1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
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
|
