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Full Discussion: Perl command in bash
Top Forums Shell Programming and Scripting Perl command in bash Post 302939760 by cmccabe on Saturday 28th of March 2015 12:28:24 PM
Old 03-28-2015
I use a perl script to add specific text to specific columns in a text file. A new file gets created in the location listed below but it is empty. So I am not sure if the script itself is incorrect or if the input file is not being used. Below is how I call the perl script:

I provide the full path to the .pl , the input and the output

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

The overall goal is use ${id}.txt.hg19_multianno.txt as the input file and after the perl script is run on that file (which adds the columns and text) and the new file is saved to the path L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt . That path is a static path and will never change, there is probably a better way but I am not expert enough to know. I attached the .pl as well. Thank you
perl.zip (548 Bytes) 
Last edited by Don Cragun; 03-28-2015 at 03:04 PM.. Reason: Fix ICODE tags.
 

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LEARN ABOUT PHP

phar.interceptfilefuncs

PHAR.INTERCEPTFILEFUNCS(3)						 1						PHAR.INTERCEPTFILEFUNCS(3)

Phar::interceptFileFuncs - instructs phar to intercept fopen, file_get_contents, opendir, and all of the stat-related functions

SYNOPSIS

       finalpublicstatic void Phar::interceptFileFuncs (void  )

DESCRIPTION

	instructs  phar  to  intercept	fopen(3),  readfile(3), file_get_contents(3), opendir(3), and all of the stat-related functions. If any of
       these functions is called from within a phar archive with a relative path, the call is modified to access a file within the  phar  archive.
       Absolute paths are assumed to be attempts to load external files from the filesystem.

	This function makes it possible to run PHP applications designed to run off of a hard disk as a phar application.

PARAMETERS

	No parameters.

RETURN VALUES

EXAMPLES

       Example #1

	      A Phar.interceptFileFuncs(3) example

	      <?php
	      Phar::interceptFileFuncs();
	      include 'phar://' . __FILE__ . '/file.php';
	      ?>

	Assuming that this phar is at /path/to/myphar.phar and it contains file.php and file2.txt, if file.php contains this code:

       Example #2

	      A Phar.interceptFileFuncs(3) example

	      <?php
	      echo file_get_contents('file2.txt');
	      ?>

	Normally  PHP  would search the current directory for file2.txt, which would translate as the directory of file.php, or the current direc-
       tory of a command-line user. Phar.interceptFileFuncs(3) instructs PHP to consider the current directory to be  phar:///path/to/myphar.phar/
       and so opens phar:///path/to/myphar.phar/file2.txt in the above example code.

PHP Documentation Group 												PHAR.INTERCEPTFILEFUNCS(3)
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