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%global _empty_manifest_terminate_build 0
Name: python-pyfastx
Version: 1.1.0
Release: 1
Summary: pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file
License: MIT
URL: https://github.com/lmdu/pyfastx
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/d2/42/116eedc4a40d96c14c6b0fb4ba0c2841b2a5a2bc65341b227521d2b27818/pyfastx-1.1.0.tar.gz
%description
The ``pyfastx`` is a lightweight Python C extension that enables users to randomly access to sequences from plain and **gzipped** FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number. The ``pyfastx`` will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the ``pyfastx`` can parse standard (*sequence is spread into multiple lines with same length*) and nonstandard (*sequence is spread into one or more lines with different length*) FASTA format. This module used `kseq.h <https://github.com/attractivechaos/klib/blob/master/kseq.h>`_ written by `@attractivechaos <https://github.com/attractivechaos>`_ in `klib <https://github.com/attractivechaos/klib>`_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy <https://github.com/pauldmccarthy>`_ in project `indexed_gzip <https://github.com/pauldmccarthy/indexed_gzip>`_ to index gzipped file for random access.
This project was heavily inspired by `@mdshw5 <https://github.com/mdshw5>`_'s project `pyfaidx <https://github.com/mdshw5/pyfaidx>`_ and `@brentp <https://github.com/brentp>`_'s project `pyfasta <https://github.com/brentp/pyfasta>`_.
%package -n python3-pyfastx
Summary: pyfastx is a python module for fast random access to sequences from plain and gzipped FASTA/Q file
Provides: python-pyfastx
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
BuildRequires: python3-cffi
BuildRequires: gcc
BuildRequires: gdb
%description -n python3-pyfastx
The ``pyfastx`` is a lightweight Python C extension that enables users to randomly access to sequences from plain and **gzipped** FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number. The ``pyfastx`` will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the ``pyfastx`` can parse standard (*sequence is spread into multiple lines with same length*) and nonstandard (*sequence is spread into one or more lines with different length*) FASTA format. This module used `kseq.h <https://github.com/attractivechaos/klib/blob/master/kseq.h>`_ written by `@attractivechaos <https://github.com/attractivechaos>`_ in `klib <https://github.com/attractivechaos/klib>`_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy <https://github.com/pauldmccarthy>`_ in project `indexed_gzip <https://github.com/pauldmccarthy/indexed_gzip>`_ to index gzipped file for random access.
This project was heavily inspired by `@mdshw5 <https://github.com/mdshw5>`_'s project `pyfaidx <https://github.com/mdshw5/pyfaidx>`_ and `@brentp <https://github.com/brentp>`_'s project `pyfasta <https://github.com/brentp/pyfasta>`_.
%package help
Summary: Development documents and examples for pyfastx
Provides: python3-pyfastx-doc
%description help
The ``pyfastx`` is a lightweight Python C extension that enables users to randomly access to sequences from plain and **gzipped** FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number. The ``pyfastx`` will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the ``pyfastx`` can parse standard (*sequence is spread into multiple lines with same length*) and nonstandard (*sequence is spread into one or more lines with different length*) FASTA format. This module used `kseq.h <https://github.com/attractivechaos/klib/blob/master/kseq.h>`_ written by `@attractivechaos <https://github.com/attractivechaos>`_ in `klib <https://github.com/attractivechaos/klib>`_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy <https://github.com/pauldmccarthy>`_ in project `indexed_gzip <https://github.com/pauldmccarthy/indexed_gzip>`_ to index gzipped file for random access.
This project was heavily inspired by `@mdshw5 <https://github.com/mdshw5>`_'s project `pyfaidx <https://github.com/mdshw5/pyfaidx>`_ and `@brentp <https://github.com/brentp>`_'s project `pyfasta <https://github.com/brentp/pyfasta>`_.
%prep
%autosetup -n pyfastx-1.1.0
%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-pyfastx -f filelist.lst
%dir %{python3_sitearch}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Sun Apr 23 2023 Python_Bot <Python_Bot@openeuler.org> - 1.1.0-1
- Package Spec generated
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