%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