search

bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
46 stars 15 forks source link

Input prodigal GFF/output prophage call in GFF format? #10

Closed jdwinkler-lanzatech closed 4 years ago

jdwinkler-lanzatech commented 4 years ago

Hi,

Thanks for your work on this tool-just found it in a search for prophage annotation pipelines and I like your approach versus the other tools in the field. Some request that would make it easier to integrate into our annotation pipeline, if possible:

  1. Is it possible to provide the Prodigal annotations as an input? We already routinely run prodigal, so it would be helpful to avoid duplication.
  2. Is it possible to output a GFF file with the prophage calls in addition to html/tsv?

No worries if these are not possible.

PollyTikhonova commented 4 years ago

I'm very sorry for long time no answer, I was intended to implement the features you asked for, but occasionally it took much mofre time then I realized. So, I wanted to say that I heard you we are in process. By the way, thanks for your feedback! Stay tuned)

jdwinkler-lanzatech commented 4 years ago

No problem! Thank you for your help.

From: PollyTikhonova notifications@github.com Sent: Friday, September 27, 2019 10:31 AM To: bobeobibo/phigaro phigaro@noreply.github.com Cc: James Winkler james.winkler@lanzatech.com; Author author@noreply.github.com Subject: Re: [bobeobibo/phigaro] Input prodigal GFF/output prophage call in GFF format? (#10)

-- EXTERNAL SENDER --

I'm very sorry for long time no answer, I was intended to implement the features you asked for, but occasionally it took much mofre time then I realized. So, I wanted to say that I heard you we are in process. By the way, thanks for your feedback! Stay tuned)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbobeobibo%2Fphigaro%2Fissues%2F10%3Femail_source%3Dnotifications%26email_token%3DALP33DH3ZWUBX276QHNTCO3QLYRLXA5CNFSM4IUSDCT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ZITYQ%23issuecomment-535988706&data=02%7C01%7Cjames.winkler%40lanzatech.com%7Ce2c5788fd4a04be44e3e08d7435fb873%7C213ac3b92d864223aa17c7727e2e175f%7C0%7C0%7C637051950723478446&sdata=FqSPez5FnfAqP8b8gzl%2BExUNfkNmnyIOynZQiSfeEmI%3D&reserved=0, or mute the threadhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FALP33DE4GIS255PT4UKQDDDQLYRLXANCNFSM4IUSDCTQ&data=02%7C01%7Cjames.winkler%40lanzatech.com%7Ce2c5788fd4a04be44e3e08d7435fb873%7C213ac3b92d864223aa17c7727e2e175f%7C0%7C0%7C637051950723478446&sdata=0ooQHDl2fEoIgK0ypwPc9HySdVXWpP%2BP39qk9xesf10%3D&reserved=0.

James Winkler PhD | LanzaTech Computational Biologist Modeler james.winkler@lanzatech.com Phone: +1 (847) 324-2400 Mobile: 8045 Lamon Ave, Suite 400, Skokie, IL 60077 http://www.lanzatech.com http://www.lanzatech.com/

The information in this e-mail and any attachments is confidential to LanzaTech. If you are not the intended recipient, you are not authorized to disclose, copy, distribute or retain this information. P Be carbon smart. Please consider the environment before printing this email

PollyTikhonova commented 4 years ago

Do you mean that gff file should contain data about genes from prophage regions? or just info about start and end of a prophage in a gff format?

jdwinkler-lanzatech commented 4 years ago

I think I meant just start, stop orientation (if possible), and then maybe the name/p-value of the best match in the info section?

PollyTikhonova commented 4 years ago

Outputs in gff and bed formats are implemented in version 2.1.9

jdwinkler-lanzatech commented 4 years ago

Thank you! I'll give it a shot in the next few days.

jdwinkler-lanzatech commented 3 years ago

Hi, apologies for the (massively) delayed response. Works great for me!

PollyTikhonova commented 3 years ago

@jdwinkler-lanzatech glad to hear that!