%global _empty_manifest_terminate_build 0 Name: python-MGEmasker Version: 0.1.13 Release: 1 Summary: please add a summary manually as the author left a blank one License: MIT URL: https://pypi.org/project/MGEmasker/ Source0: https://mirrors.nju.edu.cn/pypi/web/packages/3f/0b/a6f655a5427e08ff6bf8401c4a6835e54ec11c892d4b1f2fea888068d892/MGEmasker-0.1.13.tar.gz BuildArch: noarch Requires: python3-biopython Requires: python3-rich %description ## MGE Masker This package finds MGEs based on annotations in a rich sequence file (Genbank or EMBL). There are 3 subcommands 1. **find_mges** Search a rich sequence file for features annotated with text that suggests a MGE-associated element 2. **mask_mges** Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command 1. **default_matches** Show the default regex patterns used when searching for MGEs. This can be overridden by providing a similarly formatted file using the -m parameter with the find_mges command ### Deafult patterns matched ``` .*\b[tT]ranspos .*\b[pP]hage .*\b[rR]epeat .*\b[rR]eptitive .*\b[iI]nsertion sequence .*\bIS .*\b[tT]n .*\b[iI]ntegr .*\b[Cc]onjug .*\b[Pp]lasmid ``` ### Installation Python3 only ``` pip install MGEmasker ``` or ``` pip3 install MGEmasker ``` ### Usage ``` usage: mgemasker [-h] {find_mges,mask_mges,default_matches} ... A module to find MGEs in a rich sequence file and mask regions corresponding to the MGEs in a pseudogenome alignment. The find_mges command searches a gbk or embl file for features that have MGE-associated annotations. It writes a GFF file containing the positions of the matched features. The mask_mges command takes a GFF file produced using the find_mges command and masks those regions in all sequences of a pseudogenome alignment based on the reference sequence used to find MGEs. positional arguments: {find_mges,mask_mges,default_matches} The following commands are available. Type mge_masker -h for more help on a specific commands find_mges Search a rich sequence file for features annotated with text that suggests a MGE-associated element mask_mges Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command default_matches Show the default regex patterns used when searching for MGEs optional arguments: -h, --help show this help message and exit ``` #### find_mges usage ``` usage: mgemasker find_mges [-h] -g GENOME_FILE_PATH [-f {genbank,embl}] [-i MERGE_INTERVAL] [-m MGE_FILE_PATH] optional arguments: -h, --help show this help message and exit -g GENOME_FILE_PATH, --genome_file_path GENOME_FILE_PATH path to a genome file -f {genbank,embl}, --file_format {genbank,embl} genome file format -i MERGE_INTERVAL, --merge_interval MERGE_INTERVAL The maximum distance between MGEs when performing the merging step (Default 1000bp) -m MGE_FILE_PATH, --mge_file_path MGE_FILE_PATH path to a file containing regex MGE annotations ``` #### mask_mges usage ``` usage: mgemasker mask_mges [-h] -f FASTA_PATH -g GFF_FILE_PATH [-m MASKING_CHARACTER] optional arguments: -h, --help show this help message and exit -f FASTA_PATH, --fasta_path FASTA_PATH path to either a single fasta reference or a pseudogenome alignment file -g GFF_FILE_PATH, --gff_file_path GFF_FILE_PATH path to a gff file containing MGE regions to be masked -m MASKING_CHARACTER, --masking_character MASKING_CHARACTER character used to mask (default: N) ``` %package -n python3-MGEmasker Summary: please add a summary manually as the author left a blank one Provides: python-MGEmasker BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-MGEmasker ## MGE Masker This package finds MGEs based on annotations in a rich sequence file (Genbank or EMBL). There are 3 subcommands 1. **find_mges** Search a rich sequence file for features annotated with text that suggests a MGE-associated element 2. **mask_mges** Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command 1. **default_matches** Show the default regex patterns used when searching for MGEs. This can be overridden by providing a similarly formatted file using the -m parameter with the find_mges command ### Deafult patterns matched ``` .*\b[tT]ranspos .*\b[pP]hage .*\b[rR]epeat .*\b[rR]eptitive .*\b[iI]nsertion sequence .*\bIS .*\b[tT]n .*\b[iI]ntegr .*\b[Cc]onjug .*\b[Pp]lasmid ``` ### Installation Python3 only ``` pip install MGEmasker ``` or ``` pip3 install MGEmasker ``` ### Usage ``` usage: mgemasker [-h] {find_mges,mask_mges,default_matches} ... A module to find MGEs in a rich sequence file and mask regions corresponding to the MGEs in a pseudogenome alignment. The find_mges command searches a gbk or embl file for features that have MGE-associated annotations. It writes a GFF file containing the positions of the matched features. The mask_mges command takes a GFF file produced using the find_mges command and masks those regions in all sequences of a pseudogenome alignment based on the reference sequence used to find MGEs. positional arguments: {find_mges,mask_mges,default_matches} The following commands are available. Type mge_masker -h for more help on a specific commands find_mges Search a rich sequence file for features annotated with text that suggests a MGE-associated element mask_mges Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command default_matches Show the default regex patterns used when searching for MGEs optional arguments: -h, --help show this help message and exit ``` #### find_mges usage ``` usage: mgemasker find_mges [-h] -g GENOME_FILE_PATH [-f {genbank,embl}] [-i MERGE_INTERVAL] [-m MGE_FILE_PATH] optional arguments: -h, --help show this help message and exit -g GENOME_FILE_PATH, --genome_file_path GENOME_FILE_PATH path to a genome file -f {genbank,embl}, --file_format {genbank,embl} genome file format -i MERGE_INTERVAL, --merge_interval MERGE_INTERVAL The maximum distance between MGEs when performing the merging step (Default 1000bp) -m MGE_FILE_PATH, --mge_file_path MGE_FILE_PATH path to a file containing regex MGE annotations ``` #### mask_mges usage ``` usage: mgemasker mask_mges [-h] -f FASTA_PATH -g GFF_FILE_PATH [-m MASKING_CHARACTER] optional arguments: -h, --help show this help message and exit -f FASTA_PATH, --fasta_path FASTA_PATH path to either a single fasta reference or a pseudogenome alignment file -g GFF_FILE_PATH, --gff_file_path GFF_FILE_PATH path to a gff file containing MGE regions to be masked -m MASKING_CHARACTER, --masking_character MASKING_CHARACTER character used to mask (default: N) ``` %package help Summary: Development documents and examples for MGEmasker Provides: python3-MGEmasker-doc %description help ## MGE Masker This package finds MGEs based on annotations in a rich sequence file (Genbank or EMBL). There are 3 subcommands 1. **find_mges** Search a rich sequence file for features annotated with text that suggests a MGE-associated element 2. **mask_mges** Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command 1. **default_matches** Show the default regex patterns used when searching for MGEs. This can be overridden by providing a similarly formatted file using the -m parameter with the find_mges command ### Deafult patterns matched ``` .*\b[tT]ranspos .*\b[pP]hage .*\b[rR]epeat .*\b[rR]eptitive .*\b[iI]nsertion sequence .*\bIS .*\b[tT]n .*\b[iI]ntegr .*\b[Cc]onjug .*\b[Pp]lasmid ``` ### Installation Python3 only ``` pip install MGEmasker ``` or ``` pip3 install MGEmasker ``` ### Usage ``` usage: mgemasker [-h] {find_mges,mask_mges,default_matches} ... A module to find MGEs in a rich sequence file and mask regions corresponding to the MGEs in a pseudogenome alignment. The find_mges command searches a gbk or embl file for features that have MGE-associated annotations. It writes a GFF file containing the positions of the matched features. The mask_mges command takes a GFF file produced using the find_mges command and masks those regions in all sequences of a pseudogenome alignment based on the reference sequence used to find MGEs. positional arguments: {find_mges,mask_mges,default_matches} The following commands are available. Type mge_masker -h for more help on a specific commands find_mges Search a rich sequence file for features annotated with text that suggests a MGE-associated element mask_mges Mask regions from a pseudogenome alignment with the regions in a GFF file produced using the find_mges command default_matches Show the default regex patterns used when searching for MGEs optional arguments: -h, --help show this help message and exit ``` #### find_mges usage ``` usage: mgemasker find_mges [-h] -g GENOME_FILE_PATH [-f {genbank,embl}] [-i MERGE_INTERVAL] [-m MGE_FILE_PATH] optional arguments: -h, --help show this help message and exit -g GENOME_FILE_PATH, --genome_file_path GENOME_FILE_PATH path to a genome file -f {genbank,embl}, --file_format {genbank,embl} genome file format -i MERGE_INTERVAL, --merge_interval MERGE_INTERVAL The maximum distance between MGEs when performing the merging step (Default 1000bp) -m MGE_FILE_PATH, --mge_file_path MGE_FILE_PATH path to a file containing regex MGE annotations ``` #### mask_mges usage ``` usage: mgemasker mask_mges [-h] -f FASTA_PATH -g GFF_FILE_PATH [-m MASKING_CHARACTER] optional arguments: -h, --help show this help message and exit -f FASTA_PATH, --fasta_path FASTA_PATH path to either a single fasta reference or a pseudogenome alignment file -g GFF_FILE_PATH, --gff_file_path GFF_FILE_PATH path to a gff file containing MGE regions to be masked -m MASKING_CHARACTER, --masking_character MASKING_CHARACTER character used to mask (default: N) ``` %prep %autosetup -n MGEmasker-0.1.13 %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-MGEmasker -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 31 2023 Python_Bot - 0.1.13-1 - Package Spec generated