Hi, Love the package, I'm keen to try it out for myself. Just wante

Not python 3 friendly about basset HOT 2 OPEN

davek44 commented on September 25, 2024 2

Not python 3 friendly

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Comments (2)

onceupon commented on September 25, 2024 1

i met the same problem using the docker image, with Python 2.7.6.
But seems to be solved by editing the file Basset/src/seq_hdf5.py, line 81-89,
adding int() to test_count, train_count and valid_count

    train_count = seqs.shape[0] - test_count - valid_count
    train_count = int(batch_round(train_count, options.batch_size))
    print >> sys.stderr, '%d training sequences ' % train_count
 
    test_count = int(batch_round(test_count, options.batch_size))
    print >> sys.stderr, '%d test sequences ' % test_count
 
    valid_count = int(batch_round(valid_count, options.batch_size))
    print >> sys.stderr, '%d validation sequences ' % valid_count

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CesarArenas-Mena commented on September 25, 2024

I guess the error in line 92 of current seq_hdf5.py while running python 2.7.5 is related. Onceupon, could your request a pull?

[ca445@cbsugpu01 bassetfiles]$ python /usr/local/Basset-0.1.0/src/seq_hdf5.py -r -c -v 3000 -t 3000 learn_cd4.fa lt.txt learn_cd4.h5
85261 training sequences
3000 test sequences
3000 validation sequences
Traceback (most recent call last):
  File "/usr/local/Basset-0.1.0/src/seq_hdf5.py", line 130, in <module>
    main()
  File "/usr/local/Basset-0.1.0/src/seq_hdf5.py", line 92, in main
    train_seqs, train_targets = seqs[i:i+train_count,:], targets[i:i+train_count,:]
TypeError: slice indices must be integers or None or have an __index__ method

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