rammappy.align¶

`Aligner` ¶

The Aligner orchestrates the alignment process.

It encapsulates the alignment configuration and the index to map query sequences against reference targets.

Examples:

>>> from rammappy import Index, Aligner, Preset
>>> index = Index.build([(b"target1", b"ATGC...")])
>>> aligner = Aligner(index, preset=Preset.MapOnt)
>>> for mapping in aligner.map(b"query1", b"ATGC..."):
...     print(mapping.score)

`options` `property` ¶

Get the current mapping options.

Returns:

Name	Type	Description
`MapOptions`	`MapOptions`	A copy of the current mapping options.

`new(*args, **kwargs)` `builtin` ¶

Create and return a new object. See help(type) for accurate signature.

`from_fasta(path, preset=Ellipsis)` `staticmethod` ¶

Create an aligner from a FASTA file.

Parameters:

Name	Type	Description	Default
`path`	`PathLike`	The file path to the FASTA file.	required
`preset`	`Preset`	The preset configuration (e.g. `Preset.MapOnt`). Defaults to `Preset.MapOnt`.	`Ellipsis`

Returns:

Name	Type	Description
`Aligner`	`Aligner`	The initialized aligner object.

`from_index(path, preset=Ellipsis)` `staticmethod` ¶

Create an aligner from an index file.

Parameters:

Name	Type	Description	Default
`path`	`PathLike`	The file path to the saved index file.	required
`preset`	`Preset`	The preset configuration (e.g. `Preset.MapOnt`). Defaults to `Preset.MapOnt`.	`Ellipsis`

Returns:

Name	Type	Description
`Aligner`	`Aligner`	The initialized aligner object.

`load_junctions_bed(path)` `method descriptor` ¶

Load splice junctions from a BED file.

Parameters:

Name	Type	Description	Default
`path`	`PathLike \| str`	Path to the BED file.	required

`load_junctions_spsc(path, scale=None)` `method descriptor` ¶

Load splice junctions from a SPSC file.

Parameters:

Name	Type	Description	Default
`path`	`PathLike \| str`	Path to the SPSC file.	required
`scale`	`float \| None`	Optional scaling factor.	`None`

`map(query_name, query_seq)` `method descriptor` ¶

Maps a single query sequence sequentially to the targets.

Parameters:

Name	Type	Description	Default
`query_name`	`bytes`	The name of the query sequence.	required
`query_seq`	`bytes`	The query sequence.	required

Returns:

Name	Type	Description
`MappingIterator`	`MappingIterator`	An iterator over the generated mappings.

`map_batch(queries)` `method descriptor` ¶

Performs highly parallelized batch alignments mapping over multiple queries.

Bypasses the GIL to utilize multiple threads for parallelism (via Rayon).

Parameters:

Name	Type	Description	Default
`queries`	`list[tuple[bytes, bytes]]`	A list of tuples containing `(name, sequence)` as bytes.	required

Returns:

Type	Description
`list[MappingIterator]`	list[MappingIterator]: A list of iterators, one for each query sequence.

`seq(name, start=None, end=None)` `method descriptor` ¶

Returns the sequence for a given target name.

Parameters:

Name	Type	Description	Default
`name`	`str`	The name of the target sequence.	required
`start`	`int`	The 0-based start coordinate. Defaults to 0.	`None`
`end`	`int`	The 0-based end coordinate. Defaults to the end of the sequence.	`None`

Returns:

Name	Type	Description
`str`	`str`	The requested sequence.

Raises:

Type	Description
`ValueError`	If the sequence name is not found in the index.

`CigarElement` ¶

Structured CIGAR operation element (length and operation type).

Attributes:

Name	Type	Description
`len`	`int`	Operation length.
`op`	`CigarOp`	Operation type enum.