未提供项目说明
MGEmasker的Python项目详细描述
MGE掩蔽器
此包根据富序列文件（Genbank或EMBL）中的注释查找mge。 有3个子命令
- find_mges在富序列文件中搜索带有提示与MGE相关元素的文本注释的特性
- mask_mges将伪基因组比对的区域与使用find_mges命令生成的GFF文件中的区域进行屏蔽
- default_matches显示搜索MGE时使用的默认regex模式。这可以通过在find\umges命令中使用-m参数提供一个格式类似的文件来覆盖
死亡模式匹配
.*\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
安装
仅Python3
^{pr2}$或者
pip3 install MGEmasker
用法
usage: mge_masker [-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
查找使用情况
usage: mge_masker 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
掩码用法
usage: mge_masker 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)
- 项目
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