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biocore / micronota

annotation pipeline for microbial genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
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add infernal and HMMer wrappers #7

Closed RNAer closed 8 years ago

RNAer commented 8 years ago

related to issue #6

mortonjt commented 8 years ago

I'll get started on the HMMER wrapper

RNAer commented 8 years ago

awesome!

On Tue, Oct 13, 2015 at 5:43 PM, mortonjt notifications@github.com wrote:

I'll get started on the HMMER wrapper

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-147893020.

RNAer commented 8 years ago

@mortonjt , have you got a chance to start working on it? it is probably good to issue pull request of your code as work in progress?

mortonjt commented 8 years ago

No I haven't gotten around to working on it. Will push probably sometime this weekend.

On Thu, Oct 15, 2015 at 11:04 AM, Zech Xu notifications@github.com wrote:

@mortonjt https://github.com/mortonjt , have you got a chance to start working on it? it is probably good to issue pull request of your code as work in progress?

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-148474680.

mortonjt commented 8 years ago

btw, it looks like infernal is already in bfillings

RNAer commented 8 years ago

needs lots of update. I am doing it.

On Thu, Oct 15, 2015 at 12:01 PM, mortonjt notifications@github.com wrote:

btw, it looks like infernal is already in bfillings https://github.com/biocore/burrito-fillings/blob/master/bfillings/infernal.py

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-148489281.

wasade commented 8 years ago

@RNAer, would it make sense to also include ssu-align? It's based on Infernal but includes SSU specific models, or is there a better method at the moment for annotating SSU?

RNAer commented 8 years ago

RNAmmer? but it is a perl script and I am reluctant to use, although it is very highly cited. I plan to just use infernal to do that as it speeds up quite a lot in recent versions. obviously SSU-Align is more accurate, but SSU-Align is designed for aligning many SSU sequences, not for genome annotation. It assumes there's at most 1 SSU in each input sequence, which defeat the purpose.

wasade commented 8 years ago

I thought it would annotate all SSU in a sequence? I'm vaguely remembering this now...

On Tue, Oct 20, 2015 at 11:46 AM, Zech Xu notifications@github.com wrote:

RNAmmer? but it is a perl script and I am reluctant to use, although it is very highly cited. I plan to just use infernal to do that as it speeds up quite a lot in recent versions. obviously SSU-Align is more accurate, but SSU-Align is designed for aligning many SSU sequences, not for genome annotation. It assumes there's at most 1 SSU in each input sequence, which defeat the purpose.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149644865.

RNAer commented 8 years ago

nope. I got that from Eric.

On Tue, Oct 20, 2015 at 10:48 AM, Daniel McDonald notifications@github.com wrote:

I thought it would annotate all SSU in a sequence? I'm vaguely remembering this now...

On Tue, Oct 20, 2015 at 11:46 AM, Zech Xu notifications@github.com wrote:

RNAmmer? but it is a perl script and I am reluctant to use, although it is very highly cited. I plan to just use infernal to do that as it speeds up quite a lot in recent versions. obviously SSU-Align is more accurate, but SSU-Align is designed for aligning many SSU sequences, not for genome annotation. It assumes there's at most 1 SSU in each input sequence, which defeat the purpose.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149644865.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149645411.

wasade commented 8 years ago

Would it be possible to just use the models from SSU-Align?

On Tue, Oct 20, 2015 at 11:49 AM, Zech Xu notifications@github.com wrote:

nope. I got that from Eric.

On Tue, Oct 20, 2015 at 10:48 AM, Daniel McDonald < notifications@github.com> wrote:

I thought it would annotate all SSU in a sequence? I'm vaguely remembering this now...

On Tue, Oct 20, 2015 at 11:46 AM, Zech Xu notifications@github.com wrote:

RNAmmer? but it is a perl script and I am reluctant to use, although it is very highly cited. I plan to just use infernal to do that as it speeds up quite a lot in recent versions. obviously SSU-Align is more accurate, but SSU-Align is designed for aligning many SSU sequences, not for genome annotation. It assumes there's at most 1 SSU in each input sequence, which defeat the purpose.

— Reply to this email directly or view it on GitHub <https://github.com/biocore/micronota/issues/7#issuecomment-149644865 .

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149645411.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149645745.

RNAer commented 8 years ago

don't think so. I remember the CM model is the same (otherwise, the model in Rfam would be updated with it), but ssualign does something smart in aligning the seq.

wasade commented 8 years ago

oh, lame

On Tue, Oct 20, 2015 at 11:52 AM, Zech Xu notifications@github.com wrote:

don't think so. I remember the CM model is the same (otherwise, the model in Rfam would be updated with it), but ssualign does something smart in aligning the seq.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/issues/7#issuecomment-149646501.