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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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specify genetic code? #38

Open nathanerank opened 3 years ago

nathanerank commented 3 years ago

Hi,

I would like to specify invertebrate mitochondrial genetic code (translation table = 5, I think). It looks like your program assumes standard genetic code and I see no where to alter that. Can I get it specified?

singing-scientist commented 3 years ago

Dear @nathanerank: thanks very much for this question and for your interest in SNPGenie. The unfortunate reality is that I hard-coded much of SNPGenie with respect to the standard code, such that implementing another code will be quite a big endeavor and likely to cause unforeseen errors. This was naive and I would have done it differently another time round, but unfortunately support for another code is beyond my bandwidth at the moment — but I will certainly keep this open and add it to my to-do list. I am truly sorry to have such a disappointing answer. I do hope implement a new instantiation of SNPGenie in coming years, in Python this time, and I will certainly include this option when I do. In the meantime, if you're willing to describe your data a bit, it's possible we could hack a quick solution.

nathanerank commented 3 years ago

Hi,

thanks for your quick response. It's reassuring for me to know that I didn't just miss it. I am working with mitochondrial data and the number of snps involved is actually pretty small. I will attach a copy of an alignment with the mt genome. My guess is that we can't get to the right kinds of substitutions without looking at every snp individually, which is what I will probably do if I can't find a script to do it. Thanks again and if you do issue a revision of the program I look forward to trying it!

best, Nathan

On Thu, Aug 13, 2020 at 12:28 AM Chase W. Nelson notifications@github.com wrote:

Dear @nathanerank https://github.com/nathanerank: thanks very much for this question and for your interest in SNPGenie. The unfortunate reality is that I hard-coded much of SNPGenie with respect to the standard code, such that implementing another code will be quite a big endeavor and likely to cause unforeseen errors. This was naive and I would have done it differently another time round, but unfortunately support for another code is beyond my bandwidth at the moment — but I will certainly keep this open and add it to my to-do list. I am truly sorry to have such a disappointing answer. I do hope implement a new instantiation of SNPGenie in coming years, in Python this time, and I will certainly include this option when I do. In the meantime, if you're willing to describe your data a bit, it's possible we could hack a quick solution.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chasewnelson/SNPGenie/issues/38#issuecomment-673311498, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP6USEZBHP2Y4CPHBXQT5I3SAOIYFANCNFSM4P3WPVBA .

singing-scientist commented 3 years ago

Hey Nathan @nathanerank ! Thanks again. I actually don't see an attachment — was it perhaps left off by accident? If you're working off a multiple sequence alignment, there may be other programs that can easily do what you need. Let me know.