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Full Discussion: awk to match file1 and extract specific tag values
Top Forums Shell Programming and Scripting awk to match file1 and extract specific tag values Post 303028307 by MadeInGermany on Friday 4th of January 2019 04:42:44 AM
Old 01-04-2019
I think you want a lookup table from file1: $1 is the lookup key and $2 the returned value.
Code:
# in file 1 store the $2 values in s[$1] (s[] indexed by $1)
FNR==NR {
  s[$1]=$2
  next
}

Now you can test existence with (key in s) or get the value with s[key] or loop through the keys with for (key in s).

I think the following captures the wanted values in file2:
Code:
{
  match($8,/'normalizedPos':'([^']+)'/, pos)  # extract value after : into pos[]
  match((";" $8),/;(AF=[^;]+).*;(FDP=[^;]+)/, info) # extract values after AF= and FDP= into info[]
  match($8,/'gene':'([^']+)'/,gene) # extract the value after gene into gene[]
  print "pos[1]="pos[1], "info[1]="info[1], "info[2]="info[2], "gene[1]="gene[1]
}

Note1: the target array as 3rd argument is an extension in GNU-awk. (Maybe you want to consider perl? Then it works on all platforms that have perl.)
Note2: for a most exact string match use a "border character". I have even prepended a ";" to the input string for match() in order to ensure it exists even at the beginning.
This User Gave Thanks to MadeInGermany For This Post:
cmccabe
 

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LEARN ABOUT BSD

join

JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME

       join - relational database operator

SYNOPSIS

       join [ options ] file1 file2

DESCRIPTION

       Join  forms,  on the standard output, a join of the two relations specified by the lines of file1 and file2.  If file1 is `-', the standard
       input is used.

       File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the  first	in
       each line.

       There  is  one line in the output for each pair of lines in file1 and file2 that have identical join fields.  The output line normally con-
       sists of the common field, then the rest of the line from file1, then the rest of the line from file2.

       Fields are normally separated by blank, tab or newline.	In this case, multiple separators count as one, and leading  separators  are  dis-
       carded.

       These options are recognized:

       -an    In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2.

       -e s   Replace empty output fields by string s.

       -jn m  Join on the mth field of file n.	If n is missing, use the mth field in each file.

       -o list
	      Each output line comprises the fields specified in list, each element of which has the form n.m, where n is a file number and m is a
	      field number.

       -tc    Use character c as a separator (tab character).  Every appearance of c in a line is significant.

SEE ALSO

       sort(1), comm(1), awk(1)

BUGS

       With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort.

       The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous.

7th Edition							  April 29, 1985							   JOIN(1)
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