#!/bin/sh
#PBS -N CNVpair_cnvkit
#PBS -j oe
#PBS -l ncpus=12
#PBS -l nodes=1
#PBS -l mem=20G

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
target=/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
includhg19=/cgdata/liuxiangqiong/database/cnvkit/data/access-5k-mappable.grch37.bed
outputdir=${inputpath}/2CNV_cnvkit_pair
cnvkit.py batch \
${bam_dir}/${tumor}_clean.bam \
--normal ${bam_dir}/${normal}_clean.bam \
--targets ${target} \
--fasta ${hg19} \
--access ${includhg19} \
--output-reference ${outputdir}/${normal}_my_reference.cnn \
--output-dir ${outputdir}/${sample}_cnvkit/ \
--diagram --scatter
###extract the cnr data for multi-region of gene
python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cnr_gene20220525.py -i ${inputpath} -s ${sample} -t ${tumor}
####do the cnvkit segment for the multi-region gene
cnvdir=${inputpath}/2CNV_cnvkit_pair/${sample}_cnvkit
cat ${cnvdir}/${tumor}_seggene.list |while read gene;do cnvkit.py segment ${cnvdir}/${tumor}_${gene}_gene.cnr -o ${cnvdir}/${tumor}_${gene}_gene.seg.cns --smooth-cbs;done
###merge the cns data
#python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cns_merge_20220525.py -i ${inputpath} -s ${sample} -t ${tumor}
python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cns_merge_20220823.py -i ${inputpath} -s ${sample} -t ${tumor}

#del the file 
rm -rf ${cnvdir}/*gene.seg.cns
rm -rf ${cnvdir}/*gene.cnr