Commits

Giovanni Marco Dall'Olio committed 3075fc0

REFACT: renaming output files

Comments (0)

Files changed (4)

 run_on_folder:
-	python generate_cosi_simulations.py -f -folder params/ -nsim 10 -length 21 
+	python generate_cosi_simulations.py -f -folder params/ -nsim 10 -length 21 > cnag_job.sh
 
 run_selection_sims:
 	python generate_cosi_simulations.py -s -nsim 2 -length 1000 -pop EUR -mutAge 0 -mutFreq 0.5 -selCoeff 0.2 -pos 0.5
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 # per bp per generation
 mutation_rate 1.5e-8
 
-#recomb_file /lustre/scratch103/sanger/igr/simulations/model.test_12
+#recomb_file /lustre/scratch103/sanger/igr/simulations/model.test_77
 gene_conversion_rate 4.5e-9
 
 # population info
 
 pop_event change_size "african pop size" 3 17000 12500
 
-pop_event sweep "selective sweep" 3 0 0.0415 0.5 0.4
+pop_event sweep "selective sweep" 1 0 0.0064 0.5 0.4
  

generate_cosi_simulations.py

 
 # General parameters (paths, etc.) (modify them to fit to your system)!!!!!!!!!!!! 
 simulationDataFolder = '/home/gioby/workspace/cnag-simulations/cosi_1.2/examples/bestfit/'
-outputFolder = '/home/gioby/workspace/cnag-simulations/results/plink_files/'
+outputFolder = '/home/gioby/workspace/cnag-simulations/results/'
 
 paramsFile = simulationDataFolder + 'params'
 run_simulations = simulationDataFolder + 'run.pl'
         # Move out.pos-1/2/3 and out.hap-1/2/3 files
         print('mkdir %s' % outputFolder + '/param_' + scenario_id)
 
-        print('mv %s %s' % ("out.hap-1", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.hap-1')) 
-        print('mv %s %s' % ("out.hap-2", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.hap-2')) 
-        print('mv %s %s' % ("out.hap-3", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.hap-3')) 
-        print('mv %s %s' % ("out.pos-1", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.pos-1')) 
-        print('mv %s %s' % ("out.pos-2", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.pos-2')) 
-        print('mv %s %s' % ("out.pos-3", outputFolder + '/param_' + scenario_id + '/bestfit_neutral_params_' + population + '_neutral_' + str(scenario_id) + '.pos-3')) 
+        print('mv %s %s' % ("out.hap-1", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.hap-1')) 
+        print('mv %s %s' % ("out.hap-2", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.hap-2')) 
+        print('mv %s %s' % ("out.hap-3", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.hap-3')) 
+        print('mv %s %s' % ("out.pos-1", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.pos-1')) 
+        print('mv %s %s' % ("out.pos-2", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.pos-2')) 
+        print('mv %s %s' % ("out.pos-3", outputFolder + '/param_' + scenario_id + '/selection_params_' + str(scenario_id) + '.pos-3')) 
 
 #        print( 'rm ' + 'out*' )
 #        print( 'rm ' + coreName + '*')