"-am True" edits the sequence

DarrenObbard commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

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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

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mtisza1 commented 2 years ago

Great. I'll close this issue for now.

mtisza1 / Cenote-Taker2

"-am True" edits the sequence #29

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