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author | CoprDistGit <infra@openeuler.org> | 2023-05-18 05:50:42 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-18 05:50:42 +0000 |
commit | e1995cfc7f119432031137a4620a57fad32fe95e (patch) | |
tree | 8dcb4511e2805c98dc870776bf8e17ca5813fcdf | |
parent | 9e8905ab50d5de4deea7466408b088f169f616f9 (diff) |
automatic import of python-aiv
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-aiv.spec | 279 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 281 insertions, 0 deletions
@@ -0,0 +1 @@ +/aiv-0.4.3.tar.gz diff --git a/python-aiv.spec b/python-aiv.spec new file mode 100644 index 0000000..f87fb58 --- /dev/null +++ b/python-aiv.spec @@ -0,0 +1,279 @@ +%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 +[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/) +[](https://pypi.org/project/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 + + + + +## Report Preview + + + +## 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 +[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/) +[](https://pypi.org/project/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 + + + + +## Report Preview + + + +## 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 +[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/) +[](https://pypi.org/project/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 + + + + +## Report Preview + + + +## 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 @@ -0,0 +1 @@ +4154b757e3326911922ee1b164032cba aiv-0.4.3.tar.gz |