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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:
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [-an] [-e s] [-o list] [-tc] 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. -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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