ChimeraGenerator.py

#!python
#
# Code 2023 by Jamel Simpson
"""Routines to generate chimeric sequences."""

from pathlib import Path

def sequence_splice(fasta_file, boundary_tuple, python_index='Yes'):
    """Takes a fasta sequence and returns the section of the sequence between indexes specified by the boundary one and two,
    as well as the sequence with the specified section replaced with a '-'.
    ABCDEFGH, boundary_one=0, boundary_two=3 Returns ABC and -DEFGH
    The residue at boundary_two is the first residue not included in the splice. If you're using alignment_finder, this is already accounted for."""
    if python_index == 'No':
        boundary_two = boundary_tuple[1] - 1
        boundary_one = boundary_tuple[0] - 1
    else:
        boundary_one = boundary_tuple[0]
        boundary_two = boundary_tuple[1]
    with open(fasta_file, "r") as fasta:
        sequence = ''.join([x for x in fasta if x[0] != '>' if x != '']).strip().replace('\n', '')
    # The spliced region between the 2 specified boundaries is the first sequence
    # in the list followed by the sequence with the spliced region replace by a '-'
    spliced_region = ''.join(sequence[boundary_one:boundary_two])
    non_spliced_region = sequence.replace(spliced_region, '-')
    return spliced_region, non_spliced_region


def chimera_sequence_creation(section_being_spliced_in, marked_sequence, mark_in_the_sequence='-'):
    """Returns a completed sequence after replacing the '-' in a marked sequence with another sequence fragment"""
    chimera_sequence = marked_sequence.replace(mark_in_the_sequence, section_being_spliced_in)
    return chimera_sequence


def fasta_creation(file_name, sequence, subunits):
    """Creates a fasta file with the given file_name, and replicates the sequence within it the specified number of times
    to create a homo multimer if subunits is greater than 1."""
    with open(file_name, 'w') as outfile:
        for _unused_x in range(subunits):
            outfile.write('>{0}\n{1}\n'.format(Path(file_name).stem, sequence))