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streptomyces / ripper

Searching for precursor peptide genes for ribosomally synthesized and post-translationally modified peptides (RiPPs).
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ripper_local readme #1

Open TomNEU opened 4 years ago

TomNEU commented 4 years ago

Hello,

I've been getting a lot of use out of the main ripper program, but would really like to start running it on some local metagenomic datasets of mine. Am I correct in thinking that is what ripper_local is for?

If it is, what exactly should I be supplying as the input? I've been trying to run it with a query file containing my RTE of interest in fasta format and a GenBank file of a test organism that I know has the RiPP I'm looking for, but to no avail.

As you can probably tell I'm a bit of a novice, so apologies if this isn't the right place to ask this question.

Thanks, Tom

streptomyces commented 2 years ago

Hi Tom, Try https://hub.docker.com/repository/docker/streptomyces/ripdock-local Cheers Govind

AltairDemond414 commented 1 year ago

Hello, What if more than one bait protein in my GenBank file? I can only see one output in the result (ripout), I know there is a precursor peptide in my GenBank file. But I can't see it in the SSN. What can I do to solve the problem? Thanks, Eric

streptomyces commented 1 year ago

Hi Eric, If you are not already using the Docker image then please do so (https://hub.docker.com/repository/docker/streptomyces/ripdock-local). The code and the functionality in the Docker image is slightly different from the code in this repository. If this does not solve your problem then I will have to ask someone. I have written the code based on requirements described to me. I also runs tests on sample input data but I am not a regular user of ripper. I will ask someone in the lab who uses ripper regularly about your problem and get back to you. Cheers Govind

AltairDemond414 commented 1 year ago

Thank you very much! Actually, the ripdock-local is what I use before. The problem is from it.😂 Anyway, thanks for your reply. Your script is great.

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发件人: @.> 发送时间: 2023年1月16日 1:55 收件人: @.> 抄送: @.>; @.> 主题: Re: [streptomyces/ripper] ripper_local readme (#1)

Hi Eric, If you are not already using the Docker image then please do so (https://hub.docker.com/repository/docker/streptomyces/ripdock-local). The code and the functionality in the Docker image is slightly different from the code in this repository. If this does not solve your problem then I will have to ask someone. I have written the code based on requirements described to me. I also runs tests on sample input data but I am not a regular user of ripper. I will ask someone in the lab who uses ripper regularly about your problem and get back to you. Cheers Govind

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