In the awk below I use $2 of filet to search filea for a match. If the values in $2 are exact match this works great. However, that is not always the case, so I need to perform the search using a range of + or - 2. That is if the value in filea $2 is within + or - 2 of filet $2 then it is matched. Thank you .
awk 'FNR==1 { next }
> FNR == NR { file1[$2,$3] = $2 " " $3} # filet search
> FNR != NR { file2[$2,$3] = $2 " " $3 } # in filea
> END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
> print "Missing in annovar but found in tvc:"; for (k in file2) if (!(k in file1)) print file2[k]
> print "Missing in tvc but found in annovar:"; for (k in file1) if (!(k in file2)) print file1[k]
> }' filea filet > match
current output
Code:
Match:
6637518 TPP1
6638506 TPP1
Missing in filea but found in filet:
1776024 CTSD
Missing in filet but found in filea:
1776025 CTSD
desired output
Code:
Match:
6637518 TPP1
6638506 TPP1
1776024 CTSD --> within 2 margin
Missing in filea but found in filet:
Missing in tvc but found in annovar:
awk trued to get the desired output
Code:
awk 'FNR==1 { next }
> FNR == NR { file1[$2,$3] = $2 " " $3 } # filea search
> FNR != NR { file2[$2,$3] = $2 " " $3 } # in filet
> END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
> print "Missing in filea but found in filet:"; for (k in file2) if (!(k in file1)) print file2[k]
> print "Missing in filet but found in filea:"; for (k in file1) if (!(k in file2)) print file1[k]
> if((k-$2)^2<=2^2) {print $0, " --> within 2 margin"; next}
> }' filea filet > match
awk: cmd. line:7: error: `next' used in END action
Last edited by cmccabe; 09-01-2016 at 02:40 PM..
Reason: fixed format
Hi,
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09-01-2016
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