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

Ok, bear with me. I have used the suggestion:

my $dssp_obj = new Bio::Structure::SecStr::DSSP::Res('-file'=>$ARGV[0]
+);
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Which works (and I'm ignoring several filehandle warnings). Now, I have written a shell script:

#!/bin/bash
while read DSSPLine ; do
echo $DSSPLine
DSSP_Output.pl $DSSPLine.dssp
done
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QUESTION: In each interation, the output of DSSP_Output.pl is written to a CSV file. Is there a way such that (in perl) this output is written for all 30,000 iterations to one file only?

The very obvious answer is to use a DSSP array like you mentioned, I have tried that (in a way):

use strict; # 'use strict' requires that you use 'my' for all local va
+riables, or explicitely qualify all globals.
use warnings;
use Bio::Structure::SecStr::DSSP::Res;

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

foreach my $dssp_obj(@dssp_objs)
{
#Get PDB ID and Compound representation for each 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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But when I do this, and run the commandline with a txt file of the DSSP filenames:

DSSP_Output.pl DSSP_codes.txt

I get an exception!

Please let me know what you think...apologies for all the headache...

A <slowly deconfusing> InfoSeeker

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Re^3: Confused when reading Input within Perl and Shell Scripts by gwadej (Chaplain) on Nov 17, 2008 at 01:04 UTC
The approach I gave would have worked if you had all of the list of filenames on the command line. If you want to take the list of filenames from a file, then we need to modify the input loop somewhat: `my @dssp_objs =(); #reads the files from the command line one line at a time. while(<>) { chomp; # remove the newline. push @dssp_objs, Bio::Structure::SecStr::DSSP::Res->new('-file'=>$_); }` [download] This code would read a line at a time out of DSSP_codes.txt (using your example). I changed to the `while(<>)` loop just to be consistent with the way most people do this kind of loop. Since it automatically loads the `$_` variable (and the loop is pretty short), I removed the `$file` variable. Otherwise, this is a drop-in replacement for the previous loop that should meet your needs. G. Wade	[reply] [d/l] [select]

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Re^3: Confused when reading Input within Perl and Shell Scripts
by gwadej (Chaplain) on Nov 17, 2008 at 01:04 UTC

The approach I gave would have worked if you had all of the list of filenames on the command line. If you want to take the list of filenames from a file, then we need to modify the input loop somewhat:

my @dssp_objs =();
#reads the files from the command line one line at a time.
while(<>)
{
    chomp; # remove the newline.
push @dssp_objs, Bio::Structure::SecStr::DSSP::Res->new('-file'=>$_);
}
[download]

This code would read a line at a time out of DSSP_codes.txt (using your example).

I changed to the while(<>) loop just to be consistent with the way most people do this kind of loop. Since it automatically loads the $_ variable (and the loop is pretty short), I removed the $file variable. Otherwise, this is a drop-in replacement for the previous loop that should meet your needs.

G. Wade

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