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authorCoprDistGit <infra@openeuler.org>2023-05-18 05:50:42 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-18 05:50:42 +0000
commite1995cfc7f119432031137a4620a57fad32fe95e (patch)
tree8dcb4511e2805c98dc870776bf8e17ca5813fcdf
parent9e8905ab50d5de4deea7466408b088f169f616f9 (diff)
automatic import of python-aiv
-rw-r--r--.gitignore1
-rw-r--r--python-aiv.spec279
-rw-r--r--sources1
3 files changed, 281 insertions, 0 deletions
diff --git a/.gitignore b/.gitignore
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+/aiv-0.4.3.tar.gz
diff --git a/python-aiv.spec b/python-aiv.spec
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+++ b/python-aiv.spec
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+%global _empty_manifest_terminate_build 0
+Name: python-aiv
+Version: 0.4.3
+Release: 1
+Summary: A variant annotation package
+License: MIT License
+URL: https://github.com/nesegunes/aiv
+Source0: https://mirrors.nju.edu.cn/pypi/web/packages/e5/85/70ce5d038978be8ec2ebb02ec88963d579c5c1be24864866bed13f48ee9f/aiv-0.4.3.tar.gz
+BuildArch: noarch
+
+Requires: python3-myvariant
+Requires: python3-pandas
+Requires: python3-reportlab
+
+%description
+[![PyPI](https://img.shields.io/pypi/v/aiv)](https://pypi.org/project/aiv/) [![GitHub](https://img.shields.io/github/license/nesegunes/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Format](https://img.shields.io/pypi/format/aiv)](https://pypi.org/project/aiv/)
+
+
+## AIV: Annotation of Identified Variants
+
+Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
+
+## Prerequisites
+
+It requires three main modules: pandas, myvariant and reportlab
+
+```
+pip install pandas
+pip install myvariant
+pip install reportlab
+```
+
+## Installation
+
+```
+pip install aiv
+```
+
+## Upgrade
+
+```
+pip install aiv --upgrade
+```
+
+## Usage
+
+```javascript
+import aiv
+
+# Get variant info
+aiv.getvariant('chr1', 69635, 'G', 'C')
+
+# Annotate variants, reference genome: hg38
+aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
+
+# Annotate variants, reference genome: hg19
+aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
+```
+## Tests
+
+You can test your installation with sample variant call files. Input test files can be found at:
+
+```
+./tests/test_annotate_variants.tsv
+./tests/bwa_mutect2_nb09_50_lines.txt
+./tests/my_data.txt
+```
+## Input File Format
+
+![Input file](https://github.com/nesegunes/aiv/blob/master/images/input.png?raw=true)
+
+
+## Report Preview
+
+![Output file](https://github.com/nesegunes/aiv/blob/master/output/test_annotate_variants_AIV_Report-01.png?raw=true)
+
+## Future Work
+
+- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
+
+
+
+
+%package -n python3-aiv
+Summary: A variant annotation package
+Provides: python-aiv
+BuildRequires: python3-devel
+BuildRequires: python3-setuptools
+BuildRequires: python3-pip
+%description -n python3-aiv
+[![PyPI](https://img.shields.io/pypi/v/aiv)](https://pypi.org/project/aiv/) [![GitHub](https://img.shields.io/github/license/nesegunes/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Format](https://img.shields.io/pypi/format/aiv)](https://pypi.org/project/aiv/)
+
+
+## AIV: Annotation of Identified Variants
+
+Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
+
+## Prerequisites
+
+It requires three main modules: pandas, myvariant and reportlab
+
+```
+pip install pandas
+pip install myvariant
+pip install reportlab
+```
+
+## Installation
+
+```
+pip install aiv
+```
+
+## Upgrade
+
+```
+pip install aiv --upgrade
+```
+
+## Usage
+
+```javascript
+import aiv
+
+# Get variant info
+aiv.getvariant('chr1', 69635, 'G', 'C')
+
+# Annotate variants, reference genome: hg38
+aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
+
+# Annotate variants, reference genome: hg19
+aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
+```
+## Tests
+
+You can test your installation with sample variant call files. Input test files can be found at:
+
+```
+./tests/test_annotate_variants.tsv
+./tests/bwa_mutect2_nb09_50_lines.txt
+./tests/my_data.txt
+```
+## Input File Format
+
+![Input file](https://github.com/nesegunes/aiv/blob/master/images/input.png?raw=true)
+
+
+## Report Preview
+
+![Output file](https://github.com/nesegunes/aiv/blob/master/output/test_annotate_variants_AIV_Report-01.png?raw=true)
+
+## Future Work
+
+- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
+
+
+
+
+%package help
+Summary: Development documents and examples for aiv
+Provides: python3-aiv-doc
+%description help
+[![PyPI](https://img.shields.io/pypi/v/aiv)](https://pypi.org/project/aiv/) [![GitHub](https://img.shields.io/github/license/nesegunes/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/aiv)](https://pypi.org/project/aiv/)
+[![PyPI - Format](https://img.shields.io/pypi/format/aiv)](https://pypi.org/project/aiv/)
+
+
+## AIV: Annotation of Identified Variants
+
+Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
+
+## Prerequisites
+
+It requires three main modules: pandas, myvariant and reportlab
+
+```
+pip install pandas
+pip install myvariant
+pip install reportlab
+```
+
+## Installation
+
+```
+pip install aiv
+```
+
+## Upgrade
+
+```
+pip install aiv --upgrade
+```
+
+## Usage
+
+```javascript
+import aiv
+
+# Get variant info
+aiv.getvariant('chr1', 69635, 'G', 'C')
+
+# Annotate variants, reference genome: hg38
+aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
+
+# Annotate variants, reference genome: hg19
+aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
+```
+## Tests
+
+You can test your installation with sample variant call files. Input test files can be found at:
+
+```
+./tests/test_annotate_variants.tsv
+./tests/bwa_mutect2_nb09_50_lines.txt
+./tests/my_data.txt
+```
+## Input File Format
+
+![Input file](https://github.com/nesegunes/aiv/blob/master/images/input.png?raw=true)
+
+
+## Report Preview
+
+![Output file](https://github.com/nesegunes/aiv/blob/master/output/test_annotate_variants_AIV_Report-01.png?raw=true)
+
+## Future Work
+
+- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
+
+
+
+
+%prep
+%autosetup -n aiv-0.4.3
+
+%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-aiv -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.3-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..3961e94
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+4154b757e3326911922ee1b164032cba aiv-0.4.3.tar.gz