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Top Forums Shell Programming and Scripting awk to calculate fields only if match is found Post 302973779 by cmccabe on Saturday 21st of May 2016 11:56:02 AM
Old 05-21-2016
awk to calculate fields only if match is found

Trying to combine the matching $5 values between file1 and file2. If a match is found then the last $6 value in the match and the sum of $7 are outputted to a new file. The awk below I hope is a good start. Thank you Smilie.

file1
Code:
chr12    9221325    9221448    chr12:9221325-9221448    A2M    1    125
chr12    9221325    9221448    chr12:9221325-9221448    A2M    2    125
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    1    120
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    2    120
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    3    130

file2
Code:
chr12    9221325    9221448    chr12:9221325-9221448    A2M    1    120
chr12    9221325    9221448    chr12:9221325-9221448    A2M    2    120
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    1    125
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    2    125
chr12    9221800    9221999    chr12:9221800-9221999    A2M1    3    135

awk tried with error
Code:
awk '{sum[$4]+=$6; count[$7]++} 
>     END{for(k in sum) printf "%s %.1f\n",  k, sum[k]/count[k]}' file1 file2 > out
awk: cmd. line:2: (FILENAME=file2 FNR=5) fatal: division by zero attempted

desired output
Code:
chr12    9221325    9221448    chr12:9221325-9221448    A2M    2    250
chr12    9221800    9221999    chr12:9221800-9221999     A2M1    3    385


Last edited by cmccabe; 05-21-2016 at 01:02 PM.. Reason: fixed format
 

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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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