squigglepull scale and pA_convert functions does not work with multifast5 files

[Akanksha2511]

Hi James,

Just wondering if the scale and pA_convert functions in squigglepull are not yet available for multi fast5 files?

Thanks, Akanksha

[Psy-Fer]

Hello Akanksha,

It seems you are right. How lazy of me. Would you like me to update that for you?

James

[Akanksha2511]

Hi James,

could you please update it.

Thanks, Akanksha

[Psy-Fer]

Hello Akanksha.

The latest commit to SquigglePull should add both pA_convert and scale (z-scaling or med-mad scaling) to the outputs for multi-fast5 files.

Let me know if there are any issues.

James

[Akanksha2511]

Thanks, James. I am getting an error saying " for i in pA_sig: TypeError: 'int' object is not iterable". Command I am giving is python SquigglePull.py --multi -c -p

[Psy-Fer]

Ahh that was my bad.

Please pull the latest change and try again. Should work this time.

[Akanksha2511]

Awesome. Thanks for the quick response, James

[Akanksha2511]

Hi James,

Sorry to bother you but I get the same error as before if I use both -s and -c options.

The error says

for i in pA_sig: TypeError: 'int' object is not iterable

Thanks, Akanksha

[Psy-Fer]

Hello Akanksha,

Sorry about that. There was an issue with numpy translating float vs int. That should be fixed now.

I would suggest caution scaling already pA converted data. But it's very use case dependant.

Let me know if you have any other troubles.

James