Shell Programming and Scripting

file2

ABCA3
ACVRL1
BMPR1B
BMPR2
CAV1

20	ABCA3	100.00
101	ACVRL1	100.00
596	BMPR1B	100.00
597	BMPR3	100.00
733	CAV1	100.00
734	CAV3	100.00
735	CBFB	100.00
736	CBL	100.00
737	CBLB	100.00
738	CBR1	100.00

awk -F'\t' 'NR==FNR{A[$1];next}$2 in A' file1 file2

20	ABCA3	100.00
101	ACVRL1	100.00
596	BMPR1B	100.00
733	CAV1	100.00

awk -F'\t' 'NR==FNR{a[$1]; next}$2 in a{delete a[$2]}
     END{for(i in a) print ++FNR,i,"missing"}1' file1 OFS='\t' file2

1	ABCA3	100.00
2	ACVRL1	100.00
3	BMPR1B	100.00
4	CAV1	100.00
5	BMPR2	missing

awk -F"\t" '
NR==FNR {a[$1]=$1; b[$1]=$1; next; }
a[$2] {$1=++l; print $0; delete b[$2]; }
END {for(i in b) {$0=++l OFS b[i] OFS "missing"; print $0; }}
' file1 OFS="\t" file2

awk '
 BEGIN {FS=OFS="\t"}
 (NR==FNR){A[$1]=0; next}
 ($2 in A){A[$2]++; print ++cnt,$2,$3}
 END {for (i in A) if (A[i]==0) print ++cnt,i,"missing"}
' file1 file2

awk '
  NR==FNR{
    A[$2]=$3
    next
  } 
  $1 in A {
    print ++c, $1, A[$1]
    next
  }
  {
    M[$1]
  }
  END {
    for(i in M) print ++c, i, "missing"
  }
' FS='\t' OFS='\t' file2 file1