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Merged
merged 2 commits into from
Aug 20, 2016
Merged

cosi sims from seltraj #70

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ae820fb
env COSI_NEWSIM
josephvitti Aug 20, 2016
7d70b3f
Merge branch 'master' into jv
josephvitti Aug 20, 2016
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8 changes: 2 additions & 6 deletions cms/dists/freqbins_func.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,13 @@ def write_slurm_array(writefilename = "slurm_array.sh", arrayCmd = "./my_process
writefile.write(arrayCmd)
writefile.write('\n')
writefile.close()

subcommand = "sbatch --array=1-" + str(numTasks) + " " + writefilename
print(subcommand)
if dispatch:
subprocess.check_output(subcommand.split())
#print('wrote to: ' + writefilename)
return

def run_seltraj_arrays(trajdir, cosibuild, paramfile, numSims, scriptDir = "/home/users/vitti/cms/cms/", taskIndexStr = "$SLURM_ARRAY_TASK_ID", maxAttempts = 1000):
'''I think I may be over-complicating things with Snakemake.'''
if trajdir [-1] != "/":
trajdir += "/"
traj_outputname = trajdir + 'rep' + taskIndexStr + '.txt'
Expand All @@ -31,14 +28,13 @@ def run_selsim_arrays(trajdir, cosibuild, paramfile, numSims, runDir, scriptDir
#traj_outputname = trajdir + 'rep' + taskIndexStr + '.txt'
if runDir [-1] != "/":
runDir += "/"

sim_cmd = "env COSI_LOAD_TRAJ=" + trajdir + "/rep" + taskIndexStr + ".txt " + cosibuild + " -p " + paramfile + " --output-gen-map "
sim_cmd = "env COSI_NEWSIM=1 env COSI_LOAD_TRAJ=" + trajdir + "/rep" + taskIndexStr + ".txt " + cosibuild + " -p " + paramfile + " --output-gen-map "
if genmapRandomRegions:
sim_cmd += " --genmapRandomRegions"
if dropSings is not None:
sim_cmd += " --drop-singletons " + str(dropSings)
sim_cmd += " --tped " + runDir + 'rep' + taskIndexStr
write_slurm_array(runDir + "run_sel_sims.sh", sim_cmd, numSims)
write_slurm_array(runDir + "run_sel_sims.sh", sim_cmd, numSims, dispatch=True)
return
def run_sel_trajs_snakemake(outputdir, cosibuild, paramfile, numSims, cluster="", jobs=1, maxAttempts=10000, waitSec = 1000, scriptDir = "/home/users/vitti/cms/cms/"):
'''this happens in each folder to be populated'''
Expand Down
41 changes: 30 additions & 11 deletions cms/likes_from_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,8 @@ def full_parser_likes_from_model():
###############################
get_sel_trajs_parser = subparsers.add_parser('get_sel_trajs', help='run forward simulations of selection trajectories and perform rejection sampling to populate selscenarios by final allele frequency before running coalescent simulations for entire sample')
#get_sel_trajs_parser.add_argument('nSimsPerBin', type=int, help="number of selection trajectories to generate per allele frequency bin")

get_sel_trajs_parser.add_argument('--maxSteps', action='store', help='')

run_sel_sims_parser = subparsers.add_parser('run_sel_sims', help='run sel. simulations')
#run_sel_sims_parser.add_argument('n', action='store', type=int, help='num replicates to run per sel scenario')
run_sel_sims_parser.add_argument('trajDir', action='store', help='location of simulated trajectories (i.e. outputDir from get_sel_trajs)')
Expand Down Expand Up @@ -132,29 +133,29 @@ def execute_get_sel_trajs(args):
selTrajDir = args.outputDir
if selTrajDir[-1] != "/":
selTrajDir += "/"
#selTrajDir += "sel_trajs/"
selTrajDir += "sel_trajs/"
runDir = check_make_dir(selTrajDir)
fullrange, bin_starts, bin_ends, bin_medians, bin_medians_str = get_bins(args.freqRange, args.nBins)

print(prefixstring + "running " + str(args.n) + " selection trajectories per for each of " + str(args.nBins) + " frequency bins, using model: \n\t\t" + args.inputParamFile)
print(prefixstring + "outputting to " + runDir)

######################
## USE SLURM ARRAYS ##
######################
for ibin in range(args.nBins):
populateDir = runDir + "sel_" + bin_medians_str[ibin]
binDir = check_make_dir(populateDir)
bounds = bin_starts[ibin], bin_ends[ibin]
paramfilename = populateDir + "/params"
write_bin_paramfile(args.inputParamFile, paramfilename, bounds) #rewrite paramfile here? to give rejection sampling
run_seltraj_arrays(binDir, args.cosiBuild, paramfilename, args.n)

'''

#DEBUG SNAKEMAKE
run_sel_trajs_allbins(bin_starts, bin_ends, bin_medians_str, args.cosiBuild,)
'''
run_seltraj_arrays(binDir, args.cosiBuild, paramfilename, args.n, maxAttempts = args.maxSteps)

"""
for ibin in range(args.nBins): ### DEBUG ##### !!!!
###################
## USE SNAKEMAKE ##
###################
#print('\n\n' + str(ibin)+'\n') ## DBEUG
populateDir = runDir + "sel_" + bin_medians_str[ibin]
binDir = check_make_dir(populateDir)
Expand All @@ -164,6 +165,10 @@ def execute_get_sel_trajs(args):
write_bin_paramfile(args.inputParamFile, paramfilename, bounds) #rewrite paramfile here? to give rejection sampling
#print("wrote bin paramfile\n")
run_sel_trajs_snakemake(binDir, args.cosiBuild, paramfilename, args.n, cluster=args.cluster, jobs=args.jobs) #ISSUE HERE args.maxSteps,
'''
#DEBUG SNAKEMAKE- use this instead??
run_sel_trajs_allbins(bin_starts, bin_ends, bin_medians_str, args.cosiBuild,)
'''
"""
return
def execute_run_sel_sims(args):
Expand All @@ -173,14 +178,28 @@ def execute_run_sel_sims(args):
selSimDir += "/"
selSimDir += "sel_sims/"
runDir = check_make_dir(selSimDir)
fullrange, bin_starts, bin_ends, bin_medians, bin_medians_str = get_bins(args.freqRange, args.nBins)

print(prefixstring + "loading trajectories from " + args.trajDir)
print(prefixstring + "outputting to " + runDir)
fullrange, bin_starts, bin_ends, bin_medians, bin_medians_str = get_bins(args.freqRange, args.nBins)

run_selsim_arrays(args.trajDir, args.cosiBuild, args.inputParamFile, args.n, runDir, dropSings=args.dropSings) #scriptDir = "/home/users/vitti/cms/cms/", taskIndexStr = "$SLURM_ARRAY_TASK_ID", maxAttempts = 1000, genmapRandomRegions
######################
## USE SLURM ARRAYS ##
######################
for ibin in range(args.nBins):
binTrajDir = args.trajDir + "sel_" + bin_medians_str[ibin]
populateDir = runDir + "sel_" + bin_medians_str[ibin]
populateDir = check_make_dir(populateDir)
trajectoryFilenames = os.listdir(binTrajDir)
paramfilename = binTrajDir + "/params"
assert os.path.isfile(paramfilename)
run_selsim_arrays(binTrajDir, args.cosiBuild, paramfilename, args.n, populateDir, dropSings=args.dropSings)

"""
for ibin in range(args.nBins):
###################
## USE SNAKEMAKE ##
###################
binTrajDir = args.trajDir + "sel_" + bin_medians_str[ibin]
populateDir = runDir + "sel_" + bin_medians_str[ibin]
populateDir = check_make_dir(populateDir)
Expand Down