In the awk I am trying to add :p.=? to the end of each $9 that matches the pattern NM_. The below executes andis close but I can not seem to figure out why the :p.=? repeats in the split as in the green in the current output. I have added comments as well. Thank you .
file
Code:
R_Index Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene Inheritance ExonicFunc.refGene AAChange.refGene
1 chr1 155870416 155870416 G A splicing RIT1 NM_001256821:exon6:c.481-7C>T;NM_001256820:exon5:c.322-7C>T;NM_006912:exon6:c.430-7C>T
9 chr10 112760138 112760138 A - splicing SHOC2 NM_007373:exon4:c.842-35A>-;NM_001269039:exon2:c.704-35A>-
11 chr18 53070914 53070914 G A exonic TCF4 . AD nonsynonymous SNV TCF4:NM_001243232:exon1:c.32C>T:p.A11V;TCF4:NM_001306208:exon1:c.32C>T:p.A11V
awk
Code:
awk '
BEGIN { FS=OFS="\t" } # define FS and OFS as tab and start processing
$9 ~ /NM/ { # look for pattern NM in $9
# split $9 by ";" and cycle through them
out="" # array out is empty
i=split($9,NM,/;/)
for (n=1; n<=i; n++) {
sub(/$/, ":p=", NM[i]) # add :p. to end off each NM[i] before the ;
out = (out=="" ? "" : out";") NM[i] # add ? to each NM[i] and store in array out
}
$9 = out # update with array out
}1' file
desired output
Code:
R_Index Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene Inheritance ExonicFunc.refGene AAChange.refGene
1 chr1 155870416 155870416 G A splicing RIT1 NM_001256821:exon6:c.481-7C>T:p=?;NM_001256820:exon5:c.322-7C>T:p=?;NM_006912:exon6:c.430-7C>T:p=?
9 chr10 112760138 112760138 A - splicing SHOC2 NM_007373:exon4:c.842-35A>-:p=?;NM_001269039:exon2:c.704-35A>-:p=?
11 chr18 53070914 53070914 G A exonic TCF4 . AD nonsynonymous SNV TCF4:NM_001243232:exon1:c.32C>T:p.A11V;TCF4:NM_001306208:exon1:c.32C>T:p.A11V
current output
Code:
R_Index Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene Inheritance ExonicFunc.refGene AAChange.refGene
1 chr1 155870416 155870416 G A splicing RIT1 NM_006912:exon6:c.430-7C>T:p=?;NM_006912:exon6:c.430-7C>T:p=?:p=?;NM_006912:exon6:c.430-7C>T:p=?:p=?:p=?
9 chr10 112760138 112760138 A - splicing SHOC2 NM_001269039:exon2:c.704-35A>-:p=?;NM_001269039:exon2:c.704-35A>-:p=?:p=?
11 chr18 53070914 53070914 G A exonic TCF4 .AD nonsynonymous SNV TCF4:NM_001243232:exon1:c.32C>T:p.A11V;TCF4:NM_001306208:exon1:c.32C>T:p.A11V
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01-23-2018
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