API Reference

This section documents the full public API of pyprego. Functions are organized by module.

Modules

Module	Description
Regression	Motif discovery via iterative PWM regression
PWM Scoring	Score sequences against a known PSSM
K-mer Operations	K-mer generation, counting, and screening
PSSM Utilities	PSSM manipulation, comparison, and analysis
Motif Database	Motif database management and querying
Visualization	Sequence logos and regression diagnostics
Genomic	Genomic interval integration (requires pymisha)
Export/Import	Model serialization and deserialization
Types	Core data structures and type definitions

Quick Import

All public functions are available directly from the top-level pyprego namespace:

import pyprego

result = pyprego.regress_pwm(sequences, response)
scores = pyprego.compute_pwm(sequences, pssm)
kmers  = pyprego.screen_kmers(sequences, response, kmer_len=8)

Alternatively, import from submodules:

from pyprego.regression import regress_pwm
from pyprego.compute import compute_pwm
from pyprego.kmers import screen_kmers