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Top Forums Shell Programming and Scripting awk to update field in file based of match in another Post 302986085 by cmccabe on Saturday 19th of November 2016 08:31:44 PM
Old 11-19-2016
awk to update field in file based of match in another

I am trying to use awk to match two files that are tab-delimited. When a match is found between file1 $1 and file2 $4, $4 in file2 is updated using the $2 value in file1. If no match is found then the next line is processed. Thank you Smilie.

file1
Code:
uc001bwr.3    ADC
uc001bws.3    ADC
uc001bwt.1    ADC
uc001bwu.3    ADC
uc001bwv.3    ADC
uc001bwx.1    ADC
uc001bwy.1    ADC
uc001bwz.1    ADC
uc001chv.2    LEPRE1
uc001chw.2    LEPRE1
uc001chx.4    LEPRE1
uc001chy.4    LEPRE1

file2
Code:
chr1    33546703    33546905    uc001bwr.3
chr1    33546978    33547119    uc001bwr.3
chr1    33547191    33547423    uc001bwr.3
chr1    43211995    43212533    uc001chw.2
chr1    43212913    43213093    uc001chw.2

desired output tab-delimeted
Code:
chr1    33546703    33546905    ADC
chr1    33546978    33547119    ADC
chr1    33547191    33547423    ADC
chr1    43211995    43212533    LEPRE1
chr1    43212913    43213093    LEPRE1

awk
Code:
awk -F'\t' -v OFS='\t'  'NR==FNR{a[$1]=4}NR!=FNR{if(a[$4])' file1 file2
awk: cmd. line:1: NR==FNR{a[$1]=4}NR!=FNR{if(a[$4])
awk: cmd. line:1:                                  ^ unexpected newline or end of string

 

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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 one of the file names 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. Input fields are normally separated spaces or tabs; output fields by space. In this case, multiple separators count as one, and leading separators are discarded. The following options are recognized, with POSIX syntax. -a n In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -v n Like -a, omitting output for paired lines. -e s Replace empty output fields by string s. -1 m -2 m Join on the mth field of file1 or file2. -jn m Archaic equivalent for -n m. -ofields Each output line comprises the designated fields. The comma-separated field designators are either 0, meaning the join field, or have the form n.m, where n is a file number and m is a field number. Archaic usage allows separate arguments for field designators. -tc Use character c as the only separator (tab character) on input and output. Every appearance of c in a line is significant. EXAMPLES
sort /etc/passwd | join -t: -1 1 -a 1 -e "" - bdays Add birthdays to the /etc/passwd file, leaving unknown birthdays empty. The layout of /adm/users is given in passwd(5); bdays con- tains sorted lines like tr : ' ' </etc/passwd | sort -k 3 3 >temp join -1 3 -2 3 -o 1.1,2.1 temp temp | awk '$1 < $2' Print all pairs of users with identical userids. SOURCE
/src/cmd/join.c SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b -ky,y; with -t, the sequence is that of sort -tx -ky,y. One of the files must be randomly accessible. JOIN(1)
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