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bschiffthaler / seidr

Toolkit to create crowd networks
GNU General Public License v3.0
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Warn instead of fail when `seidr neighbours` encounters a gene absent from the header #16

Closed nicolasDelhomme closed 4 years ago

nicolasDelhomme commented 5 years ago

Maybe the default behaviour of seidr neighbours should be to warn about a gene missing in the header rather than fail.

[ ERROR ][ 2019-09-02T13:57:48 ][ seidr ]: Gene AT5G40212 not found in header.

Because we typically filter genes prior to generate the network, we cannot assume that all genes might be in the header and as such the ground for the error will rather be a constant than an exception. It does not harm to ignore the missing genes and proceed with the rest of the provided IDs.

bschiffthaler commented 5 years ago

I will add a flag (--lax ?) for this and #15 That way the default behaviour is strict with regard to correctness, but users whoa re confident can circumvent it.

bschiffthaler commented 4 years ago

Now default behavious for seidr view and seidr neighbours. You can revert to old behaviour (failure on bad lookup) with seidr neighbours --strict or seidr view --strict