Intervene venn –save-overlaps not working

[jharrison0123]

Hi,

Running the command intervene venn -I <bed files> --names=<> generated a Venn diagram but when I add --save-overlaps to get the intersections I get an error regardless if I do the default (False) or True to get the intersections.

intervene venn -I --names=<> --save-overlaps False usage: intervene [options] intervene: error: unrecognized arguments: False

intervene venn -I --names=<> --save-overlaps True usage: intervene [options] intervene: error: unrecognized arguments: True

[asntech]

The --save-overlaps argument does not require a parameter. By simply adding --save-overlaps without True or False will work.

[jharrison0123]

Hi Aziz,

Thank you for your quick reply. When I only have the —save-overlaps argument, it only generates a folder with a .pdf of the Venn diagram.

Get Outlook for iOShttps://aka.ms/o0ukef

---

From: Aziz Khan @.> Sent: Saturday, May 14, 2022 1:55:12 AM To: asntech/intervene @.> Cc: Harrison, Jessica @.>; Author @.> Subject: Re: [asntech/intervene] Intervene venn –save-overlaps not working (Issue #49)

The --save-overlaps argument does not require a parameter. By simply adding --save-overlaps without True or False will work.

— Reply to this email directly, view it on GitHubhttps://github.com/asntech/intervene/issues/49#issuecomment-1126657550, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO2HCX4BKQT3FXAXUBISRWDVJ5E5BANCNFSM5V4PBD2Q. You are receiving this because you authored the thread.Message ID: @.***>

[asntech]

What version you're using? And can you try upset with intervene upset -i *.bed --save-overlaps

[jharrison0123]

I am using intervene version 0.6.5. I was getting an error because I did "-save-overlaps" instead of "--save-overlaps". Thank you for your help! It is a very helpful tool.

Jessica

[asntech]

That's great you figured it out, Jessica!

Cheers!