Reading history

[manulera]

Hello,

Really nice library, I was wondering if you could give some hint on how to decode the history of the files. I see that the byte indicator is number 7, but how did you figure out how to decode the other fields? Is there any reference somewhere of the encoding, or you just trial and errored?

Thanks!

[merv1n34k]

Hey!

In case you're still interested, I have recently decided to take on this project. As of now, my current parser can decode ~90% of all blocks in the file, including history nodes and compressed DNA sequences.

I am not sure about the author's approach, but I was doing good ol' trial and error with hex editor, I found one resource who also attempted to reverse engineer it, see it on my GH page.

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

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Cheers

[manulera]

Hi @merv1n34k I was able to parse the history as well, the problem is how to access the sequences that the history refers to. For example, if the main sequence is a PCR product, did you figure out how to access the sequence of the template (upstream in the history)?

[merv1n34k]

@manulera from what I see you don't need history node at all, this information is located in history tree (type:7). This is a nested xml, where the outer node tag is the latest node and the most nested is the earliest. For each node the modification action is written in node's class operation, e.g.

<Node name="Your.dna" type="DNA" seqLen="777" strandedness="double" ID="111" circular="0"
upstreamModification="Unmodified" downstreamModification="Unmodified" resurrectable="1"
operation="amplifyFragment">

Then oligos and polymerase contained as separate tags. All history nodes have id from 0 to n, and 0 is the latest, so probably this is enough to find the referenced sequence.

IMHO, history nodes (type:11) are existed soley for node resurrection, which usually contains 2 variations:

1. Sequence (type:1/0/32/21 - compressed dna/dna/rna/protein) + Node information (type:30) - nested SnapGene file without magic header
2. Node modifier (type:29) - as I understand this is a modifier for the action on the node, this may contain information you are interested in, as well as history tree, but I haven't looked yet.

Is this what you was looking for?

BTW, have you managed to decode enzyme cutters library (type:3) or mystery blocks (type:13 and type:27)? These are the last blocks I can't figure out. Once I decode them I can create a proper SnapGene writer.

EDIT: To get the actual sequence of the template you do need to see the node content, usually SnapGene compresses its sequences into octet format (e.g. 2 bits per base - 00:01:10:11-G:A:C:T). I have managed to decompress them, but this part also have strange flags which I can't figure out, if you want to give a hand on this issue I can give more verbose explanation.

[manulera]

Hi @merv1n34k thanks for the detailed followup. Honestly I don't think I would be of much help. These decoding things are definitely above my paygrade, but I am happy to help with tasks that don't involve trying to figure out the binary data. You can ping me in an issue where you think I can help.

[merv1n34k]

@manulera great, thank you! I am planning to use my reader for another project - biological data browser for local construct libraries, which do involves parsing SnapGene files to make searches at least feature-, sequence- and history-aware.

As of now it's all concepts in alpha state, but when I make it more or less playable I can ping you if you're interested. That project is build on FastAPI + MongoDB, and I am also searching for nice python library to add "biological awareness" to the browser.

[manulera]

Hi @merv1n34k, you may want to look into OpenCloning, the project I am working on.

OpenCloning is an Open Source web application for DNA engineering. Think of it as an open source SnapGene / Benchling with an intuitive interface (see example) that also supports automation via Python scripting. The key features are:

• 🦠 Support for methods like homologous recombination, CRISPR, and Cre-Lox — which Snapgene and Benchling don’t support.
• 🧬 Import gene sequences directly from NCBI by name and plasmids from Addgene.
• 🧰 Design and track cloning strategies using Gibson, Golden Gate, Gateway, etc.
• 🤖 Automate routine tasks (cloning/primer design) via scripts or forms.
• 💾 Export as GenBank or FASTA, or store the full history of the project (see example).

🌐 opencloning.org  | 📽️ Demo video

[merv1n34k]

Looks interesting. I will check it out, thanks!