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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 SUNOS

comm

comm(1) 							   User Commands							   comm(1)

NAME

       comm - select or reject lines common to two files

SYNOPSIS

       comm [-123] file1 file2

DESCRIPTION

       The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output:
       lines only in file1; lines only in file2; and lines in both files.

       If the input files were ordered according to the collating sequence of the current locale, the lines  written  will  be	in  the  collating
       sequence of the original lines. If not, the results are unspecified.

OPTIONS

       The following options are supported:

       -1	Suppresses the output column of lines unique to file1.

       -2	Suppresses the output column of lines unique to file2.

       -3	Suppresses the output column of lines duplicated in file1 and file2.

OPERANDS

       The following operands are supported:

       file1	A path name of the first file to be compared. If file1 is -, the standard input is used.

       file2	A path name of the second file to be compared. If file2 is -, the standard input is used.

USAGE

       See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2**31 bytes).

EXAMPLES

       Example 1: Printing a list of utilities specified by files

       If file1, file2, and file3 each contain a sorted list of utilities, the command

       example% comm -23 file1 file2  | comm -23 - file3

       prints a list of utilities in file1 not specified by either of the other files. The entry:

       example% comm -12 file1 file2 | comm -12 - file3

       prints a list of utilities specified by all three files. And the entry:

       example% comm -12  file2 file3 | comm -23 -file1

       prints a list of utilities specified by both file2 and file3, but not specified in file1.

ENVIRONMENT VARIABLES

       See  environ(5)	for  descriptions  of  the  following  environment  variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE,
       LC_CTYPE, LC_MESSAGES, and NLSPATH.

EXIT STATUS

       The following exit values are returned:

       0	All input files were successfully output as specified.

       >0	An error occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWesu			   |
       +-----------------------------+-----------------------------+
       |CSI			     |enabled			   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Standard			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5)

SunOS 5.10							    3 Mar 2004								   comm(1)
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