Re^2: parsing blast output

#!/usr/bin/perl 
use warnings;
use strict;
use Bio::SearchIO;
use Bio::AlignIO;

my $out = ">C:/Documents and Settings/mgavi.brathwaite/Desktop/current
+/bl2seq/13117_aln1.out";
my $dir = 'C:/Documents and Settings/mgavi.brathwaite/Desktop/current/
+bl2seq/';
my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => $dir.'13117_2.out',
                           -report_type => 'bl2seq');
while( my $result = $in->next_result ) {
  while( my $hit = $result->next_hit ) {
   while( my $hsp = $hit->next_hsp ) { 
     if( $hsp->length('total') > 1000 ) {
      if ( $hsp->percent_identity >= 90 ) {
       if(    $hsp->score ){
        if(     $hsp->gaps ){
         if(  $hsp->expect ){
            print  "Hit= ",    $hit->name, 
                    " Length=",     $hsp->length('total'), 
                    " Score=",        $hsp->score,"\n";
            print " Gaps=",    $hsp->gaps,
                    " Expect=",        $hsp->expect,
                    " Percent_id=", $hsp->percent_identity, "\n";
=cut
                    # $hit->name, $hit->hsps,
                                $hit->name, 
                                $hsp->length('total'), 
                                $hsp->score,
                                $hsp->gaps,
                                $hsp->expect,
                                $hsp->percent_identity;    
=cut                                
                    my $aln = $hsp->get_aln;    
                    my $alnIO = Bio::AlignIO->new(-format =>"clustalw"
+, -file => $out);
                    $alnIO->write_aln($aln);
          }
         }
        }
      }
    }
   }  
  }
}
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I can get the alignment, but I also need the print data
to be prepended at the top of the $out file.

Comment on Re^2: parsing blast output Download Code

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Re^3: parsing blast output by Marshall (Canon) on May 05, 2009 at 15:50 UTC
So, if I understand the question, you've got what you want except that instead of print going to screen, you want that print to go to the file that the Bio module is writing to? First one thing that might be helpful here is to do a $\|=1; at the top of the program, this turns Autoflush on. This slows the output down a bit, but until you get this working, this might be a good idea to do. I'm not familiar with the module that you are using, but one suggestion is to see if you can give this Bio thing a filehandle instead of a text filepath. If that's true, then you open the output file, use the handle for your printing and give the handle to Bio for its printing. This is the easiest thing if this module allows it.(eg. open say $outhandle to the $out filepath (open ($outhandle, ">", "path) or die .....) In Perl you can use a scalar as a filehandle instead of a bareword like OUT).. Anyway before speculating about more complex scenarios, try the simple approach first.	[reply]

Replies are listed 'Best First'.

Re^3: parsing blast output
by Marshall (Canon) on May 05, 2009 at 15:50 UTC

First one thing that might be helpful here is to do a $|=1; at the top of the program, this turns Autoflush on. This slows the output down a bit, but until you get this working, this might be a good idea to do.

I'm not familiar with the module that you are using, but one suggestion is to see if you can give this Bio thing a filehandle instead of a text filepath. If that's true, then you open the output file, use the handle for your printing and give the handle to Bio for its printing. This is the easiest thing if this module allows it.(eg. open say $outhandle to the $out filepath (open ($outhandle, ">", "path) or die .....) In Perl you can use a scalar as a filehandle instead of a bareword like OUT)..

Anyway before speculating about more complex scenarios, try the simple approach first.

[reply]