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For example, I have 1796 motifs in the pfm file, but I got the following warning:
2023-12-16 10:23:46 (1569572) [INFO] Reading motifs from file
2023-12-16 10:23:47 (1569572) [INFO] - Read 5531 motifs
2023-12-16 10:23:47 (1569572) [WARNING] The motif output names (as given by --naming) are not unique.
2023-12-16 10:23:47 (1569572) [WARNING] The following names occur more than once: ['_']
2023-12-16 10:23:47 (1569572) [WARNING] These motifs will be renamed with '_1', '_2' etc. To prevent this renaming, please make the names of the input --motifs unique
And I got results with the directories named as such:
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: pip install git+https://github.com/loosolab/TOBIAS@dev
After testing, the functionality will be included in the next version of TOBIAS. Hope that helps 🙏
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: