%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 - 0.4.3-1 - Package Spec generated