automatic import of python-mgemasker

1 files changed, 365 insertions, 0 deletions

diff --git a/python-mgemasker.spec b/python-mgemasker.spec
new file mode 100644
index 0000000..805d0e1
--- /dev/null
+++ b/python-mgemasker.spec
@@ -0,0 +1,365 @@
+%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
+                        <COMMAND> -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
+                        <COMMAND> -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
+                        <COMMAND> -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 <Python_Bot@openeuler.org> - 0.1.13-1
+- Package Spec generated