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Top Forums UNIX for Beginners Questions & Answers awk to average matching lines in file Post 303041704 by cmccabe on Monday 2nd of December 2019 09:22:44 AM
Old 12-02-2019
awk to average matching lines in file

The awk below executes and is close (producing the first 4 columns in desired). However, when I add the sum of $7, I get nothing returned. Basically, I am trying to combine all the matching $4 in f1 and output them with the average of $7 in each match. Thank you Smilie.

f1
Code:
chr9	135804143	135804145	chr9:135804143-135804145	TSC1	1	128
chr9	135804143	135804145	chr9:135804143-135804145	TSC1	2	125
chr9	135819919	135819922	chr9:135819919-135819922	TSC1	1	0
chr9	135819919	135819922	chr9:135819919-135819922	TSC1	2	0
chr9	135819919	135819922	chr9:135819919-135819922	TSC1	3	0
chr16	2097885	2097890	chr16:2097885-2097890	TSC2	1	249
chr16	2097885	2097890	chr16:2097885-2097890	TSC2	2	245
chr16	2097885	2097890	chr16:2097885-2097890	TSC2	3	243
chr16	2097885	2097890	chr16:2097885-2097890	TSC2	4	237
chr16	2097885	2097890	chr16:2097885-2097890	TSC2	5	237

desired tab-delimeted
Code:
chr9	135804143	135804145 	TSC1	126
chr9	135819919	135819922 	TSC1	0
chr16	2097885	2097890 	TSC2	242

awk
Code:
awk '
# print from stored values
function prt(){
  print p1 ":" (p6start==1 ? p2 : p2+p6start) "-" p2+p6, "\t" p5
}
($4!=p4 || $6!=p6+1) {
# new sequence, print the previous sequence
  if (NR>1) prt()
  p6start=$6  
}
{
# store the values that for later
  p1=$1
  p2=$2
  p4=$4
  p5=$5
  p6=$6
}
END { prt() }
' f1 | awk -F"[:-]" ' { print $1 "\t" $2 "\t" $3 "\t" $4}' | awk -v N=7 '{ sum += $N } END { if (NR > 0) print sum / NR }' > out

 

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RAKE(1) 						 Ruby Programmers Reference Guide						   RAKE(1)

NAME
rake -- Ruby Make SYNOPSIS
rake [--f Rakefile] [--version] [-CGNPgnqstv] [-D [PATTERN]] [-E CODE] [-I LIBDIR] [-R RAKELIBDIR] [-T [PATTERN]] [-e CODE] [-p CODE] [-r MODULE] [--rules] [variable=value] target ... DESCRIPTION
Rake is a simple ruby(1) build program with capabilities similar to the regular make(1) command. Rake has the following features: o Rakefiles (Rake's version of Makefiles) are completely defined in standard Ruby syntax. No XML files to edit. No quirky Makefile syntax to worry about (is that a tab or a space?). o Users can specify tasks with prerequisites. o Rake supports rule patterns to synthesize implicit tasks. o Flexible FileLists that act like arrays but know about manipulating file names and paths. o A library of prepackaged tasks to make building rakefiles easier. OPTIONS
--version Display the program version. -C --classic-namespace Put Task and FileTask in the top level namespace -D [PATTERN] --describe [PATTERN] Describe the tasks (matching optional PATTERN), then exit. -E CODE --execute-continue CODE Execute some Ruby code, then continue with normal task processing. -G --no-system --nosystem Use standard project Rakefile search paths, ignore system wide rakefiles. -I LIBDIR --libdir LIBDIR Include LIBDIR in the search path for required modules. -N --no-search --nosearch Do not search parent directories for the Rakefile. -P --prereqs Display the tasks and dependencies, then exit. -R RAKELIBDIR --rakelib RAKELIBDIR --rakelibdir RAKELIBDIR Auto-import any .rake files in RAKELIBDIR. (default is rakelib ) -T [PATTERN] --tasks [PATTERN] Display the tasks (matching optional PATTERN) with descriptions, then exit. -e CODE --execute CODE Execute some Ruby code and exit. -f FILE --rakefile FILE Use FILE as the rakefile. -h --help Prints a summary of options. -g --system Using system wide (global) rakefiles (usually ~/.rake/*.rake ). -n --dry-run Do a dry run without executing actions. -p CODE --execute-print CODE Execute some Ruby code, print the result, then exit. -q --quiet Do not log messages to standard output. -r MODULE --require MODULE Require MODULE before executing rakefile. -s --silent Like --quiet, but also suppresses the 'in directory' announcement. -t --trace Turn on invoke/execute tracing, enable full backtrace. -v --verbose Log message to standard output (default). --rules Trace the rules resolution. SEE ALSO
ruby(1) make(1) http://rake.rubyforge.org/ REPORTING BUGS
Bugs, features requests and other issues can be logged at <http://onestepback.org/redmine/projects/show/rake>. You will need an account to before you can post issues. Register at <http://onestepback.org/redmine/account/register>. Or you can send an email to the author. AUTHOR
Rake is written by Jim Weirich <jim@weirichhouse.org> UNIX
November 7, 2012 UNIX
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