[Bioperl-l] Problem in using BioPerl module through Strawberry Perl Professional 5.10.1.3 alpha 2

2BioInfo thamanchand at yahoo.com
Fri Jan 14 14:10:44 UTC 2011


Hi all,

I am new to Perl and Bioperl, but I am trying to do something with
Perl and Bioperl. I tried to install Perl and BioPerl module
separately but didn't worked for me. Then I installed Strawberry Perl
Professional 5.10.1.3 alpha 2 which has inbuilt Bioperl module and
Padre IDE.

To check whether perl is working or not I put these command

c:\perl -v

It seems working

Then I wanted to check whether Bioperl is working

In Padre I put

use Bio::Perl; ## It seems working because it didn't complain

Then I wanted to check further more according to

http://etutorials.org/Programming/perl+bioinformatics/Part+II+Perl+and+Bioinformatics/Chapter+9.+Introduction+to+Bioperl/9.3+Testing+Bioperl/

I used following examples to test

  #!C:\strawberry\perl\bin -w
use strict;
use warnings;
use Bio::Perl;

  # this script will only work with an internet connection
  # on the computer it is run on
$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
write_sequence(">roa1.fasta",'fasta',$seq_object);

But it doesn't seems working

I got following erros

Global symbol "$seq_object" requires explicit package name at C:\......
\Perl\2.pl line 8.
Global symbol "$seq_object" requires explicit package name at C:
\.........\Perl\2.pl line 9.
Execution of C:\.................\Perl\2.pl aborted due to compilation
errors.

Further I checked in command line perldoc::Seq

It seems working too

Can anyone point out what stupid mistakes I am doing?

Thank you







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