Re^2: Problem with getting the right object

Hello Chromatic!
I have revised it to make it simpler. I need to parse a blast report. I am using an if/else to print to 2 different
out files. $hd_out should have:

Name: 13426|HD
Percent Identity: 97.0856102003643
Alignment: Bio::SimpleAlign=HASH(0x4012f2c)

and $hu_out should have:

Name: 13426|HU
Percent Identity: 99.7737556561086
Alignment: Bio::SimpleAlign=HASH(0x401965c)

Where "Bio::SimpleAlign=HASH(object)" is should have the actual data, which is an alignment.
I am confused about dereferencing the hash object since it is a scalar($hu_aln, $hd_aln) in my code

my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => $maid_dir."\\".$maid."_aln.out",
                           -report_type => 'blastn');
    open (my $hu_out,">".$maid_dir."\\".$maid."_hu_parsed.out");
    open (my $hd_out,">".$maid_dir."\\".$maid."_hd_parsed.out");
    
    while(my $result = $in->next_result){
 
    # get info about the first hit
        my $hit = $result->next_hit;
        my $hu_name = $hit->name;
        my $hd_name = $hit->name;

        if($hu_name =~ /^>.*HU/){
            
                    
            # get info about the first hsp of the first hit
            my $hsp = $hit->next_hsp;
            my $best_hsp = $hit->hsp('best');
            my $hu_Percent_id = $hsp->percent_identity;
            print $hu_out "Name: ", $hu_name, "\n";                   
+ 
            print $hu_out "Percent Identity:  ", $hu_Percent_id, "\n";
            my $hu_aln = $hsp->get_aln;
            my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file 
+=> ">$hu_out");
            $alnIO->write_aln($hu_aln);
            print $hu_out "Alignment:  ", $hu_aln, "\n";
            
        }
        else
        {
            $hd_name =~ /^>.*HD/;
            
                    
            # get info about the first hsp of the first hit
            my $hsp = $hit->next_hsp;
            my $best_hsp = $hit->hsp('best');
            my $hd_Percent_id = $hsp->percent_identity;
            print $hd_out "Name: ", $hd_name, "\n";                   
+ 
            print $hd_out "Percent Identity:  ", $hd_Percent_id, "\n";
            my $hd_aln = $hsp->get_aln;
            my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file 
+=> ">$hd_out");
            $alnIO->write_aln($hd_aln);
            print $hd_out "Alignment:  ", $hd_aln, "\n";
            
        }
    }
    close $hu_out;
    close $hd_out;
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I am expecting to get two files. Each with the name, Percent ID, and the sequence alignment.
Your help is appreciated!
LomSpace

Comment on Re^2: Problem with getting the right object Download Code

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Re^3: Problem with getting the right object by chromatic (Archbishop) on May 19, 2009 at 19:03 UTC
`$hu_aln` and `$hd_aln` contain Bio::SimpleAlign objects. If you read the linked documentation, you may find that one of the methods of that class gives you access to the data you need. It doesn't support a default stringification, so you can't print the object directly and get what you expect. (I don't know what you expect, so I can't tell you which method is likely to help.)	[reply] [d/l] [select]