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

Ulrik Stervbo ulrik.stervbo at gmail.com
Fri Jul 6 03:03:08 EDT 2012


I had the same problem, and realized it is because I am behind a proxy.

This is what I did to the Protparam module:
Changed the url to 'http://web.expasy.org/cgi-bin/protparam/protparam'
as previously found

Added:
$browser->proxy(['http'], 'http://[my proxy]/'); after initialization
of the LWP agent.

The proxy settings is what made Perl choke. (If only one could make
perl see global proxy settings).

Cheers,
Ulrik

2011/7/28 Shachi Gahoi <shachigahoimbi at gmail.com>:
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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