consequence.gene

#!/bin/bash
c=$1
p=$2

g=$3

chr=$c

if [[ ! -z "$(echo $c | grep rs)" ]]; then
## rsid
read c p <<< $(/home/agilly/scripts/rsid.to.pos.b38.sh $c| sed 's/chr//;s/:/ /')
fi

chr=$c

af=$(bcftools query -f'%AF' -r chr${c}:${p}-${p} /storage/sanger/projects/helic/t144_helic_15x/analysis/HA/release/chr$chr.vcf.gz)
read ref alt <<< $(tabix /storage/sanger/projects/helic/t144_helic_15x/analysis/HA/release/chr$chr.vcf.gz chr${c}:${p}-${p} | cut -f4,5)
#echo $af
#echo | perl -e 'print('$af' > 0.5?1:0)'
#af=0.4

#if [ "$(echo | perl -e 'print('$af' > 0.5?1:0)')" == 1 ]; then
#t=$alt
#alt=$ref
#ref=$t
#fi

#echo $c $p $alt



vep=$(wget -O- -q "http://rest.ensembl.org/vep/human/region/${c}:${p}-${p}:1/$alt?content-type=application/json")

#echo most_severe_consequence $(echo $vep | jq -r '.[].most_severe_consequence')

echo $vep | jq -r '.[].transcript_consequences[] | .gene_id + " " + .gene_symbol' | sort -u | while read ensg sym; do
if [[ "$sym" == "$g" ]]; then
canonical=$(wget -q -O- "http://rest.ensembl.org/lookup/id/${ensg}?expand=1;content-type=application/json" | jq -r '.Transcript[] | select(.is_canonical == 1)| .id')
echo canonical $sym $canonical $( echo $vep | jq -r '.[].transcript_consequences[] | select(.transcript_id=="'$canonical'").consequence_terms[]' | tr '\n' ',' | sed 's/,$/\n/')
fi
done


#wget -O- -q "http://rest.ensembl.org/vep/human/region/${c}:${p}-${p}:1/$alt?content-type=application/json"