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Full Discussion: Error in .pl
Top Forums Shell Programming and Scripting Error in .pl Post 302921813 by cmccabe on Monday 20th of October 2014 12:16:06 PM
Old 10-20-2014
The only change that was made is the file is called match.sh and is called by:
Code:
 bash ~/match.sh

The same code as in post 1 is being used with the same error resulting. Thank you Smilie.

Code:
 #!/bin/bash
echo -n "Enter ID  : "; read id
echo -n "What panel: "; read panel
OMR=Output_Mutation_Report
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})' $id_$panel_$OMR.txt < $id_$panel_$OMR_Filtered.vcf > $id_matched.vcf

 

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panel_above(3CURSES)					     Curses Library Functions					      panel_above(3CURSES)

NAME
panel_above, panel_below - panels deck traversal primitives SYNOPSIS
cc [ flag ... ] file ... -lpanel -lcurses [ library .. ] #include <panel.h> PANEL *panel_above(PANEL *panel); PANEL *panel_below(PANEL *panel); DESCRIPTION
panel_above() returns a pointer to the panel just above panel, or NULL if panel is the top panel. panel_below() returns a pointer to the panel just below panel, or NULL if panel is the bottom panel. If NULL is passed for panel, panel_above() returns a pointer to the bottom panel in the deck, and panel_below() returns a pointer to the top panel in the deck. RETURN VALUES
NULL is returned if an error occurs. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |MT-Level |Unsafe | +-----------------------------+-----------------------------+ SEE ALSO
curses(3CURSES), panels(3CURSES), attributes(5) NOTES
These routines allow traversal of the deck of currently visible panels. The header <panel.h> automatically includes the header <curses.h>. SunOS 5.11 31 Dec 1996 panel_above(3CURSES)
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