Biopython

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Here is a step wise procedure of performing the given task.
(Step 1):Download Fasta File. Retrieve genome data by downloading a Fasta file from the NCBI server.
(Step 2):Create BED File.This BED file contains sequence identifiers, start, and end positions.
(Step 3):Extracting Specific Sequence.Here i have extracted the sequence with identifier  "gi|58576|gb|X52226|Influenza" and saved it separately.
(Step 4):Eliminate or remove the selected sequence with identifier "gi|58576|gb|X52226|Influenza" from the original Fasta file.
(Step 5):Reverse Complement.Obtaining the reverse complement of the extracted sequence.
(Step 6):Insert Nucleotide Change.Introducing a single nucleotide change at 1st position of the sequence. 
(Step 7):Appending the Modified Sequence back to the original Fasta file.
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from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import requests

# Step 1: Download the fasta file
url = "https://ftp.ncbi.nlm.nih.gov/genomes/INFLUENZA/influenza.fna"
filename = "influenza.fna"
with open(filename, 'wb') as file:
    file.write(requests.get(url).content)

print("step1 completed successfully")

# Step 2: Create a bed file
bed_filename = "influenza.bed"
with open(bed_filename, 'w') as bed_file:
    for record in SeqIO.parse(filename, "fasta"):
        bed_file.write(f"{record.id}\t1\t{len(record.seq)}\n")

print("step2 completed successfully")

# Step 3: Extract the subsequence
identifier_to_extract = "gi|58576|gb|X52226|Influenza"
output_filename = "step3_extracted_sequence.fasta"

with open(filename, 'r') as fasta_file, open(output_filename, 'w') as output_file:
    for record in SeqIO.parse(fasta_file, "fasta"):
        if record.id == identifier_to_extract:
            SeqIO.write([record], output_file, "fasta")
            break

print("step3 completed successfully")

# Step 4: Remove the extracted subsequence from the original file
sequences_to_keep = [record for record in SeqIO.parse(filename, "fasta") if record.id != identifier_to_extract]
with open(filename, 'w') as updated_fasta_file:
    SeqIO.write(sequences_to_keep, updated_fasta_file, "fasta")

print("step4 completed successfully")

# Step 5: Perform reverse complement on the extracted subsequence
with open(output_filename, 'r') as extracted_file:
    extracted_record = SeqIO.read(extracted_file, "fasta")
    reversed_complement_sequence = str(extracted_record.seq.reverse_complement())

reversed_complement_filename = "step5_reversed_complement_sequence.fasta"
with open(reversed_complement_filename, 'w') as reversed_complement_file:
    reversed_complement_record = SeqRecord(Seq(reversed_complement_sequence),
                                           id=extracted_record.id + "_reversed_complement",
                                           description="Reversed complement sequence")
    SeqIO.write([reversed_complement_record], reversed_complement_file, "fasta")

print("step5 completed successfully")

# Step 6: Perform manipulation by inserting 1 nucleotide change
modified_sequence = 'X' + reversed_complement_sequence[1:]

modified_filename = "step6_modified_sequence.fasta"
with open(modified_filename, 'w') as modified_file:
    modified_record = SeqRecord(Seq(modified_sequence),
                                id=extracted_record.id + "_modified",
                                description="Modified sequence")
    SeqIO.write([modified_record], modified_file, "fasta")

print("step6 completed successfully")

# Step 7: Append the changed sequence back into the main fasta file at the top
updated_sequences = [modified_record] + sequences_to_keep

with open(filename, 'w') as fasta_file:
    SeqIO.write(updated_sequences, fasta_file, "fasta")

print("step7 completed successfully")
print("All the Output files created successfully and ready to view.")