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Smithies, Russell | 2 Mar 00:06
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Re: Remote Blast and Report

Works fine for me using the code below.
Took about 30 seconds to return a result.
==============================================

#!perl -w

use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;
use Data::Dumper;

#Here i set the parameters for blast
$prog = "tblastx";
$db = "nr";
$e_val = "1e-10";

my @params = ( '-prog' => $prog,
         '-data' => $db,
         '-expect' => $e_val,
         '-readmethod' => 'SearchIO' );

my $remoteBlast = Bio::Tools::Run::RemoteBlast->new(@params);

#Select the file and make the balst.
$infile = 'infile.fasta';
$r = $remoteBlast->submit_blast($infile);

  my $v = 1;

    print STDERR "waiting..." if( $v > 0 );  ########  WAIT FOR THE RESULTS TO RETURN!!!!!
    while ( my @rids = $remoteBlast->each_rid ) {
(Continue reading)

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Ocar Campos | 2 Mar 01:51
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Re: Remote Blast and Report

Hello, I tried your script Russel, but I still got the same error in the
console, "Can't call method "query_name" on an undefined value at ./aer2.pl
line 39, <GEN4> line 185.", I didn't do anything to it, just copy/paste and
ran it. So what I assumed is that the object for the SearchIO module was not
initialized, so I created it, but now I get an Exeption while parsing the
report:

------------- EXCEPTION  -------------
MSG: Could not open Bio::SearchIO::blast=HASH(0x8bb79bc): Doesn't exist the
file or directory.
STACK Bio::Root::IO::_initialize_io
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/IO.pm:273
STACK Bio::Root::IO::new /usr/lib/perl5/site_perl/5.8.8/Bio/Root/IO.pm:213
STACK Bio::SearchIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO.pm:135
STACK Bio::SearchIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SearchIO.pm:167
STACK toplevel ./aer2.pl:45

--------------------------------------

aer2.pl is my script, Any Idea what it could be?

The script:

#!/usr/bin/perl

use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;
use Data::Dumper;

########HERE I SET THE PARAMETERS
(Continue reading)

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Jason Stajich | 2 Mar 02:19
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Re: Remote Blast and Report

I think $rc is already a Bio::SearchIO object - you shouldn't have to  
instantiate a Bio::SearchIO object that is what the -readmethod in the  
@params at the top is for.

Try printing ref($ref) to see what it is.

-js
On Mar 1, 2009, at 4:51 PM, Ocar Campos wrote:

> Hello, I tried your script Russel, but I still got the same error in  
> the
> console, "Can't call method "query_name" on an undefined value at ./ 
> aer2.pl
> line 39, <GEN4> line 185.", I didn't do anything to it, just copy/ 
> paste and
> ran it. So what I assumed is that the object for the SearchIO module  
> was not
> initialized, so I created it, but now I get an Exeption while  
> parsing the
> report:
>
>
> ------------- EXCEPTION  -------------
> MSG: Could not open Bio::SearchIO::blast=HASH(0x8bb79bc): Doesn't  
> exist the
> file or directory.
> STACK Bio::Root::IO::_initialize_io
> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/IO.pm:273
> STACK Bio::Root::IO::new /usr/lib/perl5/site_perl/5.8.8/Bio/Root/ 
> IO.pm:213
(Continue reading)

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Ocar Campos | 2 Mar 02:35
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Re: Remote Blast and Report

Hello Jason, I printed the ref($ref), this is what i got:
Bio::SearchIO::blast

I'm going to update from version 1.4.2 of bioperl to 1.6.0, maybe that's why
is not working.

O'car

2009/3/1 Jason Stajich <jason <at> bioperl.org>

> I think $rc is already a Bio::SearchIO object - you shouldn't have to
> instantiate a Bio::SearchIO object that is what the -readmethod in the
> @params at the top is for.
>
> Try printing ref($ref) to see what it is.
>
> -js
>
> On Mar 1, 2009, at 4:51 PM, Ocar Campos wrote:
>
>  Hello, I tried your script Russel, but I still got the same error in the
>> console, "Can't call method "query_name" on an undefined value at
>> ./aer2.pl
>> line 39, <GEN4> line 185.", I didn't do anything to it, just copy/paste
>> and
>> ran it. So what I assumed is that the object for the SearchIO module was
>> not
>> initialized, so I created it, but now I get an Exeption while parsing the
>> report:
>>
(Continue reading)

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Ocar Campos | 2 Mar 03:29
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Re: Remote Blast and Report

Hello Everybody!
Finally I got the script working, It was a problem of the version of my
BioPerl, I updated to 1.6 and now the script is working fine, I use the one
that Russel send, that is this one, and got no problem

#!perl -w

use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;
use Data::Dumper;

#Here i set the parameters for blast
$prog = "tblastx";
$db = "nr";
$e_val = "1e-10";

my @params = ( '-prog' => $prog,
         '-data' => $db,
        '-expect' => $e_val,
         '-readmethod' => 'SearchIO' );

my $remoteBlast = Bio::Tools::Run::RemoteBlast->new(@params);

#Select the file and make the balst.
$infile = 'infile.fasta';
$r = $remoteBlast->submit_blast($infile);

  my $v = 1;

   print STDERR "waiting..." if( $v > 0 );  ########  WAIT FOR THE RESULTS
(Continue reading)

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Abhishek Pratap | 2 Mar 08:09
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Implementing Logistic Regression for data anaylsis

Hi All
Does any one know if there is any logistic regression module in Bioperl or
Perl for that matter. Cant find anything relevant on CPAN. I want to analyze
some data with this Algorithm.

Thanks,
-Abhi
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Bruno Vecchi | 2 Mar 19:53
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Offering to help

Hi,

I've been using BioPerl for a couple of years now, so first of all,
thanks to all the devs that made it possible.

Although I have only used a fraction of it, I think I am now acquainted
with it enough to be useful in some way. I offer then to help with any
issue that needs taken care of.

I have written a wrapper for the Qcons <http://tsailab.tamu.edu/Qcons/> (
http://tsailab.tamu.edu/Qcons/)
application (calculates protein-protein contacts), you can look at the
code at my github repository <http://github.com/brunoV/qcons/tree/master> (
http://github.com/brunoV/qcons/tree/master).
Don't know if it will be useful or not (or any of the other modules that
I've
written for my personal use, feel free to look).

If there is anything else that you feel that I would be able to do, I'd
be happy to. My current field is more involved with wet-lab work
(antibody engineering), but I like programming a lot and I think this
will be a great chance to keep learning while still contributing.

Cheers,

   Bruno.
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Alper Yilmaz | 3 Mar 04:49
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Bio::DB::GFF again

I have another question about Bio::DB::GFF module. I went through the manual
couldn't find the answer. Maybe it's easy solution and I don't know it.

Is it possible to overlay protein domain coordinates on genomic coordinates
in Bio::DB::GFF?
Let's say I want to extract -nucleotide sequence- of a protein domain. If my
input is protein domain location (as amino acid coordinates) can I have dna
sequence by using Bio::DB::GFF for the same region, (excluding intron
sequences)?

thanks,

Alper Yilmaz
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Heikki Lehvaslaiho | 3 Mar 08:11
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Re: Offering to help

Hi Bruno,

I had a quick look at your code. You have used Moose which would be a
new dependency to BioPerl. I am not too sure what to with it. The
problem is that since you are not inheriting from Bio::Root::RootI,
none of the standard BioPerl methods work.

Maybe it is time to start adding code to the trunk that replicates
Bio::Root::* functionality using Moose which will then lead the way to
Perl6?

Most probably we will be needing the full functionality of Moose,
don't you think? Meaning that his cuter and faster friends Mouse and
Squirrel are not enough? :)

   -Heikki

2009/3/2 Bruno Vecchi <vecchi.b <at> gmail.com>:
> Hi,
>
> I've been using BioPerl for a couple of years now, so first of all,
> thanks to all the devs that made it possible.
>
> Although I have only used a fraction of it, I think I am now acquainted
> with it enough to be useful in some way. I offer then to help with any
> issue that needs taken care of.
>
> I have written a wrapper for the Qcons <http://tsailab.tamu.edu/Qcons/> (
> http://tsailab.tamu.edu/Qcons/)
> application (calculates protein-protein contacts), you can look at the
(Continue reading)

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Chris Fields | 3 Mar 14:45
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Re: Offering to help


On Mar 3, 2009, at 1:11 AM, Heikki Lehvaslaiho wrote:

> Hi Bruno,
>
> I had a quick look at your code. You have used Moose which would be a
> new dependency to BioPerl. I am not too sure what to with it. The
> problem is that since you are not inheriting from Bio::Root::RootI,
> none of the standard BioPerl methods work.
>
> Maybe it is time to start adding code to the trunk that replicates
> Bio::Root::* functionality using Moose which will then lead the way to
> Perl6?

Been thinking the same thing.  Maybe biomoose?

> Most probably we will be needing the full functionality of Moose,
> don't you think? Meaning that his cuter and faster friends Mouse and
> Squirrel are not enough? :)
>
>
>   -Heikki

This would definitely be an easier transition to perl6 and, at the  
same time, would allow us to refactor code where it's needed (using  
roles instead of interfaces, etc).

chris
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