mkt.databases.app.sequences.SequenceAlignment

class mkt.databases.app.sequences.SequenceAlignment(str_kinase: str, dict_color: dict[str, str], bool_mismatch: bool = True, bool_klifs: bool = True, bool_reverse: bool = True, obj_kinase: KinaseInfo | None = None)

Bases: object

Class to generate sequence alignments for kinase sequences.

__init__(*args: Any, **kwargs: Any) → None

Methods

__eq__(other)	Return self==value.
__post_init__()
_map_single_alignment(idx_start, idx_end, ...)	Map the indices of the alignment to the original sequence.
_parse_start_end_values(start_or_end, str_seq)	Parse the start and end keys for the alignment.
generate_alignments()	Iterate through the KinaseInfo object and generate a list of sequences and a list of colors.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
__pydantic_config__
bool_klifs	If True, shade KLIFS pocket residues using KLIFS pocket colors, by default True.
bool_mismatch	If True, show mismatches with UniProt seq in crimson, by default True.
bool_reverse	Whether or not to reverse order of inputs
obj_kinase	KinaseInfo object from which to extract sequences (loaded from str_kinase if not provided).
str_kinase	Gene name of the kinase for which to generate the sequence alignment.
dict_color	Color dictionary for sequence viewer.

static _map_single_alignment(idx_start: int, idx_end: int, str_uniprot: str, seq_obj: str | None = None)

Map the indices of the alignment to the original sequence.

Parameters:

• idx_start (int) – Start index of the alignment.

• idx_end (int) – End index of the alignment.

• str_uniprot (str) – Full canonical UniProt sequence.

• seq_obj (str | None) – Seq obj provided by user or database. If None, use UniProt sequence. This is the case for Pfam, which only provides start and end indices.

Returns:

Output string with the alignment mapped to the original sequence.

Return type:

str

_parse_start_end_values(start_or_end: Any, str_seq: str) → int | None

Parse the start and end keys for the alignment.

Parameters:

• start_or_end (Any) – The start or end key to parse.

• str_seq (str) – The sequence to parse - only used if start_or_end callable.

Returns:

The parsed start or end index, or None if not found.

Return type:

int | None

bool_klifs: bool = True

If True, shade KLIFS pocket residues using KLIFS pocket colors, by default True.

bool_mismatch: bool = True

If True, show mismatches with UniProt seq in crimson, by default True.

bool_reverse: bool = True

Whether or not to reverse order of inputs

dict_color: dict[str, str]

Color dictionary for sequence viewer.

generate_alignments() → dict[str, str | list[str]]

Iterate through the KinaseInfo object and generate a list of sequences and a list of colors.

Returns:

A dictionary with keys DICT_ALIGNMENT containing the sequences and a list of colors per residue.

Return type:

dict[str, str | list[str]]

obj_kinase: KinaseInfo | None = None

KinaseInfo object from which to extract sequences (loaded from str_kinase if not provided).

str_kinase: str

Gene name of the kinase for which to generate the sequence alignment.