If I'm reading your example code correctly, you are closer than you think. When you say:

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

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it looks like you are saying that normally the name of the of the file (and not a file handle) needs to be passed to Bio::Structure::SecStr::DSSP::Res::new method as the -file argument.

If that's the case, then you could do the following:

my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>$ARGV[0]
+);

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if the file you want to open is on the command line of your script, like your example. Now, if you wanted to replicate this for all of the files on the command line, you would do something like:

  my @dssp_objs = ();
  foreach my $file (@ARGV)
  {
      push @dssp_objs, Bio::Structure::SecStr::DSSP::Res->new('-file'=
+>$file);
  }

[download]

giving you an array of DSSP objects to work with.

G. Wade

In reply to Re: Confused when reading Input within Perl and Shell Scripts by gwadej
in thread Confused when reading Input within Perl and Shell Scripts by InfoSeeker

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