[Bioperl-l] Error message.

[Jason Stajich]

This works fine for me.  You're not telling us what your actual syntax 
errors are.

#!/usr/bin/perl -w
use Bio::AlignIO;
use strict;
my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 'clustalw' );

my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 'clustalw' );

my $aln = $in->next_aln();



On Sep 15, 2004, at 3:44 PM, Sun, Jian wrote:

> Dear all:
>
>   Could anybody tell me what's the problem of the below perl codes, 
> why I always get the Syntax Error message when I run the command:> 
> perl -c file.name?
>
> **********************************************
>
> ..............
>
> my $in = new Bio::AlignIO ( -file => $ARGV[0], -format => 
> 'clustalw' );
>
> my $out = newFh Bio::AlignIO ( -fh => \*STDOUT, -format => 
> 'clustalw' );
>
> my $aln = $in->next_aln();
>
> ***************************************************
>
>
>
> ________________________________
>
> From: bioperl-l-bounces at portal.open-bio.org on behalf of Pankaj
> Sent: Wed 9/15/2004 3:40 AM
> To: bio_bulletin_board at bioinformatics.org
> Cc: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] (no subject)
>
>
>
> Hi all,
> I have a pdb file of 2 superimposed structures. I want to know the
> rmsd of a part of 1 structure to a part of the 2 structure. For this
> rmsd calculation I dont want to disturb the superimposition. how do I
> do that?
> thanking all in advance
> Pankaj Kamra
> Research Scholar
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>
>
>
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>
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/