automatic import of python-cigar

3 files changed, 218 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..358d67a 100644
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+/cigar-0.1.3.tar.gz
diff --git a/python-cigar.spec b/python-cigar.spec
new file mode 100644
index 0000000..5f657d7
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+%global _empty_manifest_terminate_build 0
+Name:		python-cigar
+Version:	0.1.3
+Release:	1
+Summary:	manipulate SAM cigar strings
+License:	MIT
+URL:		https://github.com/brentp/cigar
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/2d/5f/ffa58a8c64f811772b69a01eeab25c602b72d02a0c83006177c21abedaa3/cigar-0.1.3.tar.gz
+BuildArch:	noarch
+
+
+%description
+cigar is a simple library for dealing with cigar strings. the most useful
+feature now is soft-masking from left or right. This allows one to adjust
+a SAM record only by changing the cigar string to soft-mask a number of bases
+such that the rest of the SAM record (pos, tlen, etc.) remain valid, but
+downstream tools will not consider the soft-masked bases in further analysis.
+```Python
+>>> from cigar import Cigar
+>>> c = Cigar('100M')
+>>> len(c)
+100
+>>> str(c)
+'100M'
+>>> list(c.items())
+[(100, 'M')]
+>>> c = Cigar('20H20M20S')
+>>> len(c)
+40
+>>> str(c)
+'20H20M20S'
+>>> list(c.items())
+[(20, 'H'), (20, 'M'), (20, 'S')]
+>>> c.mask_left(29).cigar, c.cigar
+('20H9S11M20S', '20H20M20S')
+>>> c = Cigar('10M20S10M')
+>>> c.mask_left(10).cigar
+'30S10M'
+>>> c.mask_left(9).cigar
+'9S1M20S10M'
+>>> Cigar('10S').mask_left(10).cigar
+'10S'
+>>> Cigar('10H').mask_left(10).cigar
+'10H'
+>>> Cigar('10H').mask_left(11).cigar
+'10H'
+>>> Cigar('10H').mask_left(9).cigar
+'10H'
+>>> Cigar('1M10H').mask_left(9).cigar
+'1S10H'
+>>> Cigar('5M10H').mask_left(9).cigar
+'5S10H'
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_left(9).cigar == c.cigar
+True
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_right(9).cigar == c.cigar
+True
+>>> c.mask_right(11).cigar
+'1S1H1S5H1S4M1S10H'
+```
+
+%package -n python3-cigar
+Summary:	manipulate SAM cigar strings
+Provides:	python-cigar
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-cigar
+cigar is a simple library for dealing with cigar strings. the most useful
+feature now is soft-masking from left or right. This allows one to adjust
+a SAM record only by changing the cigar string to soft-mask a number of bases
+such that the rest of the SAM record (pos, tlen, etc.) remain valid, but
+downstream tools will not consider the soft-masked bases in further analysis.
+```Python
+>>> from cigar import Cigar
+>>> c = Cigar('100M')
+>>> len(c)
+100
+>>> str(c)
+'100M'
+>>> list(c.items())
+[(100, 'M')]
+>>> c = Cigar('20H20M20S')
+>>> len(c)
+40
+>>> str(c)
+'20H20M20S'
+>>> list(c.items())
+[(20, 'H'), (20, 'M'), (20, 'S')]
+>>> c.mask_left(29).cigar, c.cigar
+('20H9S11M20S', '20H20M20S')
+>>> c = Cigar('10M20S10M')
+>>> c.mask_left(10).cigar
+'30S10M'
+>>> c.mask_left(9).cigar
+'9S1M20S10M'
+>>> Cigar('10S').mask_left(10).cigar
+'10S'
+>>> Cigar('10H').mask_left(10).cigar
+'10H'
+>>> Cigar('10H').mask_left(11).cigar
+'10H'
+>>> Cigar('10H').mask_left(9).cigar
+'10H'
+>>> Cigar('1M10H').mask_left(9).cigar
+'1S10H'
+>>> Cigar('5M10H').mask_left(9).cigar
+'5S10H'
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_left(9).cigar == c.cigar
+True
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_right(9).cigar == c.cigar
+True
+>>> c.mask_right(11).cigar
+'1S1H1S5H1S4M1S10H'
+```
+
+%package help
+Summary:	Development documents and examples for cigar
+Provides:	python3-cigar-doc
+%description help
+cigar is a simple library for dealing with cigar strings. the most useful
+feature now is soft-masking from left or right. This allows one to adjust
+a SAM record only by changing the cigar string to soft-mask a number of bases
+such that the rest of the SAM record (pos, tlen, etc.) remain valid, but
+downstream tools will not consider the soft-masked bases in further analysis.
+```Python
+>>> from cigar import Cigar
+>>> c = Cigar('100M')
+>>> len(c)
+100
+>>> str(c)
+'100M'
+>>> list(c.items())
+[(100, 'M')]
+>>> c = Cigar('20H20M20S')
+>>> len(c)
+40
+>>> str(c)
+'20H20M20S'
+>>> list(c.items())
+[(20, 'H'), (20, 'M'), (20, 'S')]
+>>> c.mask_left(29).cigar, c.cigar
+('20H9S11M20S', '20H20M20S')
+>>> c = Cigar('10M20S10M')
+>>> c.mask_left(10).cigar
+'30S10M'
+>>> c.mask_left(9).cigar
+'9S1M20S10M'
+>>> Cigar('10S').mask_left(10).cigar
+'10S'
+>>> Cigar('10H').mask_left(10).cigar
+'10H'
+>>> Cigar('10H').mask_left(11).cigar
+'10H'
+>>> Cigar('10H').mask_left(9).cigar
+'10H'
+>>> Cigar('1M10H').mask_left(9).cigar
+'1S10H'
+>>> Cigar('5M10H').mask_left(9).cigar
+'5S10H'
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_left(9).cigar == c.cigar
+True
+>>> c = Cigar('1S1H1S5H1S5M10H')
+>>> c.mask_right(9).cigar == c.cigar
+True
+>>> c.mask_right(11).cigar
+'1S1H1S5H1S4M1S10H'
+```
+
+%prep
+%autosetup -n cigar-0.1.3
+
+%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-cigar -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.3-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..16fec6f
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+5c8d8ca31d80d759f67d87dcd54ec01d  cigar-0.1.3.tar.gz