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huihui1126 / drugSim-pathway

Drug similarity evaluation based on pathway fingerprints
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Data required to run `PathSim.py` is missing #3

Closed cthoyt closed 3 years ago

cthoyt commented 3 years ago

The PathSim.py script references several data files that are neither included in this repository, automatically downloaded during runtime, nor documented how the user can get them. Here are the offending lines:

https://github.com/huihui1126/drugSim-pathway/blob/6042830395bbf4dfbdea8b72dd4de11bac25e269/PathSim.py#L10-L14

As it is, this script is unusable so the results can neither be reproduced nor verified

huihui1126 commented 3 years ago

extracRelation.pl is the main program of this project which call the pathsim.py inside it. So the input files of pathsim.py were produced by extracRelation.pl. And they were deleted as the intermediate results. https://github.com/huihui1126/drugSim-pathway/blob/080178a6801a75a4df5a382935eb9fff9043ca18/v1.1/extracRelation.pl#L101