awk to parse file and display result based on text

Shell Programming and Scripting
1

I am trying using awk to open an input file and check a column 2/field $2 and if there is a warning then that is displayed (variantchecker): G not found at position 459, found A instead. The attached Sample1.txt is that file. If in that column/field there is a black space, then the text after the colon in $1 is displayed . Sample2.txt is that file.

The below code is close, but I can not seem to get it right. Thank you :).

 awk 'NR>1 {$1=""; e=$2; print "Found error: ", $0} END{if (!e) print "No error";}' C:/Users/cmccabe/Desktop/annovar/${id}_name.txt
2

It is not clear to me how to distinguish the error case from the case with no errors. In sample1 we have (variantchecker): in the second column, in sample2 it is NM_004004.5 GJB2_v001 .

Can we assume for example that parentheses at the start of the second column indicate an error?

3

Yes, the parentheses at the start of the second column does indicate an error. Thank you :).

4

Something like the following should work then:

awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); print "No error: " $1 }}' C:/Users/cmccabe/Desktop/annovar/${id}_name.txt
5

Works great.... if the text in the no warning (Sample2.txt), p.(Val27Ile) was needed as well would:

 awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1 $8); print "No error: " $1 "," $8}}' C:/Users/cmccabe/Desktop/annovar/${id}_name.txt

Desired output displayed:

 c.79G>A,p.(Val27Ile)
6

Separating the substitutions works:

 awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/annovar/${id}_name.txt
1 Like
7

Thank you, works great :).