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### Enformer Prediction (`enformer-prediction`) Predicts regulatory track activity for one or more DNA sequences. The tool accepts input in two forms. In exact-window form, each sequence is exactly 196,608 base pairs, the full Enformer model context, and is passed to the model directly. In target-range form, each sequence is longer than the model context and is paired with a target range, and the tool extracts the 196,608 base-pair context window that keeps the requested range inside the model's output bins. Each result carries the predicted activity matrix of shape 896 bins by the number of selected tracks, together with the coordinates that map the output bins back onto the source sequence. #### API Reference

Source DNA sequence(s) for Enformer inference. Each item is a sequence with an optional `target_range`, and a bare string is accepted. Without a `target_range` the sequence must already be the model context length. With one, the source must be long enough to extract a full window (no padding). DNA sequence -- an exact model-context window, or a longer source sequence paired with `target_range`. Optional sequence-relative span the tool must keep inside the model output bins. Windowing is all-or-nothing across a call: set `target_range` on every window or on none (see :func:`windows_target_ranges`).

Source Track indices to extract from the Enformer output. Species track head to use. Available options: `human`, `mouse` Number of sequences to process in each GPU batch. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device used for inference. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-sequence prediction results. Input DNA sequence that was scored. Length of the input sequence. Predicted signal matrix with shape `[896, num_tracks]`. Start coordinate of the Enformer input window in the source sequence. End coordinate of the Enformer input window in the source sequence. Source-sequence coordinate of the first Enformer output bin. Source-sequence coordinate immediately after the last Enformer output bin. Base pairs represented by each output bin. Target start coordinate supplied for this sequence. Target end coordinate supplied for this sequence. Track indices that were extracted. Species used for prediction (`"human"` or `"mouse"`).

#### Applications This tool is appropriate for analyses that relate noncoding DNA sequence to predicted regulatory activity. Representative applications include predicting the effect of a candidate variant by comparing the activity of the reference and alternate sequences, prioritizing noncoding variants for follow-up by the magnitude of their predicted regulatory change, screening designed or synthetic regulatory sequences for predicted promoter or enhancer activity, and surveying the predicted chromatin and expression landscape across a genomic locus of interest. #### Usage Tips * **Each input sequence must provide a full 196,608 base-pair model context.** A sequence supplied in exact-window form must be exactly this length. A longer sequence must be paired with a `target_range`, and the tool then extracts the model context window around that range. The tool does not pad missing context, so a sequence shorter than the model context without a target range is rejected. * **`output_tracks` selects which of the model's tracks are returned and defaults to the single track at index 0.** The human head exposes 5,313 tracks and the mouse head exposes 1,643 tracks. Selecting only the tracks of interest, rather than all of them, keeps the returned activity matrix small and the analysis focused on the relevant assays. * **`species` selects the human or mouse output head and defaults to human.** The track index meanings differ between the two heads, so the `output_tracks` indices should be chosen to match the selected species. * **`batch_size` controls how many sequences are processed together on the GPU and defaults to 1.** Larger values increase throughput when many sequences are scored in one call, subject to the available GPU memory. * **The output covers a 114,688 base-pair central window, narrower than the input context.** The 896 output bins span the central portion of the input, and the per-result `output_start` and `output_end` coordinates report exactly which part of the source sequence the bins cover. A feature of interest must fall within this central window to receive a prediction.