Shell Programming and Scripting

FILE:2

c1	1234	a t
c1	1534	a t
c1	1634	a t
c1	1654	a t
c1	2234	a t
c1	5678	g t
c1	91011	t a
c1	2444	taa blank
c1	5667	att blank
c1	34566	blank att
c1	36365	a t
c2	88777	G blank
c2	7455	T a		
c2	46445	g t
c2	74676	a c
c2	565455	c G


FILE:1
c1	g1	1234	a 
c1	g1	1234	t
c1	g1	1234	t
c1	g1	1234	a 
c1	g1	1234	a 
c1	g1	1234	a 
c1	g1	5678	g 
c1	g1	5678	C
c1	g1	5678	t
c1	g1	5678	t
c1	g1	5678	t
c1	g1	5678	g 
c1	g1	5678	g 
c1	g1	91011	t 
c1	g2	2444	random
c1	g2	2444	random
c1	g2	2444	random
c1	g2	2444	taa
c1	g2	2444	random
c1	g2	2444	taa 
c1	g2	5667	att
c1	g2	34566	random
c1	g2	36365	a 
c2	g3	88777	G 
c2	g3	88777	G 
c2	g3	88777	random
c2	g3	88777	G 
c2	g3	88777	G 
c2	g3	7455	T 		
c2	g4	46445	t
c2	g4	74676	c
c2	g4	74676	c
c2	g4	74676	a 
c2	g4	74676	a 
c2	g4	74676	c
c2	g4	565455	G
c2	g4	565455	G
c2	g4	565455	G


Expected output

c1	g1	8	5
c1	g2	5	4
c2	g3	5	1
c2	g4	2	7

awk 'END {
  for (g in gc) {
    split(g, t, SUBSEP)
    print t[1], gn[t[1], t[2]], gc[g]
    }
  }
NR == FNR {
  k[$1, $3]
  v[$1, $3, tolower($4)]
  gn[$1, $3] = $2
  next
  }
($1, $2) in k {
  for (i = 2; ++i <= 4;) {
   if ($i == "blank") {
     gc[$1, $2, $i]++
     continue
     } 
   if (($1, $2, tolower($i)) in v || ($1, $2, tolower(substr($i, 1, length($i) - 1))) in v)
      gc[$1, $2, tolower($i)]++   
    }
  }' file1 file2