Simulations #129
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Simulations #129
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suragnair
reviewed
Mar 26, 2025
src/grelu/data/dataset.py
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| Args: | ||
| seqs: DNA sequences as intervals, strings, integer encoded or one-hot encoded. | ||
| fixed_pattern: A subsequence to insert in the center of each background sequence. | ||
| variable_pattern: A subsequence to insert into the background sequences at |
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variable_pattern is a bit misleading as it suggested the pattern itself is changing-- maybe moving_pattern?
suragnair
reviewed
Mar 27, 2025
src/grelu/data/dataset.py
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| max_pos = self.seq_len - self.moving_pattern_len + 1 | ||
| excl_start = self.fixed_pattern_start - self.moving_pattern_len + 1 | ||
| excl = range(excl_start, self.fixed_pattern_end) | ||
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| positions = [x for x in range(0, max_pos, self.stride) if x not in excl] |
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This logic is shared with Tiling Shuffle Dataset. Should it be abstracted out? Do you see it being used again?
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Good idea, I will break it out
suragnair
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Mar 27, 2025
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Note: these changes were made on top of #118 which should be merged first.
Expanded the simulations module along with tutorial and tests.
shuffle_tilesto shuffle successive tiles along an input sequence, e.g. for enhancer discoverymarginalize_pattern_spacingto insert motifs at different distances in shuffled background sequencesplot_position_effectin `visualize to plot the outputs of these functionsObviously, there is a lot of unnecessary duplication and complexity in the dataset module. This will be cleaned up in later PRs.