"-am True" edits the sequence

[DarrenObbard]

I want to annotate a sequence that I am confident of. It is a densovirus, with ITRs that have internal repeat structure. I do not want cenote-take to reorientate or edit the sequence before annotating it. However, even when I run "-am True" it (mis)identifies the sequence as circular, and reverse complements it before annotating it.

How do I make it JUST annotate the sequence?

[mtisza1]

Hey Darren,

There is no way to prevent the rotation/clipping of the DTRs as of now. I'm now working on a patch that will include an option for this. Basically, the new option will allow labeling of detected DTRs but it won't rotate or clip the sequence.

[mtisza1]

Hey Darren,

I have added an option --wrap which you can set to False in order to get sequences that are not clipped or rotated. You'll have to update Cenote-Taker 2 to v2.1.5 per the instructions. You can set this in any mode, not just -am True mode.

I hope this helps, and I'm happy to fix any further issues.

Mike

[DarrenObbard]

Fantastic! Thank you - this has arrived at exactly the right moment for a project I'm working on!

-- Darren Obbard ***@***.*** Institute of Evolutionary Biology University of Edinburgh Room 2.09, Ashworth 2, Charlotte Auerbach Road Edinburgh EH9 3FL Office 0131 651 7781 Mobile: 07968 838 635 http://obbard.bio.ed.ac.uk/ 🕑 I work flexibly, and I collaborate with people in many different time zones. Please do not feel obliged to reply to this email outside of your own working hours. -------------------------------------------------------------------

-----Original Message----- From: Mike Tisza ***@***.*** Sent: 09 May 2022 19:57 To: mtisza1/Cenote-Taker2 ***@***.***> Cc: OBBARD Darren ***@***.***>; Author ***@***.***> Subject: Re: [mtisza1/Cenote-Taker2] "-am True" edits the sequence (Issue #29) This email was sent to you by someone outside the University. You should only click on links or attachments if you are certain that the email is genuine and the content is safe. Hey Darren, I have added an option --wrap which you can set to False in order to get sequences that are not clipped or rotated. You'll have to update Cenote-Taker 2 to v2.1.5 per the instructions. You can set this in any mode, not just -am True mode. I hope this helps, and I'm happy to fix any further issues. Mike — Reply to this email directly, view it on GitHub <#29 (comment)- 1121460989> , or unsubscribe <https://github.com/notifications/unsubscribe- auth/AJKOROBRXZE53V6OSKQ7CL3VJFNXXANCNFSM5QGCD3RA> . You are receiving this because you authored the thread. <https://github.com/notifications/beacon/AJKOROCYLOO5X3AGLOBKVSLVJFNX XA5CNFSM5QGCD3RKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVX HJKTDN5WW2ZLOORPWSZGOILMCF7I.gif> Message ID: <mtisza1/Cenote- ***@***.***>

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[mtisza1]

Great. I'll close this issue for now.