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Top Forums Shell Programming and Scripting Problem with writing to output - awk, echo Post 302716531 by @man on Tuesday 16th of October 2012 02:25:20 PM
Old 10-16-2012
Problem with writing to output - awk, echo

Hello all,

I wrote this command line for some calculation on my given input files based on another input file which is a txt file.
Code:
while read BAM REGION;  do samtools view $BAM $REGION | awk '{if ($2==0) print $0}' | wc -l  >>log.txt; echo "$REGION"; done >> log.txt <regions.txt

It takes each file and parse it and with wc -l I want to count the number of lines and writing to output file.
My problem is that it writes $REGION and calculation of samtools in separate lines. It gives me the output like this:

calc1
region1
calc2
region2
calc3
region3
...

But I want it to be like this:

region1 calc1
region2 calc2
region3 calc3
...

Can you help me with this?
Thanks for your consideration.
 

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BAM(1)								   User Commands							    BAM(1)

NAME
bam - fast and flexible build system SYNOPSIS
bam [OPTION]... [VARIABLE=VALUE]... [TARGET]... DESCRIPTION
Builds applications using the bam build system. Execution: -a abort on error -c clean targets -d build targets that is dependent given targets --dry dry run, don't run any jobs -j sets the number of threads to use (default: 0, disabled) -s bam file to use (default: bam.lua) Lua: -l print local variables in backtrace -t print backtrace when an error occurs Output: -r build progress report format (default: s) b = progress bar c = use ansi colors s = build steps -v be verbose Other: -n don't use cache -h, --help prints this help Debug: --debug-nodes prints all the nodes with dependencies --debug-detail prints all the nodes with dependencies and details --debug-jobs prints all the jobs that exist --debug-dot prints all nodes as a graphviz dot file --debug-jobs-dot prints all jobs as a graphviz dot file --debug-trace-vm prints a line for every instruction the vm makes --debug-dump-int prints the internals scripts to stdout --debug-no-int don't load internal scripts bam by Magnus Auvinen (magnus.auvinen@gmail.com) bam May 2011 BAM(1)
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