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workflow.py
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workflow.py
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import numpy as np
from gwf import Workflow
import os, sys
import itertools
gwf = Workflow()
def nquireRef(ploidy=2,depth=50,L=5000,nInd=1,random_seed=1):
outFolder='./ploidy_ref/ploidy_'+str(ploidy)
inputs=[]
outputs=[outFolder+'/sim.DP'+str(depth)+'.genolikes']
options = {
'cores': 1,
'memory': '24g',
'walltime': '8:00:00'
}
spec = '''
mkdir -p {outFolder}
#source activate HMMploidyNew
echo {ploidy}x{nInd} > {outFolder}/ploidy_{ploidy}.file
./HMMploidy/simulationScript.sh -p {outFolder}/ploidy_{ploidy}.file -d {depth} -l {L} -g {random_seed} -o {outFolder}/sim
echo ./{outFolder}/sim.DP{depth}.mpileup.gz > {outFolder}/file.list
if [ {ploidy}==1 ]; then
python3 ./HMMploidy/Genotype_Likelihoods.py {outFolder}/file.list -m 0
else
python3 ./HMMploidy/Genotype_Likelihoods.py {outFolder}/file.list
fi
gunzip {outFolder}/sim.DP{depth}.genolikes.gz
'''.format(ploidy=ploidy, nInd=nInd, outFolder=outFolder, depth=depth, L=L, random_seed=random_seed)
return inputs, outputs, options, spec
def simulate(ploidy=2, nInd=1, depth=10, L=5000, sim=1, random_seed=1, walltime='1:00:00', memory='8g'):
inputs = []
outFolder='ploidy_'+str(ploidy)+'/depth_'+str(depth)+'/nind_'+str(nInd)+'/run_'+str(sim)
outputs = [outFolder+'/sim.DP'+str(depth)+'.genolikes']
options = {
'cores': 1,
'memory': memory,
'walltime': walltime
}
outFolder='ploidy_'+str(ploidy)+'/depth_'+str(depth)+'/nind_'+str(nInd)+'/run_'+str(sim)
spec = '''
mkdir -p {outFolder}
#source activate HMMploidyNew
echo {ploidy}x{nInd} > {outFolder}/ploidy.file
./HMMploidy/simulationScript.sh -p {outFolder}/ploidy.file -d {depth} -l {L} -g {random_seed} -o {outFolder}/sim
echo ./{outFolder}/sim.DP{depth}.mpileup.gz > {outFolder}/file.list
if [ {ploidy}==1 ]; then
python3 ./HMMploidy/Genotype_Likelihoods.py {outFolder}/file.list -m 0
else
python3 ./HMMploidy/Genotype_Likelihoods.py {outFolder}/file.list
fi
gunzip {outFolder}/sim.DP{depth}.genolikes.gz
'''.format(ploidy=ploidy, nInd=nInd, outFolder=outFolder, depth=depth, L=L, random_seed=random_seed)
return inputs, outputs, options, spec
def runHMM(ploidy=2, nInd=1, depth=10, sim=1, walltime='1:00:00', memory='8g'):
inFolder='ploidy_'+str(ploidy)+'/depth_'+str(depth)+'/nind_'+str(nInd)+'/run_'+str(sim)
inputs = [inFolder+'/sim.DP'+str(depth)+'.genolikes']
outputs = [inFolder+'/sim.DP'+str(depth)+'.HMMploidy',
inFolder+'/sim.DP'+str(depth)+'.pdf',
inFolder+'/sim.DP'+str(depth)+'.testRate']
options = {
'cores': 1,
'memory': memory,
'walltime': walltime
}
spec = '''
mkdir -p {outFolder}
#source activate HMMploidyNew
Rscript ./HMMploidy/HMMploidy.R file={outFolder}/sim.DP{depth} maxPloidy=5 truePl={ploidy} wind=250
'''.format(outFolder=inFolder, depth=depth, ploidy=ploidy)
return inputs, outputs, options, spec
def runPloidyNGS(ploidy=2, nInd=1, depth=10, sim=1, walltime='1:00:00', memory='8g'):
inFolder='ploidy_'+str(ploidy)+'/depth_'+str(depth)+'/nind_'+str(nInd)+'/run_'+str(sim)
inputs = [inFolder+'/sim.DP'+str(depth)+'.genolikes']
outputs = [inFolder+'/sim.DP'+str(depth)+'.ploidyNGS']
options = {
'cores': 1,
'memory': memory,
'walltime': walltime
}
spec = '''
mkdir -p {outFolder}
#source activate HMMploidyNew
Rscript ./HMMploidy/tools/ploidyNGS.R {outFolder}/sim.DP{depth} {NIND} {ploidy}
'''.format(outFolder=inFolder, depth=depth, ploidy=ploidy, NIND=nInd)
return inputs, outputs, options, spec
def runNquire(ploidy=2, nInd=1, depth=10, sim=1, walltime='2:00:00', memory='16g'):
inFolder='ploidy_'+str(ploidy)+'/depth_'+str(depth)+'/nind_'+str(nInd)+'/run_'+str(sim)
inputs = [inFolder+'/sim.DP'+str(depth)+'.genolikes']
outputs = [inFolder+'/sim.DP'+str(depth)+'.noisy.gmmu']
options = {
'cores': 1,
'memory': memory,
'walltime': walltime
}
spec = '''
mkdir -p {outFolder}
#source activate HMMploidyNew
Rscript ./HMMploidy/tools/nQuire.R {outFolder}/sim.DP{depth} {NIND} {ploidy}
'''.format(outFolder=inFolder, depth=depth, ploidy=ploidy, NIND=nInd)
return inputs, outputs, options, spec
PLOIDY = [1, 2, 3, 4, 5]
for p in PLOIDY:
gwf.target_from_template('NQref_'+str(p), nquireRef(ploidy=p,
nInd=1,
depth=50,
L=5000,
random_seed=p))
DEPTH = [0.5, 1, 2, 5]
IND = [1, 2, 5, 10, 20]
PLOIDY = [1, 2, 3, 4, 5]
RUN = range(0,100)
parameter_space = itertools.product(RUN,DEPTH,IND,PLOIDY)
for run, depth, ind, ploidy in parameter_space:
name = 'depth_'+str(depth)+'_ind_'+str(ind)+'_pl_'+str(ploidy)+'_sim_'+str(run)
gwf.target_from_template(name, simulate(ploidy=ploidy,
nInd=ind,
depth=depth,
L=5000,
sim=run,
random_seed=run,
walltime='8:00:00',
memory='64g'))
gwf.target_from_template('HMM_'+name, runHMM(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('ploidyNGS_'+name, runPloidyNGS(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('nQuire_'+name, runNquire(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='3:00:00'))
DEPTH = [10, 20]
IND = [1, 2, 5]
PLOIDY = [1, 2, 3]
RUN = range(0,100)
parameter_space = itertools.product(RUN,DEPTH,IND,PLOIDY)
for run, depth, ind, ploidy in parameter_space:
name = 'depth_'+str(depth)+'_ind_'+str(ind)+'_pl_'+str(ploidy)+'_sim_'+str(run)
gwf.target_from_template(name, simulate(ploidy=ploidy,
nInd=ind,
depth=depth,
L=5000,
sim=run,
random_seed=run,
walltime='8:00:00',
memory='64g'))
gwf.target_from_template('HMM_'+name, runHMM(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='14:00:00'))
gwf.target_from_template('ploidyNGS_'+name, runPloidyNGS(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('nQuire_'+name, runNquire(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='3:00:00'))
DEPTH = [10, 20]
IND = [1, 2, 5]
PLOIDY = [4, 5]
RUN = range(0,100)
parameter_space = itertools.product(RUN,DEPTH,IND,PLOIDY)
for run, depth, ind, ploidy in parameter_space:
name = 'depth_'+str(depth)+'_ind_'+str(ind)+'_pl_'+str(ploidy)+'_sim_'+str(run)
gwf.target_from_template(name, simulate(ploidy=ploidy,
nInd=ind,
depth=depth,
L=5000,
sim=run,
random_seed=run,
walltime='20:00:00',
memory='64g'))
gwf.target_from_template('HMM_'+name, runHMM(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='14:00:00'))
gwf.target_from_template('ploidyNGS_'+name, runPloidyNGS(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('nQuire_'+name, runNquire(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='3:00:00'))
DEPTH = [10, 20]
IND = [10, 20]
PLOIDY = [1, 2, 3]
RUN = range(0,100)
parameter_space = itertools.product(RUN,DEPTH,IND,PLOIDY)
for run, depth, ind, ploidy in parameter_space:
name = 'depth_'+str(depth)+'_ind_'+str(ind)+'_pl_'+str(ploidy)+'_sim_'+str(run)
gwf.target_from_template(name, simulate(ploidy=ploidy,
nInd=ind,
depth=depth,
L=5000,
sim=run,
random_seed=run,
memory='64g',
walltime='20:00:00'))
gwf.target_from_template('HMM_'+name, runHMM(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='14:00:00'))
gwf.target_from_template('ploidyNGS_'+name, runPloidyNGS(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('nQuire_'+name, runNquire(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
DEPTH = [10, 20]
IND = [10, 20]
PLOIDY = [4, 5]
RUN = range(0,100)
parameter_space = itertools.product(RUN,DEPTH,IND,PLOIDY)
for run, depth, ind, ploidy in parameter_space:
name = 'depth_'+str(depth)+'_ind_'+str(ind)+'_pl_'+str(ploidy)+'_sim_'+str(run)
gwf.target_from_template(name, simulate(ploidy=ploidy,
nInd=ind,
depth=depth,
L=5000,
sim=run,
random_seed=run,
memory='64g',
walltime='24:00:00'))
gwf.target_from_template('HMM_'+name, runHMM(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='14:00:00'))
gwf.target_from_template('ploidyNGS_'+name, runPloidyNGS(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='6:00:00'))
gwf.target_from_template('nQuire_'+name, runNquire(ploidy=ploidy,
nInd=ind,
depth=depth,
sim=run,
memory='24g',
walltime='2:00:00'))