I have the below bash which runs great. Before I make a change I wanted to check with experts (as I am not one). After the perl code completes, I am going to display "annotation complete" then go into the remove function .
Code:
annovar() {
# combine id and position files
cd 'C:\Users\cmccabe\Desktop\annovar'
cp out_parse.txt "$(cat target.txt)"
# run annotation
$( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
printf "The annotation is complete, would you like analyze additional target gene patients? Y/N "; read match_choice
case "$match_choice" in
[yY]) id="${id}"; menu ;;
[nN]) id="${id}"; remove ;;
esac
}
My question is will something like this work: Thank you .
Code:
annovar() {
# combine id and position files
cd 'C:\Users\cmccabe\Desktop\annovar'
cp out_parse.txt "$(cat target.txt)"
# run annotation
$( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
printf "The annotation is complete "; remove
esac
}
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Discussion started by: HikingLife
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LEARN ABOUT DEBIAN
ecaccess-file-move
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)
05-28-2015
.