Adding separate query and test sequences

[nikhita-damaraju]

Hi,
I was wondering if there was a way to make the static plot for two separate sequences? As I understand it right now, it checks the identity of a sequence with itself.

[tchrisboles]

Same question as Nikhita above. Thanks.

[tchrisboles]

As in comparing pseudogenes or segdups on different chromosomes?

[nikhita-damaraju]

@tchrisboles , yes that could be one of the outcomes. I was thinking more along the lines of showing the alignment of query sequence to a reference sequence.

[alexsweeten]

Hi @nikhita-damaraju and @tchrisboles,

Sorry for the late response! I've added this functionality in the most recent update to ModDotPlot. To create an a vs. b style dotplot, add the --compare command line argument when creating static plots or using interactive mode.

[tchrisboles]

Great - will try it out soon. Thanks. Best regards, Chris Boles, Ph.D, Chief Scientific Officer Sage Science, Inc., 500 Cummings Center, Suite 2400, Beverly, MA 01915 Direct Office: +1-978-522-6284, Mobile: +1-781-856-2165 Company: +1-978-922-1832 ***@***.*** This e-mail may contain information that is confidential or privileged. If you are not the intended recipient, do not read, copy or distribute the e-mail or any attachments. Instead, please notify the sender and delete the e-mail and any attachments. Thank you.

…

On Wed, Jun 14, 2023 at 3:55 AM Alex Sweeten ***@***.***> wrote: Hi @nikhita-damaraju <https://github.com/nikhita-damaraju> and @tchrisboles <https://github.com/tchrisboles>, Sorry for the late response! I've added this functionality in the most recent update to ModDotPlot. To create an a vs. b style dotplot, add the --compare command line argument when creating static plots or using interactive mode. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH7SXXLDE6SZXIX4N3B2JATXLFU57ANCNFSM6AAAAAAXPYJRJU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[tchrisboles]

Sorry for the delay. Just tried A vs B dotplot with --compare-only option. Works great. Thanks.
Chris

[tchrisboles]

Actually, one other thing. What's the proper way to exit interactive mode?

[alexsweeten]

Running ctrl+C on the terminal ModDotPlot is being run on will exit interactive mode and kill the process.

Adding a proper exit button will make this cleaner. Will add this in the next version. Thanks and glad it's working well!

• Alex