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haotianteng / Chiron

A basecaller for Oxford Nanopore Technologies' sequencers
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Parameter inconsistency in `read_raw_data_sets()` #82

Closed franrodalg closed 5 years ago

franrodalg commented 5 years ago

Hi, The call to read_raw_data_sets in train_test.py:

https://github.com/haotianteng/Chiron/blob/70c14bccd3316bd1e84619961b8c883139354d1c/chiron/train_test.py#L61

seems to be inconsistent with the signature of the function in chiron_input.py:

https://github.com/haotianteng/Chiron/blob/70c14bccd3316bd1e84619961b8c883139354d1c/chiron/chiron_input.py#L415

This causes a TypeError exception to be thrown:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: read_raw_data_sets() got an unexpected keyword argument 'valid_reads_num'

Note that also the positional arguments don't match.

I haven't tried using chiron_cnn_train.py, but I suspect it will also cause an issue there:

https://github.com/haotianteng/Chiron/blob/b013416def86a06fb54fd66bf481fb536b1db284/chiron/chiron_cnn_train.py#L57-L59

Cheers, Fran

haotianteng commented 5 years ago

Hi, please don't use chiron_cnn_train.py and chiron_train_test.py these two are scripts no longer used. Use chiron_rcnn_train.py instead. I will remove those two scripts.