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arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
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Missing test data #1

Open mdshw5 opened 10 years ago

mdshw5 commented 10 years ago

I noticed that there is not test data containing a full Minion run. Could you please fix this?

arq5x commented 10 years ago

Will do so once I have some data that I am allowed to share.

stephenturner commented 10 years ago

+1 to this one. I may be able to add some shotgun metagenomic data in the near future, but not how sure that will be for instructional purposes.

mdshw5 commented 10 years ago

Just in case it wasn't obvious, this was only partially a joke issue.

stephenturner commented 10 years ago

must be dense - what's the joke? that minion/nanopore sequencing would be vaporware? not sure what MAP agreements look like, but as soon as i've confirmed i can release data i'll put some here.

nickloman commented 10 years ago

I will put some up, probably a full run will need to be hosted outside this repo though, as the files are quite large.

mdshw5 commented 10 years ago

"Full run" and "fix this" urgency were in jest. Seriously though, just part of a run would be fine for tool test data.

alexbw commented 10 years ago

+1 would love to see what it looks like

mdshw5 commented 10 years ago

Looks like @nickloman released some yesterday so maybe it could be linked from here?

nickloman commented 10 years ago

We could take a subset of these reads to serve for the basis of our test suite.

arq5x commented 10 years ago

I think that is a solid plan, but we want to either keep it very lightweight so that cloning the repo is easy, or we could have a test_data command that just downloads a more informaticve subset from Amazon S3. Or both.

mdshw5 commented 10 years ago

It looks like there is no testing framework in poretools currently, so maybe once there is it could be split:

  1. Unit tests that are for internal consistency and do not require external data
  2. Tests that require external data, and this data can be downloaded (and cached)
arq5x commented 10 years ago

Yep @mdshw5 - that is the way to go. We'll get there. Nick and I are both in crunch meeting and grant deadline time, but after the dust settles, we will take care of it.

gawbul commented 9 years ago

+1 to this! Need some test data for a homebrew-science formula I've been working on anyway, so will try kill 2 birds with one stone :smile:

See https://github.com/Homebrew/homebrew-science/pull/2300.

UPDATE: I've added some test data to the homebrew poretools package. Will write some tests for this in due course.

jeffhsu3 commented 8 years ago

Matt Loose has some data from his Read Until paper: https://github.com/mattloose/RUscripts . Seems pretty small and all the scripts seem to work on it.