intersect_count.sh

##takes output from bedtools intersect output tab delimted file containing all instances at which two annotations intersect 
##bedtools intersect input of alignment.bed file and gff/gtf3 annotation 
##script output count table of unique gene ID and number of intersect counts (collapsed under one gene id)

function count_intersect() {
	echo "using file name $1.tsv"
	cut -f15 $1_intersect_final.tsv |
  tail -n +2 |
  awk -F '[;]' '{print $2}' |
  awk -F '["]' '{print $2}' |
  sed 's.\\..g' |
  sort -n |
  uniq -c > $1_bedtools_count_new.txt
	echo "done"
}