from CoaSim import simulate
from CoaSim.randomMarkers import makeRandomSNPMarkers
markers = makeRandomSNPMarkers(10, 0.0, 1.0)
sequences = simulate(markers, 100, rho=400).sequences
from CoaSim.IO import printMarkerPositions, printSequences
printMarkerPositions(markers, open('positions.txt', 'w'))
printSequences(sequences, open('sequences.txt', 'w'))
from CoaSim import simulate, TraitMarker, insertSorted from CoaSim.randomMarkers import randomPosition, makeRandomSNPMarkers from CoaSim.diseaseModelling import singleMarkerDisease, split from CoaSim.IO import printSequences markers = makeRandomSNPMarkers(10, 0.0, 1.0) traitMarker = TraitMarker(randomPosition(), 0.2, 0.4) markers,traitIdx = insertSorted(markers, traitMarker) sequences = simulate(markers, 100, rho=400).sequences diseaseModel = \ singleMarkerDisease(traitIdx,wildTypeRisk=0.1,mutantRisk=0.3) affected, unaffected = split(diseaseModel,sequences) print 'Affected:' printSequences(affected) print print 'Unaffected:' printSequences(unaffected) print
from CoaSim import simulate
from CoaSim.randomMarkers import makeRandomSNPMarkers
markers = makeRandomSNPMarkers(10, 0.0, 1.0)
sequences = simulate(markers, 100, rho=400).sequences
from CoaSim.IO import printMarkerPositions, printSequences
printMarkerPositions(markers, open('positions.txt','w'))
printSequences(sequences, open('sequences.txt','w'))
