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Copy pathsimulations.mk
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67 lines (54 loc) · 2.66 KB
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#
# Simulations Makefile
#
.PHONY: seq_sim dil_sim
# General parameters:
LSF_QUEUE = research-rh6
SIMNGS_RUNFILE =$(BASE)/dat/s_8_4x.runfile
READ_LENGTH =101
INSERT_SIZE =400
INIT_POPSIZE = 5000
PCR_EFFICIENCY = 0.75
CYCLES_MUT = 20
DILF_MUT = 70000
CYCLES_CLEAN = 20
DILF_CLEAN = 16000000
CYCLES_FINAL = 30
SAMPLE_SIZE = 40
VMIN_CTGL = 400
VKMER_LENGTH = 90
VMAX_DIV = 0.1
TOTAL_COV = 4000
# seq_sim specific parameters:
SEQ_OUT_DIR =$(BASE)/seq_sim/out
SEQ_TARGET_DIR = $(BASE)/seq_sim/targets
NR_REPS = 5 # Number of replications for a given unit length/number combination.
UNIT_NR_RANGE = 4:100:4 # Unit number range and step size.
UNIT_LEN_RANGE = 4:4000:5 # Unit length range and step size.
MIN_TLEN = 500 # Minimum target sequence length.
MAX_TLEN = 30000 # Maximum target sequence length.
SEQ_SIM_PARAMS = "-n $(MUT_MODEL_FILE) -b $(BL_SCALER_FILE) -i $(INIT_POPSIZE) -e $(PCR_EFFICIENCY) -cm $(CYCLES_MUT) -dm $(DILF_MUT) \
-cc $(CYCLES_CLEAN) -dc $(DILF_CLEAN) -cf $(CYCLES_FINAL) -ss $(SAMPLE_SIZE) -vm $(VMIN_CTGL) -vk $(VKMER_LENGTH) -vi $(INSERT_SIZE) \
-vd $(VMAX_DIV) -P $(BIN) -S $(SIMNGS_RUNFILE) -L $(READ_LENGTH) -I $(INSERT_SIZE) -t $(TOTAL_COV)"
# Simulate NG-SAM experiments on random targets with varying repetitive structure:
seq_sim:
@bin/run_seq_sim -m $(MIN_TLEN) -M $(MAX_TLEN) -Q $(LSF_QUEUE) -X '$(SEQ_SIM_PARAMS)' -R $(RUN_DIR) -T $(SEQ_TARGET_DIR) -n $(NR_REPS) -u $(UNIT_NR_RANGE) -l $(UNIT_LEN_RANGE) -o $(SEQ_OUT_DIR)
# Visualise the results of seq_sim:
plot_seq_res:
@bin/plot_seq_res -i $(SEQ_OUT_DIR) -r $(REP_DIR)/seq_sim.pdf -g 27
# dil_sim spacific parameters:
DIL_OUT_DIR =$(BASE)/dil_sim/out
DIL_TARGET_DIR = $(BASE)/dil_sim/targets
NR_REPS = 5 # Number of replications for a given dm/dc combination.
D1_RANGE = 17000:280000:20000 # First dilution range.
D2_RANGE = 2000000:128000000:200000 # Second dilution range.
DIL_TARGET = $(BASE)/dat/eater_root.fas
DIL_SIM_PARAMS = "-n $(MUT_MODEL_FILE) -b $(BL_SCALER_FILE) -i $(INIT_POPSIZE) -e $(PCR_EFFICIENCY) -cm $(CYCLES_MUT) \
-cc $(CYCLES_CLEAN) -cf $(CYCLES_FINAL) -ss $(SAMPLE_SIZE) -vm $(VMIN_CTGL) -vk $(VKMER_LENGTH) -vi $(INSERT_SIZE) \
-vd $(VMAX_DIV) -P $(BIN) -S $(SIMNGS_RUNFILE) -L $(READ_LENGTH) -I $(INSERT_SIZE) -t $(TOTAL_COV)"
# Simulate NG-SAM experiments under a range of dilution factors.
dil_sim:
@bin/run_dil_sim -t $(DIL_TARGET) -m $(MIN_TLEN) -M $(MAX_TLEN) -Q $(LSF_QUEUE) -X '$(DIL_SIM_PARAMS)' -R $(RUN_DIR) -n $(NR_REPS) -o $(DIL_OUT_DIR) -d1 $(D1_RANGE) -d2 $(D2_RANGE)
# Visualise the results of dil_sim:
plot_dil_res:
@bin/plot_dil_res -i $(DIL_OUT_DIR) -r $(REP_DIR)/dil_sim.pdf -g 13