[Bioperl-l] error in Protparm module
Shachi Gahoi
shachigahoimbi at gmail.com
Sat Jul 23 06:36:25 EDT 2011
I am trying following script using Protparam.pm module
###################################################################################
#!/usr/bin/perl
use warnings;
use Bio::SeqIO;
use Bio::Tools::Protparam;
$seqfile='SHP1_At.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";
}
#########################################################################################
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, <GEN0> line 1.
Please help me to solve this problem.
Thanks in advance.
--
Regards,
Shachi
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