awk to update file based on match in 3 fields using two files
Trying to use awk to store the value of $5 in file1 in array x. That array x is then used to search $4 of file1 to find aa match (I use x[2] to skip the header in file1). Since $4 can have multiple strings in it seperated by a , (comma), I split them and iterate througn each split looking for a match. Each split is then stored in array and compared to x[2] for a match. The pattern c. is extracted and stored as VAL.
The awk below will hopefully do that but where I am struggling is in order for $6 in file1 to be updated, the $2 and $3 and array value must match $5 and $6 and $9 in file2. If that is true then $6 in file1 is updated with the values of $1 and $3 from file2. Line 4 is an example of this because the NM_000138.4 matches array x[2] and the c. value up to the : (colon) and that value matches $9 in file2. So all the conditions are meet to update $6 in file1. Line2 satisfies all but the c. value in VAL as it does not match $9 in file2, so $6 is not updated. I hope this is a good start and that I didn't over-complicate things (though I may have and there is probably a better way). Thank you .
awk '
BEGIN { FS=OFS="\t" }
FNR==NR {x[NR]=$5} # store value in $5 in array x
#{print X[2]}
$4 ~ x[2] { # if $4 matches x[2]
match($4,"NM"].*],); # regex match from NM to till , in 4rd field
val=substr($4,RSTART+1,RLENGTH-2); # store substring value that starts from RSTART+1 to RLENGTH-2 using $4 in val
NM=split($4, array,","); # Split $4 on "," and storing it's length(array's length) to variable named num.
for(i=1;i<=NM;i++){ # Starting a loop which will start from value 1 of variable i to till value of variable num
if(array[i] ~ x[2]){ # Check condition if any array's value is equal to array x[2] skipping header
if (match(NM[i],/c[.].:/)) { # extract pattern c. in each split from c. to :
VAL=substr(NM[n],RSTART+2) # store each c. from split in VAL
}
}
}
}
{a[$5,$6,$9]=$1,$3; next} a[$2,$3]{$6=a[$2,$3]}1' file1 file2 # update $6 in file1 if condition is met
Last edited by cmccabe; 03-23-2018 at 12:36 PM..
Reason: added details, updated thread title
If $1 in file1 matches $2 in file2. Then the value in $2 of file2 is updated to $1"."$2 of file2. The awk seems to only match the two files but not update. Thank you :).
awk
awk 'NR==FNR{A ; next} $1 in A { $2 = a }1' file1 file2
file1
name version
NM_000593 5
NM_001257406... (3 Replies)
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file1
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file1
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awk
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03-22-2018
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