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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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ECACCESS-FILE-MOVE(1p)					User Contributed Perl Documentation				    ECACCESS-FILE-MOVE(1p)

NAME
ecaccess-file-move - Move or Rename ECaccess Files SYNOPSIS
ecaccess-file-move -version|-help|-manual ecaccess-file-move [-debug] source-ecaccess-file target-ecaccess-file DESCRIPTION
Allow moving an ECaccess File. When the move occurs within the same ECaccess File System then it is a rename. When the move occurs across two different ECaccess File Systems then first a copy is done and then a delete of the original file is done (e.g. similar to ecaccess- file-copy ... -erase). The source-ecaccess-file and target-ecaccess-file are in the form [domain:][/user-id/]path. Please read the "Shell commands -> File Management" section of the "ecaccess" guide for more information on the ECaccess File System. ARGUMENTS
source-ecaccess-file The source ECaccess File name. target-ecaccess-file The target ECaccess File name. OPTIONS
-version Display version number and exits. -help Print a brief help message and exits. -manual Prints the manual page and exits. -debug Display the SOAP messages exchanged. EXAMPLES
ecaccess-file-move ec:test1.txt ec:test2.txt Rename the test1.txt file in the ECFS directory of the authenticated user in test2.txt. ecaccess-file-move ec:test1.txt home:test2.txt Copy the test1.txt file from the ECFS directory of the authenticated user to the test2.txt file in the $HOME directory of the authenticated user, then delete the test1.txt file from ECFS. SEE ALSO
ecaccess-file-delete, ecaccess-file-get, ecaccess-file-mget, ecaccess-file-modtime, ecaccess-file-mput, ecaccess-file-rmdir, ecaccess-file- copy, ecaccess-file-dir, ecaccess-file-mdelete, ecaccess-file-mkdir, ecaccess-file-chmod, ecaccess-file-put, ecaccess-file-size and ecaccess. perl v5.14.2 2012-04-16 ECACCESS-FILE-MOVE(1p)
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