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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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Q: More complete documentation on Python(3) bindings? #259

Closed sklages closed 3 years ago

sklages commented 3 years ago

Just wondering if you have some more complete documentation giving some more explanations on the methods available and used in each "Module"?

.... the docs are just showing some examples on how to get some data from InterOp.

Currently it is faster and more convenient for me to parse the various output csv/xml files created by bcl2fastq or bcl-convert.

ezralanglois commented 3 years ago

Ya, this has been in our backlog for a while. What we have been slowly working on are more intuitive methods for accessing the data.

For example, there will be a new module that ties together the various io to make reading in the metrics easier, with proper doc strings and examples in the doc string that double as unit tests to ensure the examples don't go out of date.

Another example would be generating the imaging table. We have a single function to wrap this that we use internally.

We do plan to release these simplified functions in the future, but I don't have a timeline yet.

Ideally, we would provide a set of 5-10 Python functions that cover most use cases that are bullet proof and rely on only numpy and pandas.

sklages commented 3 years ago

Sounds great :-) thanks for the information.

sklages commented 3 years ago

It is (for me) not obvious what has been changed in the python binding and where (version 1.1.22)? Using pip install interop on Manjaro Linux still lists 1.1.21 as current version.

What am I missing?

ezralanglois commented 3 years ago

Looks like it failed to deploy. Unfortunately, this is not something we test in the PR. I will look into it.

ezralanglois commented 3 years ago

I just retagged it, should trigger the builds again. I don't see anything obvious as to why it failed.

ezralanglois commented 3 years ago

Looks like it deployed for Linux http://illumina.github.io/interop/python_binding.html See New simplified interface

sklages commented 3 years ago 
Installing collected packages: interop
  Attempting uninstall: interop
    Found existing installation: interop 1.1.21
    Uninstalling interop-1.1.21:
      Successfully uninstalled interop-1.1.21
Successfully installed interop-1.1.22

Now it works fine. The New simplified interface looks promising :+1: thanks a lot.