Hello, I am confused about how to execute 'mass' commands when calling perl code in a shell script. I have around 30,000 DSSP files which I want to process within Perl. This entails creating a Bioperl DSSP object for every DSSP file that I will read. Part of the code (DSSP_output.pl) is as follows:

#!/usr/bin/perl -w
use strict;
use warnings;
use Bio::Structure::SecStr::DSSP::Res;

open (DSSPIN, "$ARGV[0]") || die $!;
#Create a new DSSP object
my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>DSSPIN);

# EXAMPLE OF HOW THE OBJECT IS NORMALLY DECLARED
#my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>'3bit.d
+ssp'); 

#Get PDB ID and Compound representation for each DSSP file
my $pdb_id = $dssp_obj->pdbID();
print "Analysis of PDB:: ". $pdb_id. "\n";
my $cmpd = $dssp_obj->pdbCompound();
print "Representing:: ". $cmpd. "\n";

etc...
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My dilemma is as follows: In a shell script, I want to read a list of filenames and execute DSSP_output.pl for each file. I am using in shell this would translate to:

<some loop to read each dssp filename>
dssp_output.pl filename.dssp
<end loop>
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Now how do I read each filename in perl? I can't use STDIN (I think) because I want this running automatically... the way I have written the code, DSSPIN produces the error:

Bareword "DSSPIN" not allowed when "strict subs" in use.

If I try the following:

open (DSSPIN, <>) || die $!;
my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>DSSPIN);
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Same error. And finally:

@data_from_files = <>;
#Create a new DSSP object
my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>$data_fr
+om_files);

Error: Global system @data_from_files, $data_from_files requires expli
+cit package name
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Apologies for a long post...I'm just badly confused with filehandling! What should I write to read in the DSSP filenames in the perl script? Much obliged!

A very confused InfoSeeker

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