License: Malinois is open source and free for academic and commercial use under an MIT license and may require explicit attribution when utilized. Please refer to the license for full terms.
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evo-design/proto-language/proto_language/constraint/sequence_annotation/malinois_activity_constraint.pyConstraint contributors
dguo8412
Score DNA sequences with Malinois as a bounded lower-is-better objective.
dguo8412API Reference
Configuration for Malinois regulatory DNA activity scoring.Malinois predicts MPRA activity for 200 bp DNA inserts in K562, HepG2, and
SK-N-SH contexts. This constraint maps the requested raw cell-type score to
a bounded lower-is-better objective:For
direction="max":score = 1 - sigmoid((raw_score - sigmoid_center) / sigmoid_scale)For direction="min":score = sigmoid((raw_score - sigmoid_center) / sigmoid_scale)With the default center of 4.0, raw scores above 4.0 receive penalties below
0.5 in maximization mode and above 0.5 in minimization mode.enum
default:"K562"
Malinois cell-type output to optimize.Options:
K562, HepG2, SKNSHenum
default:"max"
Use ‘max’ to encourage activity or ‘min’ to suppress activity in the selected cell type.Options:
max, minnumber
default:"4.0"
Raw Malinois score where the transformed constraint score is 0.5.
number
default:"1.0"
Positive scale for the raw-score sigmoid transform.
integer
default:"200"
Expected DNA insert length before Malinois MPRA flank padding.
string
default:""
Optional local artifact tarball path; empty uses the managed cache download.
string
HTTPS URL used to provision the Malinois artifact.
string
default:"375142a714e7df73c463b46113a65210"
Expected MD5 checksum for the downloaded Malinois artifact.
string
default:""
Optional local Malinois metadata directory; empty uses the managed cache extraction.
integer
default:"1"
Number of sequences to score simultaneously on GPU.
string
default:"cuda"
Device for Malinois inference.
Usage
python