getTIRs Class

getTIRs

getTIRs(
    fasta_file: str,
    flankdist: int = 10,
    minid: float = 80,
    minterm: int = 10,
    minseed: int = 5,
    diagfactor: float = 0.3,
    mites: bool = False,
    report: str = 'split',
    temp: Optional[str] = None,
    keeptemp: bool = False,
    alignTool: str = 'nucmer',
    verbose: bool = True,
) -> Generator[SeqRecord, None, None]

Align elements to self and attempt to identify TIRs.

Processes sequences to identify Terminal Inverted Repeats (TIRs) by performing self-alignment. Can optionally construct synthetic Miniature Inverted-repeat Transposable Elements (MITEs).

PARAMETER	DESCRIPTION
`fasta_file`	Path to the multifasta file containing sequence records. TYPE: `str`
`flankdist`	Maximum distance from element start for TIR candidates, by default 10. TYPE: `int` DEFAULT: `10`
`minid`	Minimum identity between terminal repeat pairs, by default 80. TYPE: `float` DEFAULT: `80`
`minterm`	Minimum length for a terminal repeat to be considered, by default 10. TYPE: `int` DEFAULT: `10`
`minseed`	Minimum seed length for nucmer, by default 5. TYPE: `int` DEFAULT: `5`
`diagfactor`	Diagonal factor for nucmer, by default 0.3. TYPE: `float` DEFAULT: `0.3`
`mites`	Whether to attempt to construct synthetic MITEs, by default False. TYPE: `bool` DEFAULT: `False`
`report`	Reporting mode for TIRs ('split', 'external', 'internal', 'all'), by default 'split'. TYPE: `str` DEFAULT: `'split'`
`temp`	Path to the temporary directory, by default None. TYPE: `str` DEFAULT: `None`
`keeptemp`	Whether to keep the temporary directory after processing, by default False. TYPE: `bool` DEFAULT: `False`
`alignTool`	Alignment tool to use ('nucmer' or 'blastn'), by default 'nucmer'. TYPE: `str` DEFAULT: `'nucmer'`
`verbose`	Whether to print verbose output, by default True. TYPE: `bool` DEFAULT: `True`

YIELDS	DESCRIPTION
`SeqRecord`	Segments of the sequence based on the reporting mode: - 'split': TIRs and internal regions separately - 'external': Only TIRs - 'internal': Only internal regions - 'all': Original sequences plus all segments

Notes

When mites=True, the function will also yield synthetic MITEs constructed by joining the identified TIRs.

options: members: - init

getLTRs Class

getLTRs

getLTRs(
    fasta_file: str,
    flankdist: int = 10,
    minid: float = 80,
    minterm: int = 10,
    minseed: int = 5,
    diagfactor: float = 0.3,
    report: str = 'split',
    temp: Optional[str] = None,
    keeptemp: bool = False,
    alignTool: str = 'nucmer',
    verbose: bool = True,
) -> Generator[SeqRecord, None, None]

Align elements to self and attempt to identify LTRs.

Processes sequences to identify Long Terminal Repeats (LTRs) by performing self-alignment and filtering results.

PARAMETER	DESCRIPTION
`fasta_file`	Path to the multifasta file containing sequence records. TYPE: `str`
`flankdist`	Maximum distance from element start for LTR candidates, by default 10. TYPE: `int` DEFAULT: `10`
`minid`	Minimum identity between terminal repeat pairs, by default 80. TYPE: `float` DEFAULT: `80`
`minterm`	Minimum length for a terminal repeat to be considered, by default 10. TYPE: `int` DEFAULT: `10`
`minseed`	Minimum seed length for nucmer, by default 5. TYPE: `int` DEFAULT: `5`
`diagfactor`	Diagonal factor for nucmer, by default 0.3. TYPE: `float` DEFAULT: `0.3`
`report`	Reporting mode for LTRs ('split', 'external', 'internal', 'all'), by default 'split'. TYPE: `str` DEFAULT: `'split'`
`temp`	Path to the temporary directory, by default None. TYPE: `str` DEFAULT: `None`
`keeptemp`	Whether to keep the temporary directory after processing, by default False. TYPE: `bool` DEFAULT: `False`
`alignTool`	Alignment tool to use ('nucmer' or 'blastn'), by default 'nucmer'. TYPE: `str` DEFAULT: `'nucmer'`
`verbose`	Whether to print verbose output, by default True. TYPE: `bool` DEFAULT: `True`

YIELDS	DESCRIPTION
`SeqRecord`	Segments of the sequence based on the reporting mode: - 'split': LTRs and internal regions separately - 'external': Only LTRs - 'internal': Only internal regions - 'all': Original sequences plus all segments

options: members: - init