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

Jason Stajich jason.stajich at gmail.com
Fri Jul 6 13:49:46 EDT 2012


you might try the PERL_LWP_ENV_PROXY and HTTP_PROXY env variables
http://search.cpan.org/~gaas/libwww-perl-6.04/lib/LWP/UserAgent.pm#CONSTRUCTOR_METHODS
http://search.cpan.org/~gaas/libwww-perl-6.04/lib/LWP/UserAgent.pm#Proxy_attributes

I can't test it my end though w/o a proxy service.


On Jul 6, 2012, at 12:03 AM, Ulrik Stervbo wrote:

> 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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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




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