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liwenran / DeepTACT

DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning
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IOError: [Errno 2] No such file or directory: 'hg19.fa' #2

Open sdjebali opened 4 years ago

sdjebali commented 4 years ago

Hello, Thanks for the nice paper and the associated code.

I wanted to test it on the monocyte example doing first: python $indir/DataPrepare.py $indir/Mon P-E

but I had this error message File "/..../DeepTACT/DataPrepare.py", line 119, in main() File "/.../DeepTACT/DataPrepare.py", line 115, in main sequence_dict = SeqIO.to_dict(SeqIO.parse(open('hg19.fa'), 'fasta')) IOError: [Errno 2] No such file or directory: 'hg19.fa'

So could you please provide the hg19.fa or tell me where to find the one you used? (masked or not, what type of masking... ?). And also tell me where I should place it in the tree structure ?

Also I think you should indicate that your code works with python2 and not python3.

Best regards, Sarah Djebali

Licko0909 commented 4 years ago

You can search for hg19.fa directly in the Google browser. NCBI can be downloaded as I remember.Or you can download it here: http://deepsea.princeton.edu/media/code/expecto/resources.tar.gz, this is the form a complete set of DeepSEA folder, there are hg19. Fa