Beefy Boxes and Bandwidth Generously Provided by pair Networks
Problems? Is your data what you think it is?

Bioperl _ SeqStats

by MVRS (Acolyte)
on Feb 06, 2013 at 05:35 UTC ( #1017336=perlquestion: print w/ replies, xml ) Need Help??
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/ 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;

Comment on Bioperl _ SeqStats
Download Code
Replies are listed 'Best First'.
Re: Bioperl _ SeqStats
by vinoth.ree (Prior) 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);

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: perlquestion [id://1017336]
Approved by vinoth.ree
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others surveying the Monastery: (5)
As of 2015-11-30 23:34 GMT
Find Nodes?
    Voting Booth?

    What would be the most significant thing to happen if a rope (or wire) tied the Earth and the Moon together?

    Results (788 votes), past polls