[Bioperl-l] Please help

[Barry Moore]

Angshu,

 

A couple of suggestions:  It's best to keep these mails on the list so
that others can contribute to and benefit from the discussion, and more
detail on what's not working would help (i.e. are you getting error
messages or just no output.)  Are you getting an error like, "Not a GLOB
referenece..."?  Your angle operator in this command  $in = <$seq>
shouldn't work.  The angle operator is intended for handles.  Try it
like this; $in = shift @$seq or if you query returns more than one
sequence wrap your Bio::Seq calls in a foreach my $in (@$seq) {} loop.

 

Barry

 

-----Original Message-----
From: Angshu Kar [mailto:angshu96 at gmail.com] 
Sent: Friday, October 14, 2005 1:38 PM
To: Barry Moore
Subject: Re: [Bioperl-l] Please help

 

Hi Barry,

I've written the follwing code:

use DBI;
use Bio::SeqIO;

my $db_host = 'YYYYYY;
my $db_user = 'WWWW';
my $db_pass = 'XXXXXX';
my $db_name = ''ZZZZZ';

# Connect to a PostgreSQL database.
my $db = "dbi:PgPP:dbname=${db_name};host=${db_host}";

# Connect to database.
$dbh = DBI->connect($db, $db_user, $db_pass,
                       { RaiseError => 1, AutoCommit => 0 }
       ) || die "Error connecting to the database: $DBI::errstr\n"; 

# My query.
my $query = "select seq from biosequence where biosequence_id = 12";

# Run query.
$seq = $dbh->selectcol_arrayref($query);

# Convert the raw string to fasta
$in = <$seq>;

#$in  = Bio::SeqIO->new($seq,
#                      -format => 'raw');
$out = Bio::SeqIO->new($seq,
                       -seq_name => "ABCDE01",
                       -format => 'Fasta'); 

# Print results.
print join("\n", @$seq);

Everything was running fine before I tried to convert the raw sequecne
into fasta using the code in bold. Could you please let me know where
I'm going wrong?

 

Thanks,
Angshu

 

On 10/13/05, Barry Moore <bmoore at genetics.utah.edu> wrote: 

Angshu-

Brain is right, you need to read the documentation and ask a more
specific question on the list.  I'll suggest a few extra modules for you

to study along with the ones Brian told you about.  Look for the non-bio
modules on CPAN http://search.cpan.org/.  BTW, the project you've
described and the modules that you will need to use will be a challenge 
to jump straight into if you've never used perl at all before.  You will
almost certainly want to start by reading some introductory and
intermediate perl books (or the free perl documentation)  The standard
books for perl beginners is Learning Perl by Randal Schwartz et al. and
the standard perl Bible is Programming Perl by Larry Wall et al.  You
will want read at least the first one and have the second one handy as
you jump into the documentation below.

DBI, DBD::Pg and perhaps Class::DBI - For perl communicating with your
database.
Bio::SeqIO - For reading your sequences into Bioperl
Bio::Tools::Run::Alignment::Clustalw - For aligning your sequences 
Bio::AlignIO::clustalw - For simple writing of the alignments.

Depending on what you had in mind for scoring you may have to write your
own code for that and the histogram display.  Look at the GD module for 
your graphics needs.  You mention several times that you want to display
your results, and I'm going to guess you mean via a web site.  I think
CGI::Application is a great way to build the kind of database driven 
websites that I think you are considering here.

Barry


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto: bioperl-l-bounces at portal.open-bio.org
<mailto:bioperl-l-bounces at portal.open-bio.org> ] On Behalf Of Brian
Osborne
Sent: Thursday, October 13, 2005 8:00 PM
To: Angshu Kar; bioperl-l
Subject: Re: [Bioperl-l] Please help

Angshu,

You need to study Bioperl's documentation. Take a look at relevant 
HOWTOs
(Beginners, SeqIO, SearchIO perhaps). Also, install the bioperl-run
package
and look at the Bio::Tools::Run::Clustalw module.

Brian O.


On 10/12/05 3:48 PM, "Angshu Kar" < angshu96 at gmail.com> wrote:

> Hi ,
>
> I'm completely new to perl. I'm have to work in biology using perl,
> postgresql (as database) and clustalw(as the alignment 
> tool). I'm stating my problem briefly:
>
> In the postgresql db the data is clustered using complete linkage
> clustering. I've to connect to that db, fetch those data, feed it to
> the multiple alignment tool, run it and show the results.Again,
> feed those alignments into a scoring tool and show the results in
> form of a histogram.All these needs to be automated using perl.
> I've installed bio-perl but can't get how to write code using it. 
>
> I'll be obliged if you help me with this by providing the idea of how
> to feed the db data (in fasta format) into clustalw.
>
> Thanks,
> Angshu
>
> _______________________________________________ 
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l 


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