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Full Discussion: How to run perl script on multiple files of two directories?
Top Forums Shell Programming and Scripting How to run perl script on multiple files of two directories? Post 302856711 by grace_shen on Tuesday 24th of September 2013 04:19:48 PM
Old 09-24-2013
Quote:
Originally Posted by Chubler_XL
Try a nested for loop

Code:
for A in A/*
do
    for B in b/*
    do
        perl script.pl $A $B
    done
done

Do i need to put it in my perl script?
Or it is a linux command?
Sorry for the silly question.
And I want to generate output file name according to the file in A
such as
perl script.pl A/1.txt B/name.txt > C/1.gff

---------- Post updated at 04:19 PM ---------- Previous update was at 04:16 PM ----------

Do i need to put it in my perl script?
Or it is a linux command?
Sorry for the silly question.
And I want to generate output file name according to the file in A
such as
perl script.pl A/1.txt B/name.txt > C/1.gff
 

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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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