CODEWITHSUNDEEP
awk
justaguy
justaguy

Reputation: 3022

awk to match field between two files and use conditions on match

I am trying to look for $2 of file1 (skipping the header) in $2 of file2 and if they match and the value in $10 is > 30 and $11 is > 49, then print the line to a output file. The below awk has syntax errors in it though shellcheck didn't return any. Both the input and output are tab-delimited. I think the below is close, but not sure what is wrong. Thank you :).

awk

 awk -F'\t' -v OFS='\t' 'NR==FNR{A[$2];next}$2 in A
{if($10 >.5 OFS $11 > 49)
print ; next
' file1 file2
awk: cmd. line:2: {if($10 >.5 OFS $11 > 49)
awk: cmd. line:2:                   ^ syntax error
awk: cmd. line:3: print ; next
awk: cmd. line:3:             ^ unexpected newline or end of string

file1

Missing in IDP but found in Reference:
2   166848646   G   A   exonic  SCN1A   68  13  16;20   0;0 17;15   0;0 0;0 0;0     c.[5139C>T]+[=] 52.94

file2

chr2    166245425   SCN2A   AMPL5155065355  SNP Het C/T C   T   54  100   50    23  27
chr2    166848646   SCN1A   AMPL1543060606  SNP Het        G/A   G  A   52.9411764706   100 68  32  36

desired output

2   166848646   G   A   exonic  SCN1A   68  13  16;20   0;0 17;15   0;0 0;0 0;0     c.[5139C>T]+[=] 52.94

edit with new awk

awk -F'\t' -v OFS='\t' 'NR==FNR{A[$2];next}$2 in A {
if($10 >.5 OFS $11 > 49) >>> if($10 >.5 && $11 > 49)
print }
' file1 file2 > out
awk: cmd. line:2: if($10 >.5 OFS $11 > 49) >>> if($10 >.5 && $11 > 49)
awk: cmd. line:2:                    ^ syntax error

Upvotes: 0

Views: 96

Answers (1)

karakfa
karakfa

Reputation: 67467

here you go...

$ awk 'BEGIN{FS=OFS="\t"} NR==FNR{a[$2]; next} 
                          ($2 in a) && $10>30 && $11>49 ' file1 file2

Upvotes: 1

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