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Full Discussion: Problem with writing to output - awk, echo
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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XCLIP-COPYFILE(1)					      General Commands Manual						 XCLIP-COPYFILE(1)

NAME

       xclip-copyfile, xclip-cutfile, xclip-pastefile - copy and move files via the X clipboard

SYNOPSIS

       xclip-copyfile [-p] FILES...

       xclip-cutfile [-p] FILES...

       xclip-pastefile

DESCRIPTION

       xclip-copyfile copies files into the X clipboard, recursing into directories.

       xclip-cutfile copies the files, but also deletes them afterwards.

       -p     preserve path formation

       xclip-pastefile pastes the files out of the clipboard

EXAMPLES

       Copying a file to a remote host

       [maggie.lkpg.cendio.se ~]$ echo "A file created on ${HOSTNAME}" > file1
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       [sofie.homeip.net ~/doc]$ xclip-pastefile
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       A file created on maggie.lkpg.cendio.se

       Copying an entire tree structure

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       Copying files with preserved path information

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AUTHORS

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																 XCLIP-COPYFILE(1)
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