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Full Discussion: User prompt for perl
Top Forums Shell Programming and Scripting User prompt for perl Post 302918772 by cmccabe on Thursday 25th of September 2014 11:58:10 AM
Old 09-25-2014
When I open the code using linux it is three lines, not sure why its one on here (maybe windows).

Code:
 
perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment
Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})'
W34903_Noonan14_Output_Mutation_Report.txt < W34903_Noonan14_Output_Mutation_Report_Filtered.vcf > W34903_matched.vcf

Thanks.
 

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Nagios::Plugin::Functions(3pm)				User Contributed Perl Documentation			    Nagios::Plugin::Functions(3pm)

NAME
Nagios::Plugin::Functions - functions to simplify the creation of Nagios plugins SYNOPSIS
# Constants OK, WARNING, CRITICAL, and UNKNOWN exported by default use Nagios::Plugin::Functions; # nagios_exit( CODE, $message ) - exit with error code CODE, # and message "PLUGIN CODE - $message" nagios_exit( CRITICAL, $critical_error ) if $critical_error; nagios_exit( WARNING, $warning_error ) if $warning_error; nagios_exit( OK, $result ); # nagios_die( $message, [$CODE] ) - just like nagios_exit(), # but CODE is optional, defaulting to UNKNOWN do_something() or nagios_die("do_something() failed horribly"); do_something_critical() or nagios_die("do_something_critical() failed", CRITICAL); # check_messages - check a set of message arrays, returning a # CODE and/or a result message $code = check_messages(critical => @crit, warning => @warn); ($code, $message) = check_messages( critical => @crit, warning => @warn, ok => @ok ); # get_shortname - return the default short name for this plugin # (as used by nagios_exit/die; not exported by default) $shortname = get_shortname(); DESCRIPTION
This module is part of the Nagios::Plugin family, a set of modules for simplifying the creation of Nagios plugins. This module exports convenience functions for the class methods provided by Nagios::Plugin. It is intended for those who prefer a simpler functional interface, and who do not need the additional functionality of Nagios::Plugin. EXPORTS Nagios status code constants are exported by default: OK WARNING CRITICAL UNKNOWN DEPENDENT as are the following functions: nagios_exit nagios_die check_messages The following variables and functions are exported only on request: %ERRORS %STATUS_TEXT get_shortname max_state max_state_alt FUNCTIONS The following functions are supported: nagios_exit( <CODE>, $message ) Exit with return code CODE, and a standard nagios message of the form "PLUGIN CODE - $message". nagios_die( $message, [CODE] ) Same as nagios_exit(), except that CODE is optional, defaulting to UNKNOWN. NOTE: exceptions are not raised by default to calling code. Set $_use_die flag if this functionality is required (see test code). check_messages( critical => @crit, warning => @warn ) Convenience function to check a set of message arrays and return an appropriate nagios return code and/or a result message. Returns only a return code in scalar context; returns a return code and an error message in list context i.e. # Scalar context $code = check_messages(critical => @crit, warning => @warn); # List context ($code, $msg) = check_messages(critical => @crit, warning => @warn); check_messages() accepts the following named arguments: critical => ARRAYREF An arrayref of critical error messages - check_messages() returns CRITICAL if this arrayref is non-empty. Mandatory. warning => ARRAYREF An arrayref of warning error messages - check_messages() returns WARNING if this arrayref is non-empty ('critical' is checked first). Mandatory. ok => ARRAYREF | SCALAR An arrayref of informational messages (or a single scalar message), used in list context if both the 'critical' and 'warning' arrayrefs are empty. Optional. join => SCALAR A string used to join the relevant array to generate the message string returned in list context i.e. if the 'critical' array @crit is non-empty, check_messages would return: join( $join, @crit ) as the result message. Optional; default: ' ' (space). join_all => SCALAR By default, only one set of messages are joined and returned in the result message i.e. if the result is CRITICAL, only the 'critical' messages are included in the result; if WARNING, only the 'warning' messages are included; if OK, the 'ok' messages are included (if supplied) i.e. the default is to return an 'errors-only' type message. If join_all is supplied, however, it will be used as a string to join the resultant critical, warning, and ok messages together i.e. all messages are joined and returned. get_shortname Return the default shortname used for this plugin i.e. the first token reported by nagios_exit/nagios_die. The default is basically uc basename( $ENV{NAGIOS_PLUGIN} || $0 ) with any leading 'CHECK_' and trailing file suffixes removed. get_shortname is not exported by default, so must be explicitly imported. max_state(@a) Returns the worst state in the array. Order is: CRITICAL, WARNING, OK, UNKNOWN, DEPENDENT The typical usage of max_state is to initialise the state as UNKNOWN and use it on the result of various test. If no test were performed successfully the state will still be UNKNOWN. max_state_alt(@a) Returns the worst state in the array. Order is: CRITICAL, WARNING, UNKNOWN, DEPENDENT, OK This is a true definition of a max state (OK last) and should be used if the internal tests performed can return UNKNOWN. SEE ALSO
Nagios::Plugin; the nagios plugin developer guidelines at http://nagiosplug.sourceforge.net/developer-guidelines.html. AUTHORS
This code is maintained by the Nagios Plugin Development Team: http://nagiosplug.sourceforge.net COPYRIGHT AND LICENSE
Copyright (C) 2006 by Nagios Plugin Development Team This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2011-12-23 Nagios::Plugin::Functions(3pm)
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