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Full Discussion: Perl command in bash
Top Forums Shell Programming and Scripting Perl command in bash Post 302939698 by cmccabe on Friday 27th of March 2015 05:24:15 PM
Old 03-27-2015
Perl command in bash

I have the below perl script that runs (I think):

Code:
 'C:\Users\cmccabe\Desktop\annovar\matrix.pl' < "${id}".txt.hg19_multianno.txt > "L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt"

The problem is I get an error that the ${id}.txt does not exist. I have tried "${id}.txt as well. There is a file (attached) with the id in it as well but can sed or awk be used to extract this id from the file and put it in the perl command?

For example, snp.txt is the first line of target.txt - can that value be extracted and substituted for the ${id).txt in the perl . Also, if there are multiple lines can it loop through one at a time? Thank you Smilie.
 

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Perl::Critic::Policy::InputOutput::ProhibitTwoArgOpen(3pUser Contributed Perl DocumentatPerl::Critic::Policy::InputOutput::ProhibitTwoArgOpen(3pm)

NAME
Perl::Critic::Policy::InputOutput::ProhibitTwoArgOpen - Write "open $fh, q{<}, $filename;" instead of "open $fh, "<$filename";". AFFILIATION
This Policy is part of the core Perl::Critic distribution. DESCRIPTION
The three-argument form of "open" (introduced in Perl 5.6) prevents subtle bugs that occur when the filename starts with funny characters like '>' or '<'. The IO::File module provides a nice object-oriented interface to filehandles, which I think is more elegant anyway. open( $fh, '>output.txt' ); # not ok open( $fh, q{>}, 'output.txt' ); # ok use IO::File; my $fh = IO::File->new( 'output.txt', q{>} ); # even better! It's also more explicitly clear to define the input mode of the file, as in the difference between these two: open( $fh, 'foo.txt' ); # BAD: Reader must think what default mode is open( $fh, '<', 'foo.txt' ); # GOOD: Reader can see open mode This policy will not complain if the file explicitly states that it is compatible with a version of perl prior to 5.6 via an include statement, e.g. by having "require 5.005" in it. CONFIGURATION
This Policy is not configurable except for the standard options. NOTES
There are two cases in which you are forced to use the two-argument form of open. When re-opening STDIN, STDOUT, or STDERR, and when doing a safe pipe open, as described in perlipc. SEE ALSO
IO::Handle IO::File AUTHOR
Jeffrey Ryan Thalhammer <jeff@imaginative-software.com> COPYRIGHT
Copyright (c) 2005-2011 Imaginative Software Systems. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2012-06-07 Perl::Critic::Policy::InputOutput::ProhibitTwoArgOpen(3pm)
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