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BINDetect not giving out error when the motif file is "deformed" #248
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Thank you for this issue - indeed it looks related to #78. There seems to be a bug in the reading of these files using biopython, which creates additional "empty" motifs with "_"-names. We have now changed it to manually parse and check the length, and will then write an error in case a deformed motif is found: The code is not thoroughly tested yet, but you can have a look already by installing the version directly from the dev branch as: After testing, the functionality will be included in the next version of TOBIAS. Hope that helps 🙏 |
Perfect, thanks so much! |
Might be a continuation of issue #78. When I tried to run BINDetect using "pfm" motif file created by gimmemotifs, i get a problem where
The pfm file looks something like:
For example, I have 1796 motifs in the pfm file, but I got the following warning:
And I got results with the directories named as such:
or
Maybe this pfm file is not a standard pfm file, but maybe it would be nice if BINDetect gives an error that the motif file is not standard.
My current workaround is to run
chen2meme
, because it seems that it is a chen motif file. Now BINDetect seems to work fine.The text was updated successfully, but these errors were encountered: