pxblat.Client(host: str, port: int, seq_dir: str | Path, *, ttype: str = 'dna', qtype: str = 'dna', dots: int = 0, nohead: bool = False, min_score: int = 30, min_identity: float = 90.0, output_format: str = 'psl', max_intron: int = 750000, is_dynamic: bool = False, genome: str | None = None, genome_data_dir: str | None = None, server_option: ServerOption | None = None, wait_ready: bool = False, wait_timeout: int = 60, parse: bool = True)[source]

A class for querying a gfServer using a separate thread.

Parameters:
host : str

The hostname or IP address of the server.

port : int

The port number of the server.

seq_dir : Union[str, Path]

The directory where sequence data is stored.

ttype : str, optional

Database type. One of ‘dna’, ‘prot’, ‘dnax’. Default is ‘dna’.

qtype : str, optional

Query type. One of ‘dna’, ‘rna’, ‘prot’, ‘dnax’, ‘rnax’. Default is ‘dna’.

dots : int, optional

Output a dot every N query sequences. Default is 0.

nohead : bool, optional

If True, suppresses 5-line psl header. Default is False.

min_score : int, optional

Sets minimum score. Default is 30.

min_identity : float, optional

Sets minimum sequence identity (in percent). Default is 90.

output_format : str, optional

Controls output file format. One of ‘psl’, ‘pslx’, ‘axt’, ‘maf’, ‘sim4’, ‘wublast’, ‘blast’, ‘blast8’, ‘blast9’. Default is ‘psl’.

max_intron : int, optional

Sets maximum intron size. Default is 750000.

is_dynamic : bool, optional

If True, the client is expected to interact with a dynamic gfServer. Default is False.

genome : Optional[str], optional

The genome name when using a dynamic gfServer. Defaults to None.

genome_data_dir : Optional[str], optional

The root directory containing the genome data files for a dynamic gfServer. Defaults to None.

server_option : Optional[ServerOption], optional

The server options to use if a server is not provided. Defaults to None.

wait_ready : bool, optional

If True, wait until the server is ready before sending a query. Default is False.

wait_timeout : int, optional

The number of seconds to wait for the server to be ready. Default is 60.

parse : bool, optional

If True, parse the result of the query. Default is True.

Raises:

ValueError – If any of the input values are invalid.

Examples

>>> from pxblat import Client
>>> host = "localhost"
>>> port = 65000
>>> seq_dir = "."
>>> two_bit = "./test_ref.2bit"
>>> client = Client(
...     host=host,
...     port=port,
...     seq_dir=seq_dir,
...     min_score=20,
...     min_identity=90,
... )