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awk to parse file and display result based on text

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# 1  
Old 03-13-2015
awk to parse file and display result based on text
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 Smilie.

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

Sample1.txt (431 Bytes) 
Sample2.txt (571 Bytes) 
# 2  
Old 03-14-2015
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  
Old 03-14-2015
Yes, the parentheses at the start of the second column does indicate an error. Thank you Smilie.
# 4  
Old 03-14-2015
Something like the following should work then:

Code:
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  
Old 03-14-2015
Works great.... if the text in the no warning (Sample2.txt), p.(Val27Ile) was needed as well would:

Code:
 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:

Code:
 c.79G>A,p.(Val27Ile)

# 6  
Old 03-16-2015
Separating the substitutions works:

Code:
 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

This User Gave Thanks to Walter Misar For This Post:
cmccabe
# 7  
Old 03-16-2015
Thank you, works great Smilie.
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