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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;

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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);

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