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EnSpec / SpecDAL

Website landing page for SpecDAL project. https://specdal.github.io now redirects here.
MIT License
28 stars 17 forks source link

Let specdal_pipeline output raw data #9

Closed DancingQuanta closed 6 years ago

DancingQuanta commented 6 years ago

I am only interested in raw data and I find that specdal_pipeline output csv files like this

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pct_reflect,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

Can this script be more flexible as specdal_info in choosing measure_type?

DancingQuanta commented 6 years ago

I have been reading through the source code. So tgt_count is raw data I think. In order to make specdal_pipeline to use tgt_count, I have to put measure_type=tgt_count in both Collection() and Collection.read() in specdal_pipeline at lines https://github.com/EnSpec/SpecDAL/blob/f15b2040da2317dd77acbc253fb7101e1d4abf2f/bin/specdal_pipeline#L146 and https://github.com/EnSpec/SpecDAL/blob/f15b2040da2317dd77acbc253fb7101e1d4abf2f/bin/specdal_pipeline#L148

This made me think, why does Collection.read() not use the information such as measure_type passed to Collection()?

DancingQuanta commented 6 years ago

I think I should close this because this script is an example of how specdal library works. Now that I understand it!