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Enformer Chromatin Accessibility MORSE
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evo-design/proto-language/proto_language/constraint/sequence_annotation/enformer_chromatin_accessibility_morse_constraint.py
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Score target proposals against an Enformer chromatin accessibility MORSE objective.

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API Reference

ConfigEnformerChromatinAccessibilityMorseConfig Source
Configuration for Enformer chromatin accessibility MORSE scoring.
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enum
default:"human"
Enformer species head to use: human or mouse.Options: human, mouse
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string
default:".--. .-. --- - ---"
Morse pattern; use ’.’, ’-’, and spaces between letters.
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integer
default:"25"
Length of each dot window.
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integer
default:"75"
Length of each dash window.
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integer
default:"25"
Gap between symbols within a letter.
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integer
default:"75"
Gap between letters in the Morse pattern.
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integer
default:"0"
Target-relative start coordinate where the Morse pattern begins.
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enum
default:"global_max"
Scale signal by full-output max, target-region max, or not at all.Options: global_max, region_max, none
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number
default:"0.0"
Minimum normalized high-minus-low signal margin to reward.
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number
default:"0.0"
Penalty weight when the normalized contrast margin is too small.
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number
default:"0.0"
Reward weight for larger raw target signal range.
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number
default:"0.0"
Reward weight for larger raw signal in dot and dash windows.
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number
default:"0.0"
Penalty weight for larger raw signal in gap windows.
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enum
default:"log1p"
Transform for raw amplitude and window-mean reward terms.Options: log1p, identity
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string
default:"cuda"
CUDA device for Enformer inference.
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integer
default:"1"
Candidate sequences per Enformer model batch.
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integer
default:"0"
Leading target bases to ignore before accessibility scoring.
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List[integer]
default:"[121]"
Enformer chromatin-accessibility tracks; defaults by organism.
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enum
default:"mean"
How to combine selected Enformer tracks.Options: mean, min, std, lcb

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Usage

python

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Metadata