Limit to subpeak regions for motif scanning (and output them).

[j-andrews7]

Pretty simple with pyfaidx, something like:

import pyfaidx

def extract_sequences_from_bed(fasta_path, bed_path, output_path):
    # Open the FASTA file
    fasta = pyfaidx.Fasta(fasta_path)

    # Open the output file
    with open(output_path, 'w') as output_file:
        # Open the BED file
        with open(bed_path, 'r') as bed_file:
            for line in bed_file:
                fields = line.strip().split('\t')
                chrom = fields[0]
                start = int(fields[1])
                end = int(fields[2])
                # Use pyfaidx to extract the sequence
                sequence = fasta[chrom][start:end]
                # Write the sequence to the output file
                output_file.write(f'>{chrom}:{start}-{end}\n')
                output_file.write(str(sequence) + '\n')

Actually probably want two output files, one in BED format, the other in FASTA format.