[Bioperl-l] print alignment from blast results file

[Brian Osborne]

Nisa,

See:

http://www.bioperl.org/wiki/HOWTO:SearchIO

Brian O.


On Nov 15, 2011, at 7:49 PM, nisa.dar wrote:

> 
> Hi,
> 
> I am parsing a blast results file. I have found bioperl modules to get query
> string, homology string and hit string for each hit/hsp. I want to print
> them in the form of an alignment instead of aligning them individually.
> 
> this is what I am doing, but it doesn't seem correct
> 
> while (my $hsp = $hit->next_hsp) {
>                                        my
> $start_query_num=$hsp->start('query');
> 					my $query_string=$hsp->query_string;
> 					my $end_query_num=$hsp->end('query');
> 					my $homology_string=$hsp->homology_string;
> 					my $start_hit_num=$hsp->start('hit');
> 					my $hit_string=$hsp->hit_string;
> 					my $end_hit_num=$hsp->end('hit');
> 					my $aln_o = $hsp->get_aln;
> 					$query_string=~s/\n//g;#get rid of new line characters
> 					$homology_string=~s/\n//g;
> 					$hit_string=~s/\n//g;
> 
>                         print "<h3>Alignment:</h3><br />";
> 			print "$start_query_num-$query_string-$end_query_num<br />";
> 			print "   
> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;$homology_string<br />";
> 			print "$start_hit_num-$hit_string-$end_hit_num<br /><br />";
> 
> 
> 
> }
> 
> Please let me know how can I print them in the form of an alignment as seen
> in the blast results file.
> 
> Thanks
> 
> 
> -- 
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> 
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