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
|
%global _empty_manifest_terminate_build 0
Name: python-mycotools
Version: 0.27.36
Release: 1
Summary: A compilation of bioinformatic and computation biology inspired python tools
License: GNU Lesser General Public License v3 or later (LGPLv3+)
URL: https://gitlab.com/xonq/mycotools/mycotools
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/97/9e/8fde0cbb9cedd95e9d1b89137708f36fc9ea8f5f631bf5485637c952305b/mycotools-0.27.36.tar.gz
BuildArch: noarch
Requires: python3-biopython
Requires: python3-pandas
Requires: python3-requests
Requires: python3-scipy
Requires: python3-openpyxl
Requires: python3-tqdm
%description
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png"
>
</p>
Now alpha support for prokaryotes too!
<br /><br />
# NOTE
While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research.
Cheers,
Zachary Konkel
# PURPOSE
Bring broadscale comparative genomics to the masses.
Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.
- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and
incomplete databases.
- `updateDB.py --update` brings the database to the current date. No more
database obsolecence in the wake of accelerating genome availability.
- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of
the `gff`, allowing for reliable analyses and format expectations from
multiple eras.
- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis.
Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`.
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png"
>
</p>
<br />
By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`.
<br />
# USAGE
Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide.
<br />
# CITING
If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.
<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png">
<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
%package -n python3-mycotools
Summary: A compilation of bioinformatic and computation biology inspired python tools
Provides: python-mycotools
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-mycotools
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png"
>
</p>
Now alpha support for prokaryotes too!
<br /><br />
# NOTE
While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research.
Cheers,
Zachary Konkel
# PURPOSE
Bring broadscale comparative genomics to the masses.
Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.
- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and
incomplete databases.
- `updateDB.py --update` brings the database to the current date. No more
database obsolecence in the wake of accelerating genome availability.
- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of
the `gff`, allowing for reliable analyses and format expectations from
multiple eras.
- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis.
Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`.
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png"
>
</p>
<br />
By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`.
<br />
# USAGE
Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide.
<br />
# CITING
If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.
<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png">
<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
%package help
Summary: Development documents and examples for mycotools
Provides: python3-mycotools-doc
%description help
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/pictogo.white.png"
>
</p>
Now alpha support for prokaryotes too!
<br /><br />
# NOTE
While extensive alpha testing has been conducted, this software is in a beta state, and errors are expected. Kindly report these issues and remain patient for fixes - if you can find the bug, even better! This software will have longterm maintenance, although my focus is on my own research.
Cheers,
Zachary Konkel
# PURPOSE
Bring broadscale comparative genomics to the masses.
Mycotools is a compilation of computational biology tools and database [MycotoolsDB](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/MTDB.md) software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.
- Installation is as simple as `updateDB.py --init <DIR>`. No more limited and
incomplete databases.
- `updateDB.py --update` brings the database to the current date. No more
database obsolecence in the wake of accelerating genome availability.
- The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of
the `gff`, allowing for reliable analyses and format expectations from
multiple eras.
- The `.mtdb` database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis.
Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email `konkelzach@protonmail.com`.
<p align="center">
<img
src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/mtdb.png"
>
</p>
<br />
By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving `gff` or `fasta` accessions; running and compiling `fasta`s of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using `ncbiDwnld.py` and `jgiDwnld.py`.
<br />
# USAGE
Check out [README.md](https://gitlab.com/xonq/mycotools/-/tree/master/mycotools) for install and the [USAGE.md](https://gitlab.com/xonq/mycotools/-/blob/master/mycotools/USAGE.md) for a guide.
<br />
# CITING
If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.
<img align="right" src="https://gitlab.com/xonq/mycotools/-/raw/master/misc/ablogo.png">
<br /><br /><br /><br /><br /><br /><br /><br /><br /><br /><br />
%prep
%autosetup -n mycotools-0.27.36
%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-mycotools -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.27.36-1
- Package Spec generated
|
