[Bioperl-l] problem in using protparam.pm module

[Shachi Gahoi]

Please help me how to run protparam using bioperl module

On Wed, Jul 27, 2011 at 11:05 AM, Chris Fields <cjfields at illinois.edu>wrote:

> The web service appears to have changed, but it looks as if no tests have
> been written up for this module which would have caught this out.  We can
> write some basic tests up to check for simple functionality.
>
> chris
>
> On Jul 26, 2011, at 10:58 PM, Shachi Gahoi wrote:
>
> > Dear All,
> >
> > i am using protparam.pm module. but when i am running this script it is
> > printing one error message
> >
> > "Can't call method "throw" without a package or object reference at
> > /usr/share/perl5/Bio/Root/Root.pm line 368, <GEN1> line 1."
> >
> > Kindly help me to solve this problem.
> >
> >
> > Script is here----
> >
> ###################################################################################
> > #!/usr/bin/perl
> >
> > use warnings;
> > use Bio::SeqIO;
> > use Bio::Tools::Protparam;
> >
> >
> > $seqfile='test1.fasta';
> >
> > $seqio = Bio::SeqIO->new(-file => "$seqfile", -format => 'Fasta');
> >
> >
> >    while(  $seq = $seqio->next_seq() )
> > {
> >
> >
> >        my $pp = Bio::Tools::Protparam->new(-seq=>$seq->seq);
> >
> >        print
> >        "ID : ", $seq->display_id,"\n",
> >        "Amino acid number : ",$pp->amino_acid_number(),"\n",
> >        "Number of negative amino acids : ",$pp->num_neg(),"\n",
> >        "Number of positive amino acids : ",$pp->num_pos(),"\n",
> >        "Molecular weight : ",$pp->molecular_weight(),"\n",
> >        "Theoretical pI : ",$pp->theoretical_pI(),"\n",
> >        "Total number of atoms : ", $pp->total_atoms(),"\n",
> >        "Number of carbon atoms : ",$pp->num_carbon(),"\n",
> >        "Number of hydrogen atoms : ",$pp->num_hydrogen(),"\n",
> >        "Number of nitrogen atoms : ",$pp->num_nitro(),"\n",
> >        "Number of oxygen atoms : ",$pp->num_oxygen(),"\n",
> >        "Number of sulphur atoms : ",$pp->num_sulphur(),"\n",
> >        "Half life : ", $pp->half_life(),"\n",
> >        "Instability Index : ", $pp->instability_index(),"\n",
> >        "Stability class : ", $pp->stability(),"\n",
> >        "Aliphatic_index : ",$pp->aliphatic_index(),"\n",
> >        "Gravy : ", $pp->gravy(),"\n",
> >        "Composition of A : ", $pp->AA_comp('A'),"\n",
> >        "Composition of R : ", $pp->AA_comp('R'),"\n",
> >        "Composition of N : ", $pp->AA_comp('N'),"\n",
> >        "Composition of D : ", $pp->AA_comp('D'),"\n",
> >        "Composition of C : ", $pp->AA_comp('C'),"\n",
> >        "Composition of Q : ", $pp->AA_comp('Q'),"\n",
> >        "Composition of E : ", $pp->AA_comp('E'),"\n",
> >        "Composition of G : ", $pp->AA_comp('G'),"\n",
> >        "Composition of H : ", $pp->AA_comp('H'),"\n",
> >        "Composition of I : ", $pp->AA_comp('I'),"\n",
> >        "Composition of L : ", $pp->AA_comp('L'),"\n",
> >        "Composition of K : ", $pp->AA_comp('K'),"\n",
> >        "Composition of M : ", $pp->AA_comp('M'),"\n",
> >        "Composition of F : ", $pp->AA_comp('F'),"\n",
> >        "Composition of P : ", $pp->AA_comp('P'),"\n",
> >        "Composition of S : ", $pp->AA_comp('S'),"\n",
> >        "Composition of T : ", $pp->AA_comp('T'),"\n",
> >        "Composition of W : ", $pp->AA_comp('W'),"\n",
> >        "Composition of Y : ", $pp->AA_comp('Y'),"\n",
> >        "Composition of V : ", $pp->AA_comp('V'),"\n",
> >        "Composition of B : ", $pp->AA_comp('B'),"\n",
> >        "Composition of Z : ", $pp->AA_comp('Z'),"\n",
> >        "Composition of X : ", $pp->AA_comp('X'),"\n";
> > }
> >
> ###################################################################################
> >
> >
> >
> >
> > --
> > Regards,
> > Shachi
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
Regards,
Shachi