Dataloader Draft#24
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ssenan merged 9 commits intopinellolab:codebasefrom Oct 19, 2022
ssenan:codebase
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mateibejan1
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Oct 18, 2022
lucapinello
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Oct 18, 2022
src/data/sequence_dataloader.py
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| from torch.utils.data import Dataset, DataLoader | ||
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| class SequenceDatasetBase(Dataset): | ||
| def __init__(self, data_path, transform=None): |
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maybe add here sequence_lenght=200 so we have flexibility later
lucapinello
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Oct 18, 2022
src/data/sequence_dataloader.py
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| # Iterating through DNA sequences from dataset and one-hot encoding all nucleotides | ||
| current_seq = self.data["raw_sequence"][index] | ||
| if 'N' not in current_seq: | ||
| X_seq = np.array(self.one_hot_encode(current_seq, ['A','C','T','G'], 200)) |
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here we can replace 200 with self.sequence_length
lucapinello
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Oct 18, 2022
src/data/sequence_dataloader.py
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| return X_seq, X_cell_type | ||
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| # Function for one hot encoding each line of the sequence dataset | ||
| def one_hot_encode(self, seq, alphabet, max_seq_len): |
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replace max_seq_len with sequence_length
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The dataloader is now up to date with all changes regarding one-hot encoding of components and renamed to suit our new folder structure.
See #17 for earlier discussion.