biotransformers.utils.msa_utils

`biotransformers.utils.msa_utils`¶

`get_translation`() → Dict[int, Any]	get translation dict to convert unused character in MSA
`read_sequence`(filename: str) → Tuple[str, str]	Reads the first (reference) sequences from a fasta or MSA file.
`remove_insertions`(sequence: str) → str	Removes any insertions into the sequence.
`read_msa`(filename: str, nseq: int) → List[Tuple[str, str]]	Reads the first nseq sequences from an MSA file,
`get_msa_list`(path_msa: Optional[str]) → List[str]	Get all files of the msa folder and check file format
`get_msa_lengths`(list_msa: List[List[Tuple[str, str]]], nseq: int) → List[int]	Get length of an MSA list
`msa_to_remove`(path_msa: str, n_seq) → List[str]	Get list of msa with less than nseq sequence

biotransformers.utils.msa_utils.get_translation() → Dict[int, Any]¶: get translation dict to convert unused character in MSA

biotransformers.utils.msa_utils.read_sequence(filename: str) → Tuple[str, str]¶: Reads the first (reference) sequences from a fasta or MSA file.

biotransformers.utils.msa_utils.remove_insertions(sequence: str) → str¶: Removes any insertions into the sequence. Needed to load aligned sequences in an MSA.

biotransformers.utils.msa_utils.read_msa(filename: str, nseq: int) → List[Tuple[str, str]]¶: Reads the first nseq sequences from an MSA file, automatically removes insertions.

biotransformers.utils.msa_utils.get_msa_list(path_msa: Optional[str]) → List[str]¶

Get all files of the msa folder and check file format

Parameters: path_msa (Optional[str]) – path of the folder with a3m file

biotransformers.utils.msa_utils.get_msa_lengths(list_msa: List[List[Tuple[str, str]]], nseq: int) → List[int]¶

Get length of an MSA list

All MSA must have at least nseq in msa

Parameters

list_msa (List[List[Tuple[str,str]]]) – list of MSA. MSA is a list of tuple
nseq –

Returns

[description]

Return type

List[int]

biotransformers.utils.msa_utils.msa_to_remove(path_msa: str, n_seq) → List[str]¶

Get list of msa with less than nseq sequence