mkdir -p  /hive/data/genomes/eboVir3/bed/snpView	
cd /hive/data/genomes/eboVir3/bed/snpView	
awk '/^s/ {print $2}' ../multiz160way/defraged.multiz160way.maf | sed 's/\..*//' > species.lst  
mafGene -exons eboVir3 multiz160way ncbiGene species.lst nonsyn.faa

paSNP species.lst nonsyn.faa stdout | sed 's/:/ /' | sed 's/-/ /' | awk '{print $1, $2-1, $3, $4, 1583, "+", $2-1, $3, "255,0,0", 1, $3-($2 - 1), 0}' > nonsyn.bed

mafGene -uniqAA -exons eboVir3 multiz160way ncbiGene species.lst syn.faa

paSNP species.lst syn.faa stdout | sed 's/:/ /' | sed 's/-/ /' | awk '{print $1, $2-1, $3, $4, 1819, "+", $2-1, $3, "0,255,0", 1, $3 - ($2 - 1), 0}' > syn.bed

mafToSnpBed eboVir3 ../multiz160way/defraged.multiz160way.maf ../ncbiGene/ncbiGene.gp stdout |  sed 's/eboVir3.//' > single.bed

#these should all disappear on the merge
grep "1580$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "255,255,0", 1, $3 -$2, 0}' > codingVariant.bed

grep "1623$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "255,255,0", 1, $3 -$2, 0}' > utrVariant.bed
grep "1624$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "255,255,0", 1, $3 -$2, 0}' >> utrVariant.bed

grep " 0$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "240,240,180", 1, $3 -$2, 0}' > missing.bed

grep "1628$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "0,0,0", 1, $3 -$2, 0}' > intergenic.bed

grep "1627$" single.bed | awk '{print $1, $2, $3, $4, $5, "+", $2, $3, "0,0,0", 1, $3 -$2, 0}' > intron.bed

echo "select * from chromInfo" | hgsql eboVir3 | tail -n +2 > chrom.sizes
rm output.bed
for i in `cat species.lst`
do
echo $i
grep -wh "$i" nonsyn.bed syn.bed codingVariant.bed utrVariant.bed intron.bed intergenic.bed missing.bed | bedSmash stdin chrom.sizes stdout >>  output.bed
done

awk '{print $1,$2,$3,$4,$5}' output.bed > load.bed

cat load.bed | sed -f ~/kent/src/hg/makeDb/doc/eboVir3/ucscName.strainName.sed \
  | sed -e 's/G3686v1_2014/KM034562v1/' \
  > strainLoad.bed

hgLoadBed eboVir3 mafSnp160way load.bed
hgLoadBed eboVir3 mafSnpStrainName160way strainLoad.bed