespace-python-sdk)  
+
+
+%package help
+Summary:	Development documents and examples for abstar
+Provides:	python3-abstar-doc
+%description help
+![](https://img.shields.io/pypi/v/abstar.svg?colorB=blue)
+[![Build Status](https://travis-ci.com/briney/abstar.svg?branch=master)](https://app.travis-ci.com/github/briney/abstar)
+[![Documentation Status](https://readthedocs.org/projects/abstar/badge/?version=latest)](https://abstar.readthedocs.io/en/latest/?badge=latest)
+![](https://img.shields.io/pypi/pyversions/abstar.svg)
+![](https://img.shields.io/badge/license-MIT-blue.svg)
+
+# abstar  
+  
+VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.  
+  
+  - Source code: [github.com/briney/abstar](https://github.com/briney/abstar)  
+  - Documentation: [abstar.readthedocs.org](http://abstar.readthedocs.org)  
+  - Download: [pypi.python.org/pypi/abstar](https://pypi.python.org/pypi/abstar)  
+  - Docker: [hub.docker.com/r/briney/abstar/](https://hub.docker.com/r/briney/abstar/)  
+  
+### install  
+`pip install abstar`  
+  
+### use  
+
+To run abstar on a single FASTA or FASTQ file:  
+`abstar -i <input-file> -o <output-directory> -t <temp-directory>`
+
+To iteratively run abstar on all files in an input directory:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory>`
+  
+To run abstar using the included test data as input:  
+`abstar -o <output-directory> -t <temp-directory> --use-test-data`  
+  
+When using the abstar test data, note that although the test data file contains 1,000 sequences, one of the test sequences is not a valid antibody recombination. Only 999 sequences should be processed successfully.  
+
+When using BaseSpace as the input data source, you can optionally provide all of the required directories:  
+`abstar -i <input-directory> -o <output-directory> -t <temp-directory> -b`  
+  
+Or you can simply provide a single project directory, and all required directories will be created in the project directory:  
+`abstar -p <project_directory> -b`  
+  
+  
+### additional options  
+`-l LOG_LOCATION, --log LOG_LOCATION` Change the log directory location. Default is the parent directory of `<output_directory>`.  
+  
+`-m, --merge` Input directory should contain paired FASTQ (or gzipped FASTQ) files. Paired files will be merged with PANDAseq prior to processing with abstar. Note that when using the BaseSpace option (`-b, --basespace`), this option is implied.  
+  
+`-b, --basespace` Download a sequencing run from BaseSpace, which is Illumina's cloud storage environment. Since Illumina sequencers produce paired-end reads, `--merge` is implied.  
+  
+`-u N, --uaid N` Sequences contain a unique antibody ID (UAID, or molecular barcode) of length N. The uaid will be parsed from the beginning of each input sequence and added to the JSON output. Negative values result in the UAID being parsed from the end of the sequence.  
+  
+`-s SPECIES, --species SPECIES` Select the species from which the input sequences are derived. Supported options are 'human', 'mouse', and 'macaque'. Default is 'human'.  
+   
+`-c, --cluster` Runs abstar in distributed mode on a Celery cluster.  
+  
+`-h, --help` Prints detailed information about all runtime options.
+  
+`-D --debug` Much more verbose logging.  
+  
+
+### api  
+Most core abstar functions are available through a public API, making it easier to run abstar as a component of integrated analysis pipelines. See the abstar [documentation](http://abstar.readthedocs.org) for more detail about the API.  
+  
+  
+### helper scripts  
+A few helper scripts are included with abstar:  
+`batch_mongoimport` automates the import of multiple JSON output files into a MongoDB database.  
+`build_abstar_germline_db` creates abstar germline databases from IMGT-gapped FASTA files of V, D and J gene segments.  
+`make_basespace_credfile` makes a credentials file for BaseSpace, which is required if downloading sequences from BaseSpace with abstar. Developer credentials are required, and the process for obtaining them is explained [here](https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader)  
+  
+
+### testing  
+To run the test suite, clone or download the repository and run `pytest ./` from the top-level directory.  
+  
+### requirements  
+Python 3.8+   
+abutils  
+biopython  
+celery  
+nwalign3  
+pymongo  
+pytest  
+scikit-bio  
+
+All of the above dependencies can be installed with pip, and will be installed automatically when installing abstar with pip.  
+If you're new to Python, a great way to get started is to install the [Anaconda Python distribution](https://www.continuum.io/downloads), which includes pip as well as a ton of useful scientific Python packages.
+  
+sequence merging requires [PANDAseq](https://github.com/neufeld/pandaseq)  
+batch_mongoimport requires [MongoDB](http://www.mongodb.org/)  
+BaseSpace downloading requires the [BaseSpace Python SDK](https://github.com/basespace/basespace-python-sdk)  
+
+
+%prep
+%autosetup -n abstar-0.6.1
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-abstar -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.6.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..46630d1
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+192776470b478b37097ed7fc0639c5fb  abstar-0.6.1.tar.gz