[Bioperl-l] print alignment from blast results file

nisa.dar nisa.dar10 at gmail.com
Tue Nov 15 19:49:00 EST 2011


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 $query_string=$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

                         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.


View this message in context: http://old.nabble.com/print-alignment-from-blast-results-file-tp32851673p32851673.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.

More information about the Bioperl-l mailing list