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diff --git a/python-pydbsnp.spec b/python-pydbsnp.spec new file mode 100644 index 0000000..1a1836b --- /dev/null +++ b/python-pydbsnp.spec @@ -0,0 +1,346 @@ +%global _empty_manifest_terminate_build 0 +Name: python-pydbsnp +Version: 2.0.2 +Release: 1 +Summary: Interface with dbSNP VCF data +License: MIT License +URL: https://gitlab.com/aaylward/pydbsnp +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/43/64/ce2bc4b12d024b96f391b8eb677a733f8512ce68461afcfe31c66b010c60/pydbsnp-2.0.2.tar.gz +BuildArch: noarch + +Requires: python3-pysam + +%description +# pydbsnp + +Interface with dbSNP VCF data + +## Installation + +**Step 0 (optional):** If you don't want to bother with environment variables +and don't care about how `pydbsnp` works under the hood, skip this step. + +If you wish, you can determine the location where `pydbsnp` looks for relevant +data using four environment variables: `PYDBSNP_VCF_GRCH37`, +`PYDBSNP_RSID_GRCH37`, `PYDBSNP_VCF_GRCH38`, `PYDBSNP_RSID_GRCH38`. The `VCF` +variables determine the location of the VCF data, the `RSID` variables +determine the location of the rsid indices. For example, you could add this +to your `.bash_profile`: + +```bash +export PYDBSNP_VCF_GRCH37=<path of your choice> +export PYDBSNP_RSID_GRCH37=<path of your choice> +export PYDBSNP_VCF_GRCH38=<path of your choice> +export PYDBSNP_RSID_GRCH38=<path of your choice> +``` + +If you set these variables before continuing to the next step, `pydbsnp` will +use them to determine where it places downloaded VCF files and RSID indices. + +**Step 1:** install the python package via `pip3` + +```sh +pip install pydbsnp +``` +or +```sh +pip install --user pydbsnp +``` + +**Step 2:** Once the python package is installed, download and index the dbSBP +VCF data: + +```sh +pydbsnp-download +pydbsnp-index +``` + +For hg19/GRCh37 coordinates: + +```sh +pydbsnp-download --reference-build GRCh37 +pydbsnp-index +``` + +## Command line usage + +```sh +pydbsnp-query -h +``` + +```sh +pydbsnp-query rs231361 +pydbsnp-query chr8:118184783 +pydbsnp-query --reference-build GRCh37 rs231361 +pydbsnp-query rs231361 chr8:118184783 rs7903146 +``` + +## API + +Two classes are provided: `Variant` and `GeneralizedVariant`. + +An object of the `Variant` class has an attribute for each relevant field +of the VCF. +```python +from pydbsnp import Variant +v = Variant(id='rs8056814') +print(v.chrom, v.pos, v.id, v.ref, v.alt) +print(v.info) +w = Variant(id='rs8056814', reference_build='GRCh37') +print(w.chrom, w.pos) +x = Variant('chr16', 75218429) +print(x) +help(Variant) +``` + +An object of the `GeneralizedVariant` class is similar, but each attribute +is a tuple which may have multiple items. For example, one RSID may map +to two sets of coordinates. +```python +gv = GeneralizedVariant(id='rs8056814') +print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt) +``` + + + + +%package -n python3-pydbsnp +Summary: Interface with dbSNP VCF data +Provides: python-pydbsnp +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-pydbsnp +# pydbsnp + +Interface with dbSNP VCF data + +## Installation + +**Step 0 (optional):** If you don't want to bother with environment variables +and don't care about how `pydbsnp` works under the hood, skip this step. + +If you wish, you can determine the location where `pydbsnp` looks for relevant +data using four environment variables: `PYDBSNP_VCF_GRCH37`, +`PYDBSNP_RSID_GRCH37`, `PYDBSNP_VCF_GRCH38`, `PYDBSNP_RSID_GRCH38`. The `VCF` +variables determine the location of the VCF data, the `RSID` variables +determine the location of the rsid indices. For example, you could add this +to your `.bash_profile`: + +```bash +export PYDBSNP_VCF_GRCH37=<path of your choice> +export PYDBSNP_RSID_GRCH37=<path of your choice> +export PYDBSNP_VCF_GRCH38=<path of your choice> +export PYDBSNP_RSID_GRCH38=<path of your choice> +``` + +If you set these variables before continuing to the next step, `pydbsnp` will +use them to determine where it places downloaded VCF files and RSID indices. + +**Step 1:** install the python package via `pip3` + +```sh +pip install pydbsnp +``` +or +```sh +pip install --user pydbsnp +``` + +**Step 2:** Once the python package is installed, download and index the dbSBP +VCF data: + +```sh +pydbsnp-download +pydbsnp-index +``` + +For hg19/GRCh37 coordinates: + +```sh +pydbsnp-download --reference-build GRCh37 +pydbsnp-index +``` + +## Command line usage + +```sh +pydbsnp-query -h +``` + +```sh +pydbsnp-query rs231361 +pydbsnp-query chr8:118184783 +pydbsnp-query --reference-build GRCh37 rs231361 +pydbsnp-query rs231361 chr8:118184783 rs7903146 +``` + +## API + +Two classes are provided: `Variant` and `GeneralizedVariant`. + +An object of the `Variant` class has an attribute for each relevant field +of the VCF. +```python +from pydbsnp import Variant +v = Variant(id='rs8056814') +print(v.chrom, v.pos, v.id, v.ref, v.alt) +print(v.info) +w = Variant(id='rs8056814', reference_build='GRCh37') +print(w.chrom, w.pos) +x = Variant('chr16', 75218429) +print(x) +help(Variant) +``` + +An object of the `GeneralizedVariant` class is similar, but each attribute +is a tuple which may have multiple items. For example, one RSID may map +to two sets of coordinates. +```python +gv = GeneralizedVariant(id='rs8056814') +print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt) +``` + + + + +%package help +Summary: Development documents and examples for pydbsnp +Provides: python3-pydbsnp-doc +%description help +# pydbsnp + +Interface with dbSNP VCF data + +## Installation + +**Step 0 (optional):** If you don't want to bother with environment variables +and don't care about how `pydbsnp` works under the hood, skip this step. + +If you wish, you can determine the location where `pydbsnp` looks for relevant +data using four environment variables: `PYDBSNP_VCF_GRCH37`, +`PYDBSNP_RSID_GRCH37`, `PYDBSNP_VCF_GRCH38`, `PYDBSNP_RSID_GRCH38`. The `VCF` +variables determine the location of the VCF data, the `RSID` variables +determine the location of the rsid indices. For example, you could add this +to your `.bash_profile`: + +```bash +export PYDBSNP_VCF_GRCH37=<path of your choice> +export PYDBSNP_RSID_GRCH37=<path of your choice> +export PYDBSNP_VCF_GRCH38=<path of your choice> +export PYDBSNP_RSID_GRCH38=<path of your choice> +``` + +If you set these variables before continuing to the next step, `pydbsnp` will +use them to determine where it places downloaded VCF files and RSID indices. + +**Step 1:** install the python package via `pip3` + +```sh +pip install pydbsnp +``` +or +```sh +pip install --user pydbsnp +``` + +**Step 2:** Once the python package is installed, download and index the dbSBP +VCF data: + +```sh +pydbsnp-download +pydbsnp-index +``` + +For hg19/GRCh37 coordinates: + +```sh +pydbsnp-download --reference-build GRCh37 +pydbsnp-index +``` + +## Command line usage + +```sh +pydbsnp-query -h +``` + +```sh +pydbsnp-query rs231361 +pydbsnp-query chr8:118184783 +pydbsnp-query --reference-build GRCh37 rs231361 +pydbsnp-query rs231361 chr8:118184783 rs7903146 +``` + +## API + +Two classes are provided: `Variant` and `GeneralizedVariant`. + +An object of the `Variant` class has an attribute for each relevant field +of the VCF. +```python +from pydbsnp import Variant +v = Variant(id='rs8056814') +print(v.chrom, v.pos, v.id, v.ref, v.alt) +print(v.info) +w = Variant(id='rs8056814', reference_build='GRCh37') +print(w.chrom, w.pos) +x = Variant('chr16', 75218429) +print(x) +help(Variant) +``` + +An object of the `GeneralizedVariant` class is similar, but each attribute +is a tuple which may have multiple items. For example, one RSID may map +to two sets of coordinates. +```python +gv = GeneralizedVariant(id='rs8056814') +print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt) +``` + + + + +%prep +%autosetup -n pydbsnp-2.0.2 + +%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-pydbsnp -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 2.0.2-1 +- Package Spec generated |