From 17bf5072f12fde73055011db89cb4ed67dfa0cd0 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Tue, 11 Apr 2023 11:32:42 +0000 Subject: automatic import of python-pyfastx --- python-pyfastx.spec | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 python-pyfastx.spec (limited to 'python-pyfastx.spec') diff --git a/python-pyfastx.spec b/python-pyfastx.spec new file mode 100644 index 0000000..93f896e --- /dev/null +++ b/python-pyfastx.spec @@ -0,0 +1,77 @@ +%global _empty_manifest_terminate_build 0 +Name: python-pyfastx +Version: 1.0.1 +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/e5/06/6496b396dc38015fd76d253ac2b41a813950483035e4b24e048f7c3e041c/pyfastx-1.0.1.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 `_ written by `@attractivechaos `_ in `klib `_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy `_ in project `indexed_gzip `_ to index gzipped file for random access. +This project was heavily inspired by `@mdshw5 `_'s project `pyfaidx `_ and `@brentp `_'s project `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 `_ written by `@attractivechaos `_ in `klib `_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy `_ in project `indexed_gzip `_ to index gzipped file for random access. +This project was heavily inspired by `@mdshw5 `_'s project `pyfaidx `_ and `@brentp `_'s project `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 `_ written by `@attractivechaos `_ in `klib `_ project to parse plain FASTA/Q file and zran.c written by `@pauldmccarthy `_ in project `indexed_gzip `_ to index gzipped file for random access. +This project was heavily inspired by `@mdshw5 `_'s project `pyfaidx `_ and `@brentp `_'s project `pyfasta `_. + +%prep +%autosetup -n pyfastx-1.0.1 + +%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 +* Tue Apr 11 2023 Python_Bot - 1.0.1-1 +- Package Spec generated -- cgit v1.2.3