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
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
|
%global _empty_manifest_terminate_build 0
Name: python-HTSeq
Version: 2.0.2
Release: 1
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
License: GPL3
URL: https://github.com/htseq
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/de/13/cbeb753eb29d31bb252bc18443e79a3739bf5bd3dbc99e65fcf13db81be1/HTSeq-2.0.2.tar.gz
BuildArch: noarch
Requires: python3-numpy
Requires: python3-pysam
Requires: python3-matplotlib
Requires: python3-scipy
Requires: python3-pytest
Requires: python3-pandas
Requires: python3-matplotlib
%description
[](https://htseq.readthedocs.io)
# HTSeq
**DEVS**: https://github.com/htseq/htseq
**DOCS**: https://htseq.readthedocs.io
**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022).
A Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq``
is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq
and similar experiments.
## Requirements
To use ``HTSeq`` you need:
- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped)
- ``numpy``
- ``pysam``
To manipulate BigWig files, you also need:
- ``pyBigWig``
To run the ``htseq-qa`` script, you also need:
- ``matplotlib``
To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need:
- ``mtx`` file: ``scipy``
- ``h5ad`` file: ``anndata``
- ``loom`` file: ``loompy``
Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We
would like to support **Windows** but currently lack the expertise to do so. If
you would like to take on the Windows release and maintenance, please open an
issue and we'll try to help.
A source package which should not require ``Cython`` nor ``SWIG`` is also
provided on Pypi.
To **develop** `HTSeq` you will **also** need:
- ``Cython >=0.29.5``
- ``SWIG >=3.0.8``
## Installation
### PIP
To install directly from PyPI:
```bash
pip install HTSeq
```
To install a specific version:
```bash
pip install 'HTSeq==2.0.0'
```
If this fails, please install all dependencies first:
```bash
pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq
```
### setup.py (distutils/setuptools)
Install the dependencies with your favourite tool (``pip``, ``conda``,
etc.).
To install ``HTSeq`` itself, run:
```bash
python setup.py build install
```
## Testing
To test locally, run
```bash
./test.sh
```
To test `htseq-count` alone, run it with the `-o` option.
A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts.
## Authors
- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber
%package -n python3-HTSeq
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
Provides: python-HTSeq
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-HTSeq
[](https://htseq.readthedocs.io)
# HTSeq
**DEVS**: https://github.com/htseq/htseq
**DOCS**: https://htseq.readthedocs.io
**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022).
A Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq``
is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq
and similar experiments.
## Requirements
To use ``HTSeq`` you need:
- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped)
- ``numpy``
- ``pysam``
To manipulate BigWig files, you also need:
- ``pyBigWig``
To run the ``htseq-qa`` script, you also need:
- ``matplotlib``
To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need:
- ``mtx`` file: ``scipy``
- ``h5ad`` file: ``anndata``
- ``loom`` file: ``loompy``
Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We
would like to support **Windows** but currently lack the expertise to do so. If
you would like to take on the Windows release and maintenance, please open an
issue and we'll try to help.
A source package which should not require ``Cython`` nor ``SWIG`` is also
provided on Pypi.
To **develop** `HTSeq` you will **also** need:
- ``Cython >=0.29.5``
- ``SWIG >=3.0.8``
## Installation
### PIP
To install directly from PyPI:
```bash
pip install HTSeq
```
To install a specific version:
```bash
pip install 'HTSeq==2.0.0'
```
If this fails, please install all dependencies first:
```bash
pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq
```
### setup.py (distutils/setuptools)
Install the dependencies with your favourite tool (``pip``, ``conda``,
etc.).
To install ``HTSeq`` itself, run:
```bash
python setup.py build install
```
## Testing
To test locally, run
```bash
./test.sh
```
To test `htseq-count` alone, run it with the `-o` option.
A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts.
## Authors
- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber
%package help
Summary: Development documents and examples for HTSeq
Provides: python3-HTSeq-doc
%description help
[](https://htseq.readthedocs.io)
# HTSeq
**DEVS**: https://github.com/htseq/htseq
**DOCS**: https://htseq.readthedocs.io
**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022).
A Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq``
is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq
and similar experiments.
## Requirements
To use ``HTSeq`` you need:
- ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped)
- ``numpy``
- ``pysam``
To manipulate BigWig files, you also need:
- ``pyBigWig``
To run the ``htseq-qa`` script, you also need:
- ``matplotlib``
To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need:
- ``mtx`` file: ``scipy``
- ``h5ad`` file: ``anndata``
- ``loom`` file: ``loompy``
Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We
would like to support **Windows** but currently lack the expertise to do so. If
you would like to take on the Windows release and maintenance, please open an
issue and we'll try to help.
A source package which should not require ``Cython`` nor ``SWIG`` is also
provided on Pypi.
To **develop** `HTSeq` you will **also** need:
- ``Cython >=0.29.5``
- ``SWIG >=3.0.8``
## Installation
### PIP
To install directly from PyPI:
```bash
pip install HTSeq
```
To install a specific version:
```bash
pip install 'HTSeq==2.0.0'
```
If this fails, please install all dependencies first:
```bash
pip install matplotlib
pip install Cython
pip install pysam
pip install HTSeq
```
### setup.py (distutils/setuptools)
Install the dependencies with your favourite tool (``pip``, ``conda``,
etc.).
To install ``HTSeq`` itself, run:
```bash
python setup.py build install
```
## Testing
To test locally, run
```bash
./test.sh
```
To test `htseq-count` alone, run it with the `-o` option.
A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts.
## Authors
- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber
%prep
%autosetup -n HTSeq-2.0.2
%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-HTSeq -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Apr 25 2023 Python_Bot <Python_Bot@openeuler.org> - 2.0.2-1
- Package Spec generated
|
