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|
%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
|
