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

[Chris Fields]

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
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