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|
%global _empty_manifest_terminate_build 0
Name: python-FastaDist
Version: 1.0.1
Release: 1
Summary: Package to calculate a distance matrix from a multiple sequence file
License: MIT
URL: https://pypi.org/project/FastaDist/
Source0: https://mirrors.aliyun.com/pypi/web/packages/1c/b2/8f441111d5608155558652b13c0636a2d9009f7a0d4eb0e540b12e868ab3/FastaDist-1.0.1.tar.gz
BuildArch: noarch
Requires: python3-biopython
Requires: python3-bitarray
Requires: python3-parmap
Requires: python3-tqdm
Requires: python3-dendropy
%description
## FastaDist
[Github repository](https://gitlab.com/antunderwood/fastadist)
This small utility package will calculate number of differences between all samples in a fasta alignment file.
It will count any position where there is a G,A,T or C (case insensitive) in both sequences that differ as 1 SNV.
Output formats are a square distance matrix in tsv, csv or phylip formats
It is fast since it first converts sequences to bit arrays and then uses fast bit operations to calculate the differences.
On a mid-range laptop a distance matrix was produced in 11 minutes from a 764 sequence alignment of length 1,082,859 using -p 1 and 4.5 minutes with -p 4
#### Installation
FastaDist is available as [PyPi](https://pypi.org/project/FastaDist/) package for Python3
```
pip3 install fastadist
```
#### Usage
```
usage: fastadist [-h] -i ALIGNMENT_FILEPATH [-t TREE_FILEPATH] -o
OUTPUT_FILEPATH [-f FORMAT] [-p PARALLEL_PROCESSES] [-v]
A script to calculate distances by converting sequences to bit arrays.
Specify number of processes as -p N to speed up the calculation
optional arguments:
-h, --help show this help message and exit
-i ALIGNMENT_FILEPATH, --alignment_filepath ALIGNMENT_FILEPATH
path to multiple sequence alignment input file
-t TREE_FILEPATH, --tree_filepath TREE_FILEPATH
path to newick tree for distance matrix ordering
-o OUTPUT_FILEPATH, --output_filepath OUTPUT_FILEPATH
path to distance matrix output file
-f FORMAT, --format FORMAT
output format for distance matrix (one of tsv
[default], csv and phylip
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of parallel processes to run (default 1)
-v, --version print out software version
```
%package -n python3-FastaDist
Summary: Package to calculate a distance matrix from a multiple sequence file
Provides: python-FastaDist
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-FastaDist
## FastaDist
[Github repository](https://gitlab.com/antunderwood/fastadist)
This small utility package will calculate number of differences between all samples in a fasta alignment file.
It will count any position where there is a G,A,T or C (case insensitive) in both sequences that differ as 1 SNV.
Output formats are a square distance matrix in tsv, csv or phylip formats
It is fast since it first converts sequences to bit arrays and then uses fast bit operations to calculate the differences.
On a mid-range laptop a distance matrix was produced in 11 minutes from a 764 sequence alignment of length 1,082,859 using -p 1 and 4.5 minutes with -p 4
#### Installation
FastaDist is available as [PyPi](https://pypi.org/project/FastaDist/) package for Python3
```
pip3 install fastadist
```
#### Usage
```
usage: fastadist [-h] -i ALIGNMENT_FILEPATH [-t TREE_FILEPATH] -o
OUTPUT_FILEPATH [-f FORMAT] [-p PARALLEL_PROCESSES] [-v]
A script to calculate distances by converting sequences to bit arrays.
Specify number of processes as -p N to speed up the calculation
optional arguments:
-h, --help show this help message and exit
-i ALIGNMENT_FILEPATH, --alignment_filepath ALIGNMENT_FILEPATH
path to multiple sequence alignment input file
-t TREE_FILEPATH, --tree_filepath TREE_FILEPATH
path to newick tree for distance matrix ordering
-o OUTPUT_FILEPATH, --output_filepath OUTPUT_FILEPATH
path to distance matrix output file
-f FORMAT, --format FORMAT
output format for distance matrix (one of tsv
[default], csv and phylip
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of parallel processes to run (default 1)
-v, --version print out software version
```
%package help
Summary: Development documents and examples for FastaDist
Provides: python3-FastaDist-doc
%description help
## FastaDist
[Github repository](https://gitlab.com/antunderwood/fastadist)
This small utility package will calculate number of differences between all samples in a fasta alignment file.
It will count any position where there is a G,A,T or C (case insensitive) in both sequences that differ as 1 SNV.
Output formats are a square distance matrix in tsv, csv or phylip formats
It is fast since it first converts sequences to bit arrays and then uses fast bit operations to calculate the differences.
On a mid-range laptop a distance matrix was produced in 11 minutes from a 764 sequence alignment of length 1,082,859 using -p 1 and 4.5 minutes with -p 4
#### Installation
FastaDist is available as [PyPi](https://pypi.org/project/FastaDist/) package for Python3
```
pip3 install fastadist
```
#### Usage
```
usage: fastadist [-h] -i ALIGNMENT_FILEPATH [-t TREE_FILEPATH] -o
OUTPUT_FILEPATH [-f FORMAT] [-p PARALLEL_PROCESSES] [-v]
A script to calculate distances by converting sequences to bit arrays.
Specify number of processes as -p N to speed up the calculation
optional arguments:
-h, --help show this help message and exit
-i ALIGNMENT_FILEPATH, --alignment_filepath ALIGNMENT_FILEPATH
path to multiple sequence alignment input file
-t TREE_FILEPATH, --tree_filepath TREE_FILEPATH
path to newick tree for distance matrix ordering
-o OUTPUT_FILEPATH, --output_filepath OUTPUT_FILEPATH
path to distance matrix output file
-f FORMAT, --format FORMAT
output format for distance matrix (one of tsv
[default], csv and phylip
-p PARALLEL_PROCESSES, --parallel_processes PARALLEL_PROCESSES
number of parallel processes to run (default 1)
-v, --version print out software version
```
%prep
%autosetup -n FastaDist-1.0.1
%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-FastaDist -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.1-1
- Package Spec generated
|
