Closed Rungetf closed 2 years ago
Hi there,
Thanks for reaching out and pointing out those bugs regarding to our codes and sorry for the inconvenience caused by the problems when using them. We have fixed these as soon as possible. Details are listed below.
Overall, all the errors have been corrected from our end. We really appreciated your careful work and we look forward you could use the tool.
Thanks
Hi, Thanks for the fast reply and the fixes! I appreciate linking the data and just tested with your provided files. Everything works fine now, thanks.
Hi,
I wanted to run UFold on some own test data (the original TS1 data accompanying the SPOT-RNA publication. After putting the respective files in
.bpseq
format into thedata/TS1
folder, I tried running theprocess_data_newdataset.py
script to produce thecPickle
files needed. I used the following commandwhich produces a
NameError
becauseone_hot_matrix
is not defined. This results from an Error in theawk
call in line 55, which cannot find the files due to a missing/
. Changing the command tofixes the
NameError
but results in aValueError
in the list comprehension in line 69. I finally changed line 55 fromto
and ran the call without trailing
/
, which fixes the Errors. However, I got stucked in thepdb.set_trace()
call in line 127. Unfortunately, without this call there is still aFileNotFoundError
due to a hard-coded path in the finalcPickle
dump that needs to be fixed (setting the path tofile_dir + '.cPickle'
produces the desired output file).After that I tried running the
ufold_test.py
script to evaluate the performance of UFold on the produced data but ran into similar issues:pdb.set_trace()
drive
ufold_train_alldata.pt
,ufold_train_pdbfinetune.pt
, andufold_train.pt
unet_train_on_merge_alldata_98.pt
andufold_train_on_pdb_contrafold_pdbfinetune_99.pt
in lines 229 and 231, respectivelyModuleNotFoundError
when setting--nc True
becausee2efold
cannot be found (import in line 25)And maybe some more that I currently don't remember.
However, I finally managed to run the script on TS1 but the results were very poor with the provided models (in the range of 3e-13 f1-scores). Probably there is more that needs to be fix that I'm not aware of yet.
After that, I switched to the Webserver but got empty files for download with the first two sample sequences I tested (both .ct and dot-bracket files; with and without non-canonical pairs).
From a user perspective this was a very bad experience and code accompanying such a recent NAR publication should at least have running example scripts that can be used out-of-the-box I think.
Having said that, I'm looking forward to running your code once the issues have been fixed.
Best regards