Bioperl _ SeqStats

MVRS has asked for the wisdom of the Perl Monks concerning the following question:

i tried running bioperl script to find hydropathicity of a protein sequence , and am unable to fix the error >

Error : Can't use string ("Bio::Tools::SeqStats") as a HASH ref while "strict refs" in use at /usr/share/perl5/Bio/Tools/SeqStats.pm line 726.

#!/usr/bin/perl

#use SeqStats;
use Data::Dumper;
use Bio::SeqIO ;
use Bio::Seq ;
use Bio::Tools::SeqStats;
use Bio::Root::Root;  

# Calculate mean Kyte-Doolittle hydropathicity (aka "gravy" score)
  my $prot = Bio::PrimarySeq->new(-seq=>'MSFVLVAPDMLATAAADVVQIGSAVSAGS
+',-format => 'Fasta',-alphabet=>'protein', -id=>'test');
   $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj);
  print "might be hydropathic" if $gravy > 1;
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Comment on Bioperl _ SeqStats Download Code

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Re: Bioperl _ SeqStats by vinoth.ree (Monsignor) on Feb 06, 2013 at 06:25 UTC
You need to give `$prot` as argument to the `hydropathicity()` function as follows, `my $gravy = Bio::Tools::SeqStats->hydropathicity($prot);`	[reply] [d/l] [select]