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awk output is space delimeted not tab delimeted

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# 1  
Old 09-07-2016
awk output is space delimeted not tab delimeted
In the below awk the output is space delimited, but it should be tab delimited. Did I not add the correct -F and OFS? Thank you Smilie.

The input file are rather large so I did not include them, but they are tab-delimeted files as well.


awk
Code:
awk -F'\t' -v OFS='\t' 'FNR==1 { next }
>       FNR == NR { file1[$2,$4,$5] = $2 " " $4 " " $5 }
>       FNR != NR { file2[$2,$4,$5] = $2 " " $4 " " $5 }
>       END { print "Match:"; for (k in file1) if (k in file2) print file1[k] # Or file2[k]
>             print "Missing in Reference but found in IDP:"; for (k in file2) if (!(k in file1)) print file2[k]
>             print "Missing in IDP but found in Reference:"; for (k in file1) if (!(k in file2)) print file1[k]
>       }' file1 file2 > out

current output (all in one field $1)
Code:
Match:
68521889 C T
167099158 A G
Missing in Reference but found in IDP:
93521604 A G
166903445 T C
Missing in IDP but found in Reference:
166210776 C T
147183143 A G

desired output (in 3 fields $1 $2 $3)
Code:
$1       $2 $3
Match:
68521889  C   T
167099158  A G
Missing in Reference but found in IDP:
93521604  A   G
166903445 T   C
Missing in IDP but found in Reference:
166210776 C   T
147183143 A G

Last edited by cmccabe; 09-07-2016 at 11:07 AM.. Reason: fixed format
# 2  
Old 09-07-2016
Hello cmccabe,

Could you please try to change following into your mentioned code. It should fly then.
Code:
FNR == NR { file1[$2,$4,$5] = $2 FS $4 FS $5 }
FNR != NR { file2[$2,$4,$5] = $2 FS $4 FS $5 }

I had changed " "with FS above, please do let us know how it goes then.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 3  
Old 09-07-2016
I total missed that, thank you very much Smilie
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