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
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
|
%global _empty_manifest_terminate_build 0
Name: python-aiv
Version: 0.4.3
Release: 1
Summary: A variant annotation package
License: MIT License
URL: https://github.com/nesegunes/aiv
Source0: https://mirrors.aliyun.com/pypi/web/packages/e5/85/70ce5d038978be8ec2ebb02ec88963d579c5c1be24864866bed13f48ee9f/aiv-0.4.3.tar.gz
BuildArch: noarch
Requires: python3-myvariant
Requires: python3-pandas
Requires: python3-reportlab
%description
[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
## AIV: Annotation of Identified Variants
Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
## Prerequisites
It requires three main modules: pandas, myvariant and reportlab
```
pip install pandas
pip install myvariant
pip install reportlab
```
## Installation
```
pip install aiv
```
## Upgrade
```
pip install aiv --upgrade
```
## Usage
```javascript
import aiv
# Get variant info
aiv.getvariant('chr1', 69635, 'G', 'C')
# Annotate variants, reference genome: hg38
aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
# Annotate variants, reference genome: hg19
aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
```
## Tests
You can test your installation with sample variant call files. Input test files can be found at:
```
./tests/test_annotate_variants.tsv
./tests/bwa_mutect2_nb09_50_lines.txt
./tests/my_data.txt
```
## Input File Format
## Report Preview
## Future Work
- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
%package -n python3-aiv
Summary: A variant annotation package
Provides: python-aiv
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-aiv
[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
## AIV: Annotation of Identified Variants
Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
## Prerequisites
It requires three main modules: pandas, myvariant and reportlab
```
pip install pandas
pip install myvariant
pip install reportlab
```
## Installation
```
pip install aiv
```
## Upgrade
```
pip install aiv --upgrade
```
## Usage
```javascript
import aiv
# Get variant info
aiv.getvariant('chr1', 69635, 'G', 'C')
# Annotate variants, reference genome: hg38
aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
# Annotate variants, reference genome: hg19
aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
```
## Tests
You can test your installation with sample variant call files. Input test files can be found at:
```
./tests/test_annotate_variants.tsv
./tests/bwa_mutect2_nb09_50_lines.txt
./tests/my_data.txt
```
## Input File Format
## Report Preview
## Future Work
- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
%package help
Summary: Development documents and examples for aiv
Provides: python3-aiv-doc
%description help
[](https://pypi.org/project/aiv/) [](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
[](https://pypi.org/project/aiv/)
## AIV: Annotation of Identified Variants
Annotation of Identified Variants to Create Reports for Clinicians to Assist Therapeutic Decisions
## Prerequisites
It requires three main modules: pandas, myvariant and reportlab
```
pip install pandas
pip install myvariant
pip install reportlab
```
## Installation
```
pip install aiv
```
## Upgrade
```
pip install aiv --upgrade
```
## Usage
```javascript
import aiv
# Get variant info
aiv.getvariant('chr1', 69635, 'G', 'C')
# Annotate variants, reference genome: hg38
aiv.annotate_mutations('variant_calls.tsv', assembly='hg38')
# Annotate variants, reference genome: hg19
aiv.annotate_mutations('bwa_mutect2_nb09_50_lines.txt', assembly='hg19')
```
## Tests
You can test your installation with sample variant call files. Input test files can be found at:
```
./tests/test_annotate_variants.tsv
./tests/bwa_mutect2_nb09_50_lines.txt
./tests/my_data.txt
```
## Input File Format
## Report Preview
## Future Work
- Performance can be determined by calculating the running time for a given input file with 6000+ mutations.
%prep
%autosetup -n aiv-0.4.3
%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-aiv -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.3-1
- Package Spec generated
|
