Re^2: Confused when reading Input within Perl and Shell Scripts

Thank you. Initially I want to provide a txt file with the filenames, for example, DsspCodes.txt:

2bx2.dssp
3cob.dssp
1nwn.dssp
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Based on your comments and my novice use of perl, I have modified the code to:

use strict; 
use warnings;
use Bio::Structure::SecStr::DSSP::Res;

my @filenames;
for my $filename (@filenames)
{
open my $dsspIn, '<', $filename or die "Unable to open $filename: $!\n
+";

#Create a new DSSP object
my $dssp_obj = Bio::Structure::SecStr::DSSP::Res->new ('-file'=> $dssp
+In);

....
close dsspIn;
}
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But if call in the commandline:

DSSP_output.pl DsspCodes.txt

I don't get any errors but I also don't get any output??

Thanks for your patience as I learn this..

InfoSeeker

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Re^3: Confused when reading Input within Perl and Shell Scripts by GrandFather (Saint) on Nov 16, 2008 at 23:28 UTC
Think about how the contents of the external file containing the file names are going to get into the @filenames array. At present your code has nothing to do that. One way would be: `my $namesFileName = shift; # Get name of the file names file from comm +and line open my $inNames, '<', $namesFileName or die "Unable to open $namesFil +eName: $!\n"; my @filenames = <$inNames>; # Read the file names (one per line) close $inNames; chomp @filenames; # Remove the line end character from each entry ...` [download] or you could replace the for loop with a while loop and eliminate the array: `use strict; use warnings; my $namesFileName = shift; # Get name of the file names file from co +mmand line open my $inNames, '<', $namesFileName or die "Unable to open $namesFil +eName: $!\n"; while (<$inNames>) { chomp; # Remove line end character from file name open my $dsspIn, '<', $_ or die "Unable to open $_: $!\n"; ... } close $inNames;` [download] Perl reduces RSI - it saves typing	[reply] [d/l] [select]

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Re^3: Confused when reading Input within Perl and Shell Scripts
by GrandFather (Saint) on Nov 16, 2008 at 23:28 UTC

Think about how the contents of the external file containing the file names are going to get into the @filenames array. At present your code has nothing to do that. One way would be:

my $namesFileName = shift; # Get name of the file names file from comm
+and line

open my $inNames, '<', $namesFileName or die "Unable to open $namesFil
+eName: $!\n";
my @filenames = <$inNames>; # Read the file names (one per line)
close $inNames;
chomp @filenames; # Remove the line end character from each entry

...
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or you could replace the for loop with a while loop and eliminate the array:

use strict;
use warnings;

my $namesFileName = shift;   # Get name of the file names file from co
+mmand line

open my $inNames, '<', $namesFileName or die "Unable to open $namesFil
+eName: $!\n";

while (<$inNames>) {
    chomp; # Remove line end character from file name
    open my $dsspIn, '<', $_ or die "Unable to open $_: $!\n";
    ...
}

close $inNames;
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Perl reduces RSI - it saves typing

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