MGEmasker 0.1.3

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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
3. 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

Usage

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