#!/bin/bash
RUN_ID=SIMC012_AgFungi_Ribo
WORKING_DIR="/home/shichino/data/${RUN_ID}"

SAMPLE_LIST_A="pool_A.csv"
SAMPLE_LIST_B="pool_B.csv"
SAMPLE_LIST_C="pool_C.csv"
SAMPLE_LIST_D="pool_D.csv"

SAMPLE_ID_A=( $(cut -d ',' -f1 ${SAMPLE_LIST_A} ) )
SAMPLE_ID_B=( $(cut -d ',' -f1 ${SAMPLE_LIST_B} ) )
SAMPLE_ID_C=( $(cut -d ',' -f1 ${SAMPLE_LIST_C} ) )
SAMPLE_ID_D=( $(cut -d ',' -f1 ${SAMPLE_LIST_D} ) )

BED_SOURCE="/home/genome/Colletotrichum_orbiculare/5UTR_annotated/Cob_genes_with_UTRs.sort.1.bed"
BED_SOURCE_MITO="/home/genome/Colletotrichum_orbiculare/Mitochondria_Genome/Cob_mitochondrial.bed"

RAWFASTQ_SOURCE="${WORKING_DIR}/RawFastq/"

UNIQUE_READS_OUT="${WORKING_DIR}/unique"
FPCOUNT_OUT="${WORKING_DIR}/fpcount"
SHELL_IN_OUT="${WORKING_DIR}/shell_in_out"

ASITES="${WORKING_DIR}/asites.txt"
ASITES_MITO="${WORKING_DIR}/asites_mito.txt"

echo "beginning fpcount"
date +"%Y/%m/%d %H:%M:%S"

mkdir ${FPCOUNT_OUT}

for id in ${SAMPLE_ID_A[@]}
do
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/${id}.txt -b ${BED_SOURCE} -a ${ASITES} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpcountcommands.sh
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/mito.${id}.txt -b ${BED_SOURCE_MITO} -a ${ASITES_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpcountcommands.sh
done

for id in ${SAMPLE_ID_B[@]}
do
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/${id}.txt -b ${BED_SOURCE} -a ${ASITES} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpcountcommands.sh
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/mito.${id}.txt -b ${BED_SOURCE_MITO} -a ${ASITES_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpcountcommands.sh
done

for id in ${SAMPLE_ID_C[@]}
do
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/${id}.txt -b ${BED_SOURCE} -a ${ASITES} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpcountcommands.sh
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/mito.${id}.txt -b ${BED_SOURCE_MITO} -a ${ASITES_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpcountcommands.sh
done

for id in ${SAMPLE_ID_D[@]}
do
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/${id}.txt -b ${BED_SOURCE} -a ${ASITES} ${UNIQUE_READS_OUT}/${id}_unique.bam) &" >> fpcountcommands.sh
       echo "(nohup fp-count -c5,5 -o ${FPCOUNT_OUT}/mito.${id}.txt -b ${BED_SOURCE_MITO} -a ${ASITES_MITO} ${UNIQUE_READS_OUT}/mito.${id}_unique.bam) &" >> fpcountcommands.sh
done


echo "wait" >> fpcountcommands.sh


source fpcountcommands.sh

mv fpcountcommands.sh ${SHELL_IN_OUT}

echo "exiting fpcount"
date +"%Y/%m/%d %H:%M:%S"

mv nohup.out ${SHELL_IN_OUT}/nohup.out.fpcount