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@@ -0,0 +1 @@ +/swalign-0.3.7.tar.gz diff --git a/python-swalign.spec b/python-swalign.spec new file mode 100644 index 0000000..c9ec6a4 --- /dev/null +++ b/python-swalign.spec @@ -0,0 +1,141 @@ +%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 @@ -0,0 +1 @@ +6b4048b2d676f9002af984757cbdef27 swalign-0.3.7.tar.gz |