# Last edited on 2008-06-10 20:38:39 by stolfi

# TAG:TBNAME:TKMIN:TKAVG:TKDEV:TNMIN:TNMID:TNTAU:NBASES:SEED
RUNS := \
  B01:BOGUS:0003:0120:0066:0066:0120:0.00150:1000000:01

all:
	for tt in ${RUNS} ; do \
          ${MAKE} RUN="$$tt" single ; \
        done
        
        
########################################################################
# Section for recursive make 
# Client must define ${RUN}

RUN := RUN.IS.UNDEFINED
ifneq "/${RUN}" "/RUN.IS.UNDEFINED"

FIELDS := ${subst :, ,${RUN}}
TAG          := ${word  1,${FIELDS}}
TABLE_NAME   := ${word  2,${FIELDS}}
MIN_K_LENGTH := ${word  3,${FIELDS}}
AVG_K_LENGTH := ${word  4,${FIELDS}}
DEV_K_LENGTH := ${word  5,${FIELDS}}
MIN_N_LENGTH := ${word  6,${FIELDS}}
MID_N_LENGTH := ${word  7,${FIELDS}}
TAU_N_LENGTH := ${word  8,${FIELDS}}
NBASES       := ${word  9,${FIELDS}}
SEED         := ${word 10,${FIELDS}}

# The following parameter is fixed for now:
MID_N_PROB := 0.15 

# Directory where to find the probability tables for codons and junk bases:
TABLE_DIR := "prob"

TABLE_K := ${TABLE_DIR}/${TABLE_NAME}_K_3.prb
TABLE_N := ${TABLE_DIR}/${TABLE_NAME}_N_1.prb

# Name of synthetic pseudo-gene:
GENE_NAME := Y-${TAG}-${TABLE_NAME}-${SEED}

PROG_DIR := ${STOLFIHOME}/programs/c/DNA/dnabayes

single: generate-single analyze-single

generate-single: ${PROG_DIR}/dbd_synthesize_dna
	 export LC_ALL="C" ; \
           ${PROG_DIR}/dbd_synthesize_dna \
            -v tabK="${TABLE_K}" \
            -v tabN="${TABLE_N}" \
            -v nBases=${NBASES} \
            -v seed=${SEED} \
            -v tKMin=${MIN_K_LENGTH} \
            -v tKAvg=${AVG_K_LENGTH} \
            -v tKDev=${DEV_K_LENGTH} \
            -v tNMin=${MIN_N_LENGTH} \
            -v tNMid=${MID_N_LENGTH} \
            -v tNTrp=${MID_N_PROB} \
            -v tNTau=${TAU_N_LENGTH} \
            -v outName="unif/${GENE_NAME}"
            
analyze-single: unif/${GENE_NAME}.lab
	export LC_ALL="C" ; \
           ${PROG_DIR}/dbd_check_translation \
              < unif/${GENE_NAME}.trn && \
           ${PROG_DIR}/dbd_gather_region_length_stats \
             -v outName="prob/${GENE_NAME}" \
             unif/${GENE_NAME}.lab && \
           ${PROG_DIR}/dbd_plot_region_length_stats \
             prob/${GENE_NAME}

endif
# end ${RUN}
######################################################################