Cobalt Wrapper Class

Overview

The Cobalt class serves as a Python wrapper for COBALT (Constraint-based Multiple Alignment Tool), a software tool used for multiple sequence alignment (MSA). This class enables the integration of COBALT's alignment capabilities within Python applications, facilitating the automated processing of sequence alignments.

Methods

__init__(self)

Initializes a new instance of the Cobalt class. This method prepares the environment for running COBALT alignments but does not require any parameters.

run(self, hits_file: Union[str, Path], aligned_file: Union[str, Path], cobalt_home: str) -> bool

Executes the COBALT alignment process on a specified set of sequences.

  • Parameters:
  • hits_file: The path to the input file containing sequence data to be aligned, typically the output from a BLASTP search. This can be a str or Path object.
  • aligned_file: The path to the output file where the aligned sequences will be saved, in multi-FASTA format. This can be a str or Path object.

  • cobalt_home: The file system path to the COBALT installation directory, which contains the COBALT executable.

  • Returns:

  • bool: Returns True if the COBALT alignment completes successfully, otherwise returns False.