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
|
%global _empty_manifest_terminate_build 0
Name: python-treesapp
Version: 0.11.4
Release: 1
Summary: TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.
License: GPL-3.0
URL: https://github.com/hallamlab/TreeSAPP
Source0: https://mirrors.aliyun.com/pypi/web/packages/c9/22/768e33057257389a7d4e234e7910768a8ab3a44017e76990be5cca8712a4/treesapp-0.11.4.tar.gz
BuildArch: noarch
Requires: python3-biopython
Requires: python3-ete3
Requires: python3-joblib
Requires: python3-numpy
Requires: python3-packaging
Requires: python3-pyfastx
Requires: python3-pygtrie
Requires: python3-samsum
Requires: python3-scikit-learn
Requires: python3-scipy
Requires: python3-six
Requires: python3-seaborn
Requires: python3-tqdm
Requires: python3-pytest
Requires: python3-pandas
Requires: python3-matplotlib
Requires: python3-pytest
Requires: python3-pytest-cov
%description
# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler
[](https://badge.fury.io/py/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://quay.io/repository/hallamlab/treesapp)
[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade)
[](http://bioconda.github.io/recipes/treesapp/README.html)
[](https://img.shields.io/pypi/pyversions/)
[](https://codecov.io/gh/hallamlab/TreeSAPP)
[](https://anaconda.org/bioconda/treesapp)
## Overview
TreeSAPP is a python package for functional and taxonomic annotation of proteins
from genomes and metagenomes using phylogenetic placement.
## Quick start
We recommend installing TreeSAPP into its own conda environment with the following command:
```bash
conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp
conda activate treesapp_cenv
```
To list all the sub-commands run `treesapp`.
To test the `assign` workflow, run:
```bash
treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB
```
To classify sequences in your genome of interest:
```bash
treesapp assign -i my.fasta -o ~/path/to/output/directory/
```
TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes.
We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs)
and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs).
## Tutorials
All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page.
Here are some specific tutorial examples:
If we do not yet have a reference package for a gene you are interested in,
please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP).
Of course, if you run into any problems or would like to collaborate on building many reference packages
don't hesitate to email us or create a new issue with an 'enhancement' label.
To determine whether the sequences used to build your new reference package are what you think they are,
and whether it might unexpectedly annotate homologous sequences,
see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages).
If you are working with a particularly complex reference package, from an orthologous group for example, or have extra
phylogenetic information you'd like to include in your classifications,
try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`.
## Citation
If you found TreeSAPP useful in your work, please cite the following paper:
Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020).
[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588).
Bioinformatics, 1–8.
This was brought to you by the team:
- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer)
- Ryan McLaughlin ([McGlock](https://github.com/McGlock))
- Grace Zhang ([grace72](https://github.com/gracez72))
- Kevin Chan ([kevinxchan](https://github.com/kevinxchan))
- Zachary Armstrong
- Steven J. Hallam
### References
If you're feeling extra citation-happy, please consider citing the following works as well:
- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763.
- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1).
- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455.
- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658.
%package -n python3-treesapp
Summary: TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.
Provides: python-treesapp
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-treesapp
# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler
[](https://badge.fury.io/py/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://quay.io/repository/hallamlab/treesapp)
[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade)
[](http://bioconda.github.io/recipes/treesapp/README.html)
[](https://img.shields.io/pypi/pyversions/)
[](https://codecov.io/gh/hallamlab/TreeSAPP)
[](https://anaconda.org/bioconda/treesapp)
## Overview
TreeSAPP is a python package for functional and taxonomic annotation of proteins
from genomes and metagenomes using phylogenetic placement.
## Quick start
We recommend installing TreeSAPP into its own conda environment with the following command:
```bash
conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp
conda activate treesapp_cenv
```
To list all the sub-commands run `treesapp`.
To test the `assign` workflow, run:
```bash
treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB
```
To classify sequences in your genome of interest:
```bash
treesapp assign -i my.fasta -o ~/path/to/output/directory/
```
TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes.
We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs)
and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs).
## Tutorials
All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page.
Here are some specific tutorial examples:
If we do not yet have a reference package for a gene you are interested in,
please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP).
Of course, if you run into any problems or would like to collaborate on building many reference packages
don't hesitate to email us or create a new issue with an 'enhancement' label.
To determine whether the sequences used to build your new reference package are what you think they are,
and whether it might unexpectedly annotate homologous sequences,
see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages).
If you are working with a particularly complex reference package, from an orthologous group for example, or have extra
phylogenetic information you'd like to include in your classifications,
try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`.
## Citation
If you found TreeSAPP useful in your work, please cite the following paper:
Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020).
[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588).
Bioinformatics, 1–8.
This was brought to you by the team:
- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer)
- Ryan McLaughlin ([McGlock](https://github.com/McGlock))
- Grace Zhang ([grace72](https://github.com/gracez72))
- Kevin Chan ([kevinxchan](https://github.com/kevinxchan))
- Zachary Armstrong
- Steven J. Hallam
### References
If you're feeling extra citation-happy, please consider citing the following works as well:
- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763.
- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1).
- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455.
- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658.
%package help
Summary: Development documents and examples for treesapp
Provides: python3-treesapp-doc
%description help
# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler
[](https://badge.fury.io/py/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://anaconda.org/bioconda/treesapp)
[](https://quay.io/repository/hallamlab/treesapp)
[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade)
[](http://bioconda.github.io/recipes/treesapp/README.html)
[](https://img.shields.io/pypi/pyversions/)
[](https://codecov.io/gh/hallamlab/TreeSAPP)
[](https://anaconda.org/bioconda/treesapp)
## Overview
TreeSAPP is a python package for functional and taxonomic annotation of proteins
from genomes and metagenomes using phylogenetic placement.
## Quick start
We recommend installing TreeSAPP into its own conda environment with the following command:
```bash
conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp
conda activate treesapp_cenv
```
To list all the sub-commands run `treesapp`.
To test the `assign` workflow, run:
```bash
treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB
```
To classify sequences in your genome of interest:
```bash
treesapp assign -i my.fasta -o ~/path/to/output/directory/
```
TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes.
We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs)
and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs).
## Tutorials
All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page.
Here are some specific tutorial examples:
If we do not yet have a reference package for a gene you are interested in,
please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP).
Of course, if you run into any problems or would like to collaborate on building many reference packages
don't hesitate to email us or create a new issue with an 'enhancement' label.
To determine whether the sequences used to build your new reference package are what you think they are,
and whether it might unexpectedly annotate homologous sequences,
see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages).
If you are working with a particularly complex reference package, from an orthologous group for example, or have extra
phylogenetic information you'd like to include in your classifications,
try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`.
## Citation
If you found TreeSAPP useful in your work, please cite the following paper:
Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020).
[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588).
Bioinformatics, 1–8.
This was brought to you by the team:
- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer)
- Ryan McLaughlin ([McGlock](https://github.com/McGlock))
- Grace Zhang ([grace72](https://github.com/gracez72))
- Kevin Chan ([kevinxchan](https://github.com/kevinxchan))
- Zachary Armstrong
- Steven J. Hallam
### References
If you're feeling extra citation-happy, please consider citing the following works as well:
- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763.
- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1).
- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455.
- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658.
%prep
%autosetup -n treesapp-0.11.4
%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-treesapp -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.11.4-1
- Package Spec generated
|
