automatic import of python-pyfastx

3 files changed, 79 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..7240753 100644
--- a/.gitignore
+++ b/.gitignore
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+/pyfastx-1.0.1.tar.gz
diff --git a/python-pyfastx.spec b/python-pyfastx.spec
new file mode 100644
index 0000000..93f896e
--- /dev/null
+++ b/python-pyfastx.spec
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+%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 <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-1.0.1
+
+%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 <Python_Bot@openeuler.org> - 1.0.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..cb8ee22
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+e2ce9beacb895ebf6ff6d145f9354156  pyfastx-1.0.1.tar.gz