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awk to print matching lines in files that meet critera

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# 1  
Old 09-14-2016
awk to print matching lines in files that meet critera
In the tab delimited files below I am trying to match $2 in file1 to $2 of file2. If a match is found the awk checks $3 of file2 and if it is greater than 40% and $4 of file2 is greater than 49, the line in file1 is printed. In the desired output line3 of file1 is not printed because $3 off file2 is less than 40%. line4 of file1 is not printed because $4 of file2 is less than 49 Thank you Smilie.

file1
Code:
Chr    Start    Ref    Alt
1    100    A    C
1    1000    -    G
2    200    C    G
2    800    A    -

file2
Code:
Chrom    Position    Var Freq    Qual    Coverage    Ref Cov    Var Cov
1    100    50    100    100    50    50
2    800    50    40    100    50    50
2    200    30    100    50    40    10
1    1000    100    100    100    0    100

awk
Code:
awk -F'\t' -v OFS='\t' 'NR==FNR{A[$2];next}$2 in A
{if($3 >.4 OFS $4 > 49)
print ; next
' file1 file2
awk: cmd. line:2: {if($3 > .4 OFS $4 > 49)
awk: cmd. line:2:                    ^ syntax error
awk: cmd. line:3: } next
awk: cmd. line:3:   ^ syntax error

desired output
Code:
1    100    A    C
1    1000    -    G

# 2  
Old 09-14-2016
Hello cmccabe,

Could you please try following and let me know if this helps you.
Code:
awk 'FNR==NR{A[$2]=$0;next} ($2 in A){printf("%s",((($3 * 100)/$4)>40 && $4>49 && $3 ~ /[[:digit:]]/ && $4 ~ /[[:digit:]]/)?A[$2] ORS:X)}' Input_file1   Input_file2

Output will be as follows.
Code:
1    100    A    C
1    1000    -    G

Thanks,
R. Singh
# 3  
Old 09-14-2016
Try out this one liner...
Code:
awk 'BEGIN{while(getline < "f1" > 0) x[$2]=$0} {printf("%s",($2 in x && $3>40 && $4>49)?x[$2]RS:"")}' f2

# 4  
Old 09-14-2016
Small simplification of shamrock's well working proposal:
Code:
awk 'BEGIN{while(getline < "f1" > 0) x[$2]=$0} $2 in x && $3>40 && $4>49 {print x[$2]}' f2
1	100	A	C
1	1000	-	G

This User Gave Thanks to RudiC For This Post:
shamrock
# 5  
Old 09-14-2016
Quote:
Originally Posted by shamrock
Try out this one liner...
Code:
awk 'BEGIN{while(getline < "f1" > 0) x[$2]=$0} {printf("%s",($2 in x && $3>40 && $4>49)?x[$2]RS:"")}' f2

That will work on some systems, but the standards don't specify the precedence of file redirection operations and comparison operations. Some versions of awk parse the command:
Code:
getline < "f1" > 0

as:
Code:
getline < ("f1" > 0)

and others parse it as:
Code:
(getline < "f1") > 0

# 6  
Old 09-14-2016
Quote:
Originally Posted by Don Cragun
That will work on some systems, but the standards don't specify the precedence of file redirection operations and comparison operations. Some versions of awk parse the command:
Code:
getline < "f1" > 0

as:
Code:
getline < ("f1" > 0)

and others parse it as:
Code:
(getline < "f1") > 0

The left and right arrow operators have the same precedence but associate left to right so getline < "f1" > 0 has an implied parenthesization of ((getline < "f1") > 0)
I am surprised to know that there are awk(s) out there that do not comply with this rule of precedence and associativity as it predates the the very first and original awk!!!
# 7  
Old 09-14-2016
Quote:
Originally Posted by shamrock
The left and right arrow operators have the same precedence but associate left to right so getline < "f1" > 0 has an implied parenthesization of ((getline < "f1") > 0)
I am surprised to know that there are awk(s) out there that do not comply with this rule of precedence and associativity as it predates the the very first and original awk!!!
What you are saying is true if both "arrow" operators are comparison operators; but it is not true when one of the "arrow" operators is a redirection operator. Historic versions of awk based on AT&T UNIX System utility code do one thing. GNU awk does the other.
This User Gave Thanks to Don Cragun For This Post:
Scrutinizer
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