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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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LEARN ABOUT SUSE

exigrep

EXIGREP(8)                                                    System Manager's Manual                                                   EXIGREP(8)

NAME

       EXIGREP - Search Exim's main log

SYNOPSIS

       exigrep [-l] pattern [log file] ...

DESCRIPTION

       The  exigrep  utility  is  a  Perl script that searches one or more main log files for entries that match a given pattern.  When it finds a
       match, it extracts all the log entries for the relevant message, not just those that match the pattern.  Thus, exigrep can extract complete
       log entries for a given message, or all mail for a given user, or for a given host, for example.

       The -l flag means 'literal', that is, treat all characters in the pattern as standing for themselves.  Otherwise the pattern must be a Perl
       regular expression.  The pattern match is case-insensitive.  If no file names are given on the command line, the standard input is read.

       If the location of a zcat command is known from the definition of ZCAT_COMMAND in Local/Makefile, exigrep  automatically  passes  any  file
       whose name ends in COMPRESS_SUFFIX through zcat as it searches it.

BUGS

       This manual page needs a major re-work. If somebody knows better groff than us and has more experience in writing manual pages, any patches
       would be greatly appreciated.

SEE ALSO

       exim(8), perlre(1), /usr/share/doc/exim4-base/

AUTHOR

       This manual page was stitched together from spec.txt by Andreas Metzler <ametzler at downhill.at.eu.org>, for the Debian  GNU/Linux  system
       (but may be used by others).

                                                                  March 26, 2003                                                        EXIGREP(8)
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