MMseqs2

MMseqs2 module for the Rush Python client.

MMseqs2 generates multiple-sequence alignments (MSAs) from amino acid sequences.

Usage:

from rush import mmseqs2

paths = mmseqs2.search(["MKFLILLFNILCL..."]).save()

class rush.mmseqs2.Result

Parsed MMseqs2 results: one A3M text per input sequence.

alias of list[str]

class rush.mmseqs2.ResultPaths

Workspace paths for saved MMseqs2 A3M files.

alias of list[Path]

class rush.mmseqs2.ResultRef(msas)

Bases: object

Lightweight reference to MMseqs2 outputs in the Rush object store.

Parameters:

msas (list[RushObject])

classmethod from_raw_output(res)

Parse raw collect_run output into a ResultRef.

Parameters:

res (Any)

Return type:

ResultRef

fetch()

Download MMseqs2 outputs and parse into A3M strings.

Return type:

Result

save()

Download MMseqs2 outputs and save as A3M files to the workspace.

Return type:

ResultPaths

msas: list[RushObject]

rush.mmseqs2.search(sequences, prefilter_mode=None, sensitivity=None, expand_eval=None, align_eval=None, diff=None, qsc=None, max_accept=None, run_spec=RunSpec(gpus=1), run_opts=RunOpts())

Submit an MMseqs2 sequence search for the given amino acid sequences.

Returns a RushRun handle. Call .fetch() to get the parsed A3M results, or .save() to write them to disk.

Parameters:

• sequences (list[str])

• prefilter_mode (Literal['KMer', 'Ungapped', 'Exhaustive'] | None)

• sensitivity (float | None)

• expand_eval (float | None)

• align_eval (int | None)

• diff (int | None)

• qsc (float | None)

• max_accept (int | None)

• run_spec (RunSpec)

• run_opts (RunOpts)

Return type:

RushRun[ResultRef]