%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.aliyun.com/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= export PYDBSNP_RSID_GRCH37= export PYDBSNP_VCF_GRCH38= export PYDBSNP_RSID_GRCH38= ``` 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= export PYDBSNP_RSID_GRCH37= export PYDBSNP_VCF_GRCH38= export PYDBSNP_RSID_GRCH38= ``` 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= export PYDBSNP_RSID_GRCH37= export PYDBSNP_VCF_GRCH38= export PYDBSNP_RSID_GRCH38= ``` 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 * Fri Jun 09 2023 Python_Bot - 2.0.2-1 - Package Spec generated