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Top Forums Shell Programming and Scripting How to join one file with multiple files in a directory in UNIX? Post 302942021 by Don Cragun on Thursday 23rd of April 2015 03:08:05 PM
Old 04-23-2015
Quote:
Originally Posted by sajmar
Sorry Scrutinize, if I put you in the wrong way. this time the command works well. But If I need to put it inside loop, this code did not work
Code:
ls *.geno | while read FN;  awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' unlocol_accessions $FN > ${FN/geno/geno2}; done

do you have any suggestion for putting your command in loop?
Instead of saying "code did not work" it would help everyone reading your thread if you would post the diagnostics that were printed by the shell that explains why it didn't work.

In this case, using correct syntax would seem to fix your problem:
Code:
ls *.geno | while read FN
do      awk '
                NR==FNR{A[$2]=$0; next}
                $1 in A{print A[$1], $0}
        ' unlocol_accessions "$FN" > "${FN/geno/geno2}"
done

or, if you insist on single line code instead of readable code:
Code:
ls *.geno | while read FN;do awk 'NR==FNR{A[$2]=$0; next} $1 in A{print A[$1], $0}' unlocol_accessions "$FN" > "${FN/geno/geno2}"; done

Or, more simply:
Code:
for FN in *.geno
do      awk '
                NR==FNR{A[$2]=$0; next}
                $1 in A{print A[$1], $0}
        ' unlocol_accessions "$FN" > "${FN/geno/geno2}"
done


Last edited by Don Cragun; 04-23-2015 at 04:14 PM.. Reason: Add alternative without pipeline and add quotes.
 

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IO::Async::PID(3pm)					User Contributed Perl Documentation				       IO::Async::PID(3pm)

NAME
"IO::Async::PID" - event callback on exit of a child process SYNOPSIS
use IO::Async::PID; use POSIX qw( WEXITSTATUS ); use IO::Async::Loop; my $loop = IO::Async::Loop->new; my $kid = $loop->fork( code => sub { print "Child sleeping.. "; sleep 10; print "Child exiting "; return 20; }, ); print "Child process $kid started "; my $pid = IO::Async::PID->new( pid => $kid, on_exit => sub { my ( $self, $exitcode ) = @_; printf "Child process %d exited with status %d ", $self->pid, WEXITSTATUS($exitcode); }, ); $loop->add( $pid ); $loop->run; DESCRIPTION
This subclass of IO::Async::Notifier invokes its callback when a process exits. For most use cases, a IO::Async::Process object provides more control of setting up the process, connecting filehandles to it, sending data to and receiving data from it. EVENTS
The following events are invoked, either using subclass methods or CODE references in parameters: on_exit $exitcode Invoked when the watched process exits. PARAMETERS
The following named parameters may be passed to "new" or "configure": pid => INT The process ID to watch. Must be given before the object has been added to the containing "IO::Async::Loop" object. on_exit => CODE CODE reference for the "on_exit" event. Once the "on_exit" continuation has been invoked, the "IO::Async::PID" object is removed from the containing "IO::Async::Loop" object. METHODS
$process_id = $pid->pid Returns the underlying process ID $pid->kill( $signal ) Sends a signal to the process AUTHOR
Paul Evans <leonerd@leonerd.org.uk> perl v5.14.2 2012-10-24 IO::Async::PID(3pm)
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