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Top Forums Shell Programming and Scripting Perl error in batch command but works one at a time Post 302990891 by Corona688 on Thursday 2nd of February 2017 10:24:49 AM
Old 02-02-2017
That is not Perl. The membrane-thin wrapper of Perl serves literally no purpose. That is nothing but shell code. If you write the loop inside shell you'll save so much trouble and CPU time.

I too made this error when first learning to program in Perl and shell. Learn a little more shell and it will make more sense.

You can also split across multiple lines for readability by putting backslash-newline wherever you need to split it.
Code:
while read LINE
do
        echo perl table_annovar.pl -vcfinput "$LINE" humandb/ -buildver hg19 -arg '-hgvs',,,,, -remove -protocol \
                IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 \
                -operation g,f,f,f,f,f -otherinfo -nastring .
done < target.txt

Remove the echo once you've tested and made sure it does what you want.

Last edited by Corona688; 02-02-2017 at 11:32 AM..
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ECHO(1) 							   User Commands							   ECHO(1)

NAME
echo - display a line of text SYNOPSIS
echo [SHORT-OPTION]... [STRING]... echo LONG-OPTION DESCRIPTION
Echo the STRING(s) to standard output. -n do not output the trailing newline -e enable interpretation of backslash escapes -E disable interpretation of backslash escapes (default) --help display this help and exit --version output version information and exit If -e is in effect, the following sequences are recognized: NNN the character whose ASCII code is NNN (octal) \ backslash a alert (BEL)  backspace c produce no further output f form feed new line carriage return horizontal tab v vertical tab NOTE: your shell may have its own version of echo, which usually supersedes the version described here. Please refer to your shell's docu- mentation for details about the options it supports. AUTHOR
Written by Brian Fox and Chet Ramey. REPORTING BUGS
Report echo bugs to bug-coreutils@gnu.org GNU coreutils home page: <http://www.gnu.org/software/coreutils/> General help using GNU software: <http://www.gnu.org/gethelp/> COPYRIGHT
Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. SEE ALSO
The full documentation for echo is maintained as a Texinfo manual. If the info and echo programs are properly installed at your site, the command info coreutils 'echo invocation' should give you access to the complete manual. GNU coreutils 7.1 July 2010 ECHO(1)
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