[Bioperl-l] Bio::AlignIO::Pfam

[Tariq Shafi]

Hello all

I am trying to submit a sequence in Perl to a pfam flat file database and 
get a classification for the family that a peptide sequence belongs to, and 
analysis of its domains.

I am thus using the Bio::AlignIO::Pfam module in Perl but all examples I can 
find is taking input from a file. I want to (dynamically) create a Bio::Seq 
object and use that as an argument in Bio::AlignIO::Pfam and get output as I 
would do as if I submitted the sequence in the Pfam database website.

I am using CGI and dynamic web pages and want to avoid creating new files 
when a Pfam alignment is requested as that will be a little messy and 
expensive on memory.

The relevant chunk of my code so far for this is as below:

use CGI qw(:standard);
use DBI;
use Bio::AlignIO;

etc....


# Using a statement handle in Perl DBI
while ($sth->fetch())
{
	print b("PAD ID: "), b($id), p(), b("Swiss-Prot ID: "), $swissProtId,br(), 
b("Sequence:"),  br();
	   # Creating Bio::Seq object
                   $seq = Bio::Seq->new(-seq => $sequence,
		     -desc => $swissProtId,
		     -id => $id
                    );
}

$sth->finish();

print b("Pfam classification:"), p();

# This is the problem area
# I don't want files involved here. Instead of file and format I simply want 
the argument to be a
# Bio::Seq object

$in = Bio::AlignIO->new(
        '-file' => $ARGV[0],
        '-format' => 'stockholm' );

# Here I don't want files involved either. I want $out to be something 
different but have nothing
# to do with a file.

$out = Bio::AlignIO->new(
        '-file' => ">$ARGV[1]",
        '-format' => 'pfam');

$align = $in->next_aln();
$out->write_aln($align);

Regards

Tariq

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