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Full Discussion: Shell script foreach help
Top Forums UNIX for Dummies Questions & Answers Shell script foreach help Post 302711369 by dgrayman on Friday 5th of October 2012 10:50:34 PM
Old 10-05-2012
Error Shell script foreach help
I am writing a shell script to uncompress files in a directory, then call a Perl script to search the files for given terms, store those terms in a different output file , and compress the output. I get a syntax error with my use of foreach. Below is my script.
Code:
#!/bin/csh -fxv

if (! $#argv==1); then
    echo "[fail, not enough input arguments]"
    exit 10
else
    echo "the pitch and kinf will be stored in a new file called" $1
    echo " "
endif
rm $1

# uncompress output files in directory
set list= `/bin/ls *.out.gz`
foreach f ($list)
    gunzip $f
end

#run the pearl script on each output file and compress that file
set list= `/bin/ls *.out`
foreach i ($list)
    ./readfile.pl $i $1
    gzip $i
end

exit 0

Last edited by fpmurphy; 10-06-2012 at 12:38 AM..
 

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LEARN ABOUT DEBIAN

bp_process_wormbase

BP_PROCESS_WORMBASE(1p) 				User Contributed Perl Documentation				   BP_PROCESS_WORMBASE(1p)

NAME

       process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser

SYNOPSIS

	 % process_wormbase.pl ./WS61 > wormbase.gff

DESCRIPTION

       This script massages the Wormbase GFF files located at ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the GFF format
       suitable for display by the generic genome browser.  It mainly adds comments to the annotations and designates certain well-spaced genetic
       loci as framework landmarks.

       This script requires the AcePerl distribution, which is available on CPAN (look for the "Ace" module).

       To use this script, get the WormBase GFF files from the FTP site listed above and place them in a directory.  It might be a good idea to
       name the directory after the current release, such as WS61.  You do not need to uncompress the files.

       Then give that directory as the argument to this script and capture the script's output to a file:

	 % process_wormbase.pl ./WS61 > wormbase.gff

       It may take a while before you see output from this script, since it must first fetch gene and protein database from the remote AceDB
       running at www.wormbase.org.  The wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command:

	 % bulk_load_gff.pl -d <databasename> wormbase.gff

SEE ALSO

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

AUTHOR

       Lincoln Stein <lstein@cshl.org>

       Copyright (c) 2002 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.14.2							    2012-03-02						   BP_PROCESS_WORMBASE(1p)
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