awk to update value based on pattern match in another file
In the awk, thanks you @RavinderSingh13, for the help in below, hopefully it is close as I am trying to update the value in $12 of the tab-delimetedfile2 with the matching value in $1 of the space delimetedfile1. I have added comments for each line as well. Thank you .
awk
Code:
awk '$12 == /NM_/{ # search $12 for pattern NM_
match($12,/p..*/); # using match the regex will match in $12 from the p. to the end
VAL=substr($12,RSTART+1,RLENGTH-2); # Putting the values of subtring whose value starts from RSTART+1 to RSTART-2
for(i=1;i<=num;i++){ # Starting a loop which will start from value 1 of variable i to till value of variable num
awk 'FNR==NR {a[$1]=$2; next} a[$i]{VAL=a[$i]} # Store $2 value from file1 in array a and update array i matching VAL
} # close block
next # process next line
}1' OFS="\t" file1 FS'\t' file2 # define file1 as space delimited and file2 as tab-delimited with the output also being tab-delimited
file1
Code:
C Cys
D Asp
V Val
W Trp
Y Tyr
file2
Code:
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 1269554 1269554 T C exonic TAS1R3 . . nonsynonymous SNV TAS1R3:NM_152228:exon6:c.2269T>C:p.C757R rs307377
desired output the 3 lines in bold are updated because the one-letter code before and after the digit matched $1 in file1, so it is updated to the three-letter code in $2.
Code:
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 1269554 1269554 T C exonic TAS1R3 . . nonsynonymous SNV TAS1R3:NM_152228:exon6:c.2269T>C:p.Cys757Arg rs307377
Last edited by cmccabe; 09-05-2017 at 10:02 AM..
Reason: fixed format
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
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file1
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09-05-2017
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