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jglamine / phamdb

Quickly create and modify Phamerator databases.
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CTG Not Valid Start Codon #8

Open PhageGuy opened 7 years ago

PhageGuy commented 7 years ago

Hi all,

In my database some of the genomes use CTG as their start codon. This appears to not be a valid start codon in PhamDB. Is there any way I can edit the parameters of acceptable start codons to include CTG so I can add these phages to the database?

Thanks!

jglamine commented 7 years ago

Hi, thanks for reporting this issue.

I'm not actively developing PhamDB at this point, but if you want to submit a pull request I'd be happy to merge it.

The relevant line of code to change would be here:

https://github.com/jglamine/phamdb/blob/master/pham/genbank.py#L531

I'm not sure what the implications are in terms of adding that as a default start codon - would this cause problems for people who don't want CTG as a start codon?

Another work around would be to not use CTG as your start codon, but I'm aware that this isn't really helpful advice.

PhageGuy commented 7 years ago

Thanks for the response!

If I were to change the code would the change be implemented immediately, or would I have to redownload docker or something along those lines? Also, I believe that any organism that doesn't aim to have CTG as a start simply wouldn't. Start codons are highly conserved so I couldn't see a situation where someone who doesn't already want to use CTG would have an organism who's start is CTG and then gets through the filter via this change.

Thanks again

jglamine commented 7 years ago

You could make the change on your own computer and then publish your own docker image.

If I merged the change I could publish the docker image.

I'm fine with adding CTG as a start codon, worst case scenario some people accidentally have it as a start codon and don't notice.

On Oct 18, 2017 10:03 AM, "PhageGuy" notifications@github.com wrote:

Thanks for the response!

If I were to change the code would the change be implemented immediately, or would I have to redownload docker or something along those lines? Also, I believe that any organism that doesn't aim to have CTG as a start simply wouldn't. Start codons are highly conserved so I couldn't see a situation where someone who doesn't already want to use CTG would have an organism who's start is CTG and then gets through the filter via this change.

Thanks again

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jglamine/phamdb/issues/8#issuecomment-337621856, or mute the thread https://github.com/notifications/unsubscribe-auth/AA0sE-5v9QrQ3OczWrNNNWucpPew_UAdks5sthNJgaJpZM4P9BQX .

PhageGuy commented 7 years ago

Ok great!

So being I am a biologist rather than a computer scientist what if anything would I need to do for you so that the code can be changed to allow CTG as a valid start?

Thanks again for your help!

jglamine commented 7 years ago

Sorry for the late reply! Unfortunately I don't have a lot of free time to help walk you through the steps.

If there's someone in your organization who is familiar with computer science or software development, you might want to ask them for help. They'll need to know about git and Github at a minimum, and knowledge of Python and Docker would also be useful.

PhageGuy commented 6 years ago

Hi jglamine,

Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG.

Thanks!

jglamine commented 6 years ago

Ok, I'll take a look this weekend.

On Wed, Nov 8, 2017 at 10:59 AM, PhageGuy notifications@github.com wrote:

Hi jglamine,

Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG.

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jglamine/phamdb/issues/8#issuecomment-342882962, or mute the thread https://github.com/notifications/unsubscribe-auth/AA0sE9jzWOv9aAqhuUQbwKKFA8DQpHZjks5s0d30gaJpZM4P9BQX .

PhageGuy commented 6 years ago

Thanks so much!

Bobby Weisensee

Gettysburg College 18'

Merck & Co. Medical Oncology Intern

Kustos, Theta Chapter, Sigma Chi

From: James Lamine notifications@github.com Sent: Wednesday, November 8, 2017 8:09:20 PM To: jglamine/phamdb Cc: Robert A. Weisensee; Author Subject: Re: [jglamine/phamdb] CTG Not Valid Start Codon (#8)

Ok, I'll take a look this weekend.

On Wed, Nov 8, 2017 at 10:59 AM, PhageGuy notifications@github.com wrote:

Hi jglamine,

Just bumping on the issue thread as well that I made the merge request so that the docker image can be published with CTG.

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jglamine/phamdb/issues/8#issuecomment-342882962, or mute the thread https://github.com/notifications/unsubscribe-auth/AA0sE9jzWOv9aAqhuUQbwKKFA8DQpHZjks5s0d30gaJpZM4P9BQX .

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PhageGuy commented 6 years ago

Good evening, just bumping for the merge request with CTG to complete our database

Thanks!

jglamine commented 6 years ago

I've merged you change, but I'm running into a bunch of errors trying to publish a new image - it's been two years, so some stuff which used to work doesn't anymore. I'd love to help, but I don't really have the time or energy to work through these issues.

My advice is to find a workaround, perhaps by editing your genbank files or using legacy phamerator without phamdb.