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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 303028464 by Don Cragun on Tuesday 8th of January 2019 03:22:04 PM
Old 01-08-2019
Hi cmccabe ,
In post #1, you said that the desired output from your two sample input files is:
Code:
AKT1 c.49G>A p.E17K	chr5:112175324 	NOT DETECTED
AKT1 c.155T>G p.L52R	chr7:55242467	NOT DETECTED
APC c.4033G>T p.E1345*	READS=1999	AF=0.248124
EGFR c.2237_2255delAATTAAGAGAAGCAACATCinsT p.E746_S752delinsV	READS=1963	AF=0.0,0.0,0.0,0.139582

Given that there is no record in file2 that contains the file1 field 2 values as a coding value in the single-quoted sub-subfields of field 8 in file2 why were the values show in red in the above output selected as the desired output? (I note that the output produced by the perl script durden_tyler suggested omits that field from the output and you didn't comment on that discrepancy.)

Other than having no idea how the 3rd output field in the first two records of your desired output is supposed to be selected, I think I can come up with an awk script that does what you want just using standard awk features (without the gawk extensions your current code is trying to use).
This User Gave Thanks to Don Cragun For This Post:
cmccabe
 

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XZDIFF(1)							     XZ Utils								 XZDIFF(1)

NAME

       xzcmp, xzdiff, lzcmp, lzdiff - compare compressed files

SYNOPSIS

       xzcmp [cmp_options] file1 [file2]
       xzdiff [diff_options] file1 [file2]
       lzcmp [cmp_options] file1 [file2]
       lzdiff [diff_options] file1 [file2]

DESCRIPTION

       xzcmp  and  xdiff invoke cmp(1) or diff(1) on files compressed with xz(1), lzma(1), gzip(1), or bzip2(1).  All options specified are passed
       directly to cmp or diff.  If only one file is specified, then the files compared are file1 (which must have a suffix of	a  supported  com-
       pression  format)  and  file1 from which the compression format suffix has been stripped.  If two files are specified, then they are uncom-
       pressed if necessary and fed to cmp(1) or diff(1).  The exit status from cmp or diff is preserved.

       The names lzcmp and lzdiff are provided for backward compatibility with LZMA Utils.

SEE ALSO

       cmp(1), diff(1), xz(1), gzip(1), bzip2(1), zdiff(1)

BUGS

       Messages from the cmp(1) or diff(1) programs refer to temporary filenames instead of those specified.

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