docs: add documentation #222
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| # TODO example | ||
| even though it's not public (it should be?) |
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I only see this method used in this class. If there's code similar to this in other places, we can move to utility functions
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| Try GRCh38 first, then GRCh37. | ||
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| # TODO example for this? |
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Did you want to add examples in here or new issue?
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Remaining TODO
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docs/source/transcript_selection.rst
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| * "Validating reference sequences" # TODO what does this mean? | ||
| * "Validating exon structure" # TODO what does this mean? |
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@korikuzma can you clarify these two lines? They're taken from the previous markdown docs file
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IIRC validating reference sequences means ensuring actual reference sequence matches expected reference sequence for a given ac/pos. Exon structure has to deal with ensuring exon numbers are the same.
| If unable to find a match on GRCh38, this method will then attempt to drop down | ||
| to GRCh37. | ||
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| # TODO example for inputs that demonstrate this? |
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@korikuzma do you have an example set of inputs handy for this?
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Not off the top of my head. We can make a separate issue if needed.
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(sorry, this duplicates a comment you had above. Probably not necessary if there isn't a good example available -- I was just trying to illustrate different code branches based on input)
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No worries. It is good to have an example and see if our test suite covers it. I just don't know off the top of my head and would have to dig into the test data
close #209 , address #11
Because of how many different things CST can do, I tried to embed a lot of explanation/instructions directly in the API reference rather than writing it out separately.
psycopg2and is also unhappy with every one of my attempts to install the binary manually. I've gone ahead and just done a basic manual test, but the logging won't be as pretty.