%global _empty_manifest_terminate_build 0
Name:		python-swalign
Version:	0.3.7
Release:	1
Summary:	Smith-Waterman local aligner
License:	None
URL:		http://github.com/mbreese/swalign/
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/ca/5a/ad32a28285cf9046b7eea9978e7e8c6a1fbadbe71b9ccfa4db60ef06dbb7/swalign-0.3.7.tar.gz
BuildArch:	noarch


%description
# swalign

This package implements a Smith-Waterman style local alignment algorithm. You
can align a query sequence to a reference. The scoring functions can be based
on a matrix, or simple identity. Weights can be adjusted for match/mismatch
and gaps, with gap extention penalties. Additionally, the gap penalty can be
subject to a decay to prioritize long gaps.

The input files are FASTA format sequences, or strings of sequences.

Here is some skeleton code to get you started:

    import swalign
    # choose your own values here… 2 and -1 are common.
    match = 2
    mismatch = -1
    scoring = swalign.NucleotideScoringMatrix(match, mismatch)

    sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
    alignment = sw.align('ACACACTA','AGCACACA')
    alignment.dump()

For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign


%package -n python3-swalign
Summary:	Smith-Waterman local aligner
Provides:	python-swalign
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-swalign
# swalign

This package implements a Smith-Waterman style local alignment algorithm. You
can align a query sequence to a reference. The scoring functions can be based
on a matrix, or simple identity. Weights can be adjusted for match/mismatch
and gaps, with gap extention penalties. Additionally, the gap penalty can be
subject to a decay to prioritize long gaps.

The input files are FASTA format sequences, or strings of sequences.

Here is some skeleton code to get you started:

    import swalign
    # choose your own values here… 2 and -1 are common.
    match = 2
    mismatch = -1
    scoring = swalign.NucleotideScoringMatrix(match, mismatch)

    sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
    alignment = sw.align('ACACACTA','AGCACACA')
    alignment.dump()

For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign


%package help
Summary:	Development documents and examples for swalign
Provides:	python3-swalign-doc
%description help
# swalign

This package implements a Smith-Waterman style local alignment algorithm. You
can align a query sequence to a reference. The scoring functions can be based
on a matrix, or simple identity. Weights can be adjusted for match/mismatch
and gaps, with gap extention penalties. Additionally, the gap penalty can be
subject to a decay to prioritize long gaps.

The input files are FASTA format sequences, or strings of sequences.

Here is some skeleton code to get you started:

    import swalign
    # choose your own values here… 2 and -1 are common.
    match = 2
    mismatch = -1
    scoring = swalign.NucleotideScoringMatrix(match, mismatch)

    sw = swalign.LocalAlignment(scoring)  # you can also choose gap penalties, etc...
    alignment = sw.align('ACACACTA','AGCACACA')
    alignment.dump()

For other uses, see the script in bin/swalign or https://compgen.io/projects/swalign


%prep
%autosetup -n swalign-0.3.7

%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-swalign -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Thu May 18 2023 Python_Bot <Python_Bot@openeuler.org> - 0.3.7-1
- Package Spec generated