crispr_score_deephf
Read-only
Score CRISPR guides with DeepHF: a predicted knockout EFFICIENCY between 0 and 1 for wild-type SpCas9 (U6 or T7 promoter), eSpCas9(1.1) or SpCas9-HF1. It is not a z-score and not comparable with Rule Set 3 — the two answer different questions and must never be averaged or ranked together. Takes 23-nt protospacers (20-nt spacer + NGG PAM), which is what crispr_design_guides produces; a guide whose PAM is not canonical NGG comes back null rather than extrapolated, because the model was trained on NGG only. THE WEIGHTS DOWNLOAD ON FIRST USE, 3-5 MB per model, and scoring is slow by construction: each guide is folded twice, once with the 79-nt tracrRNA scaffold, before the network sees it.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| model | No | which published model to score under. This is a scientific choice about YOUR experiment — which Cas9 variant, and which promoter the sgRNA is expressed from — not a quality setting, and scores from two models are not comparable. Values: wt_u6 (WT SpCas9 · U6 promoter), wt_t7 (WT SpCas9 · T7 promoter), wt (WT SpCas9 · both promoters), esp (eSpCas9(1.1)), hf (SpCas9-HF1). | wt_u6 |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| protospacers | Yes | the 23-nt protospacers to score — 20-nt spacer plus the 3-nt PAM, exactly as DeepHF takes them. Anything that is not 23 nt of unambiguous A/C/G/T ending in GG scores null rather than being silently trimmed or extrapolated. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| best | Yes | the highest-scoring protospacer, or empty when none could be scored | |
| model | Yes | which model produced these numbers. Scores from two models are not comparable | |
| scored | Yes | how many of the inputs DeepHF is defined on — the accounting, not an assumption | |
| scores | Yes | every protospacer with its efficiency, IN THE ORDER GIVEN — null where DeepHF is not defined, with the reason beside it | |
| efficiencies | Yes | just the numbers, same order — null-preserving, so it lines up with the input |