How do I re-write data into a snapgene file?

[li1311139481]

from snapgene_reader import snapgene_file_to_dict, snapgene_file_to_seqrecord
from Bio.Seq import Seq

file_path = "/cluster/facility/hlhuang/zifeng001/snapgene/LMB.dna"
dictionary = snapgene_file_to_dict(file_path)
seqrecord = snapgene_file_to_seqrecord(file_path)

for i, value in dictionary.items():
    # print(value)
    if isinstance(value, list):
        # print(value)
        for anno in value:
            # print(anno)
            if anno["name"] == "sgRNA":
                # print(anno["name"])
                start = anno["start"]
                end = anno["end"]

dictionary["seq"] = dictionary["seq"].replace(
    dictionary["seq"][start:end], new_sgRNA_sequence
)

I used this code to find and replace the sequence. Then I want to regenerate the snapgene file. What should I do？

[merv1n34k]

Hey!

For this you will need to assemble file structure in its native format. This shouldn't be a problem, once you can decode file blocks.

SnapGene file is a TLV binary file, meaning type-length-value, so the file is just composed of blocks with this format. Ideally, you just need to:

1. Extract block(s) you want to modify
2. Modify things you need
3. Encode it into original format
4. Update block(s) length and value
5. Save file

I haven't tried this yet, but my project aims to develop complete reader and writer for SnapGene files, currently I have made only the reader.

If you plan to implement a writer I will appreciate a contribution :D

Source: https://github.com/merv1n34k/SnapGeneConverter