[Bioperl-l] Abot prot_param code :)

[Joel Martin]

you need to install bioperl-live, the protparam website has changed
since the cpan version of bioperl was released so you need the most up
to date version of bioperl.

the instructions for installing are at

http://www.bioperl.org/wiki/Using_Git

Joel

On Fri, May 4, 2012 at 10:06 AM, guillermo romero <biorges at gmail.com> wrote:
> Thanks for your reply !!!
>
> I have just run your suggestions but an error appears:
>
>  EXCEPTION: Bio::Root::Exception -------------
> MSG: http://www.expasy.org/cgi-bin/protparam error: 301 Moved Permanently
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::Tools::Protparam::new
> /usr/share/perl5/Bio/Tools/Protparam.pm:128
> STACK: prog_protparam.pl:14
>
> Would you recommend me to do something else?
>
> Thanks again :)
>
>
> On 4 May 2012 11:54, Joel Martin <j_martin at lbl.gov> wrote:
>>
>> first, use bioperl-live.  the url for protparam has changed since
>> 1.6.901 was released.
>>
>> second, the example code is a bit off, replace the start with this,
>> it's just adding the
>> use lines and changing "my $pp = Protparam..." to "my $pp =
>> Bio::Tools::Protparam..."
>>
>> use Bio::DB::GenBank;
>> use Bio::Tools::Protparam;
>>
>> my $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' ,
>>                                -format => 'Fasta');
>> my @ids=qw(O14521 O43709 O43826);
>> my $seqio = $gb->get_Stream_by_acc(\@ids );
>>  while( my $seq =  $seqio->next_seq ) {
>>    my $pp = Bio::Tools::Protparam->new(seq=>$seq->seq);
>> # it's correct from that line on down
>>
>> On Wed, May 2, 2012 at 10:49 AM, guillermo romero <biorges at gmail.com>
>> wrote:
>> > To whom it may concern,
>> >
>> > I am reading your prot param source code (
>> >
>> > http://cpansearch.perl.org/src/CJFIELDS/BioPerl-1.6.901/Bio/Tools/Protparam.pm)
>> > and i am wondering how to use it: How do I execute it? Which are the
>> > parameters needed to use it?
>> >
>> > Sincere thanks
>> >
>> > Cheers
>> >
>> >
>> > Guillermo Romero
>> > University of Mexico
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>