Shell Programming and Scripting

6	chr1	949654	949654	A	G	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.294A>G:p.=;ISG15:NM_005101:exon2:c.237C>T:p.=

R_Index	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	Inheritence	ExonicFunc.refGene	AAChange.refGene	avsnp147
1	chr1	948846	948846	-	A	upstream	ISG15	dist=1	.	.	.	rs3841266
2	chr1	948870	948870	C	G	UTR5	ISG15	NM_005101:c.-84C>G	.	.	.	rs4615788
3	chr1	948921	948921	T	C	UTR5	ISG15	NM_005101:c.-33T>C	.	.	.	rs15842
4	chr1	949597	949597	C	T	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.237C>T:p.D79D	rs61766284
5	chr1	949654	949654	A	G	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.294A>G:p.V98V	rs8997
6	chr1	949654	949654	A	G	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.294A>G:p.V98V;ISG15:NM_005101:exon2:c.237C>T:p.D79D	rs8997

R_Index	Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	Inheritence	ExonicFunc.refGene	AAChange.refGene	avsnp147
1	chr1	948846	948846	-	A	upstream	ISG15	dist=1	.	.	.	rs3841266
2	chr1	948870	948870	C	G	UTR5	ISG15	NM_005101:c.-84C>G	.	.	.	rs4615788
3	chr1	948921	948921	T	C	UTR5	ISG15	NM_005101:c.-33T>C	.	.	.	rs15842
4	chr1	949597	949597	C	T	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.237C>T:p.Asp79Asp	rs61766284
5	chr1	949654	949654	A	G	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.294A>G:p.Val98Val	rs8997
6	chr1	949654	949654	A	G	exonic	ISG15	.	.	synonymous SNV	ISG15:NM_005101:exon2:c.294A>G:p.Val98Val;ISG15:NM_005101:exon2:c.237C>T:p.Asp79Asp	rs8997

awk '
  BEGIN { OFS="\t" }
  # The input files are processed one by one and the following code runs for each line
  # FNR is equal to NR when processing file1
  # a[ ] is indexed by the one letter code, its value is the three letter code
  FNR==NR { a[$1]=$2; next }
  # The next goes to the next input cycle
  # The following code runs for file2 (and further files)
  $12 ~ /:NM_/ {
    ostring=""
    # split $12 by ";" and cycle through them
    nNM=split($12,NM,";")
    for (n=1; n<=nNM; n++) {
      if (n>1) ostring=(ostring ";") # append ";"
      if (match(NM[n],/p[.].*/)) {
        # copy up to "p."
        ostring=(ostring substr(NM[n],1,RSTART+1))
        # Get the substring after "p."
        VAL=substr(NM[n],RSTART+2)
        # Get its length
        lenVAL=length(VAL)
        # Cycle through each character, append to ostring, if in a[ ] replace by its value
        for (i=1; i<=lenVAL; i++) {
          c=substr(VAL,i,1)
          ostring=(ostring ((c in a) ? a[c] : c))
        }
      } else {
        # append the unchanged string
        ostring=(ostring NM[n])   
      }
    }
    # copy ostring back to $12 (unconditionally)
    $12=ostring
  }
  # always print
  { print }
' file1 FS="\t" file2