%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 ![build](https://gitlab.com/antunderwood/fastadist/badges/master/pipeline.svg) ![coverage](https://gitlab.com/antunderwood/fastadist/badges/master/coverage.svg?job=coverage) [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 ![build](https://gitlab.com/antunderwood/fastadist/badges/master/pipeline.svg) ![coverage](https://gitlab.com/antunderwood/fastadist/badges/master/coverage.svg?job=coverage) [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 ![build](https://gitlab.com/antunderwood/fastadist/badges/master/pipeline.svg) ![coverage](https://gitlab.com/antunderwood/fastadist/badges/master/coverage.svg?job=coverage) [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 - 1.0.1-1 - Package Spec generated