[Bioperl-guts-l] bioperl commit

[Steve Chervitz]

sac
Wed May  5 22:08:18 EDT 2004
Update of /home/repository/bioperl/bioperl-live/examples/searchio
In directory pub.open-bio.org:/tmp/cvs-serv23830/examples/searchio

Modified Files:
      Tag: branch-1-4
	hitwriter.pl 
Log Message:
Exercising the interfaces a little more.

bioperl-live/examples/searchio hitwriter.pl,1.2,1.2.2.1
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/examples/searchio/hitwriter.pl,v
retrieving revision 1.2
retrieving revision 1.2.2.1
diff -u -r1.2 -r1.2.2.1
--- /home/repository/bioperl/bioperl-live/examples/searchio/hitwriter.pl	2003/06/04 02:26:48	1.2
+++ /home/repository/bioperl/bioperl-live/examples/searchio/hitwriter.pl	2004/05/06 02:08:18	1.2.2.1
@@ -54,6 +54,7 @@
                  hit_length
 		 num_hsps
                  expect
+                 frac_aligned_query
                  frac_identical_query
                  length_aln_query
                  gaps_total
@@ -61,6 +62,14 @@
                  strand_hit
 		);
 
+# The following columns require HSP alignment data:
+# 		  num_hsps
+#                 frac_identical_query
+#                 length_aln_query
+#                 gaps_total
+#                 strand_query
+#                 strand_hit
+
 print STDERR "\nUsing SearchIO->new()\n";
 
 # Note that all parameters for the $in, $out, and $writer objects are optional.
@@ -69,8 +78,10 @@
 # called "hitwriter.out"
 # TODO: write hitless reports to STDERR and note if filtered.
 my $in     = Bio::SearchIO->new( -format => 'blast', 
+				 -fh => \*ARGV,
 				 -signif => 0.1, 
-				 -verbose=> 0 );
+				# -verbose=> 2
+                               );
 my $writer = Bio::SearchIO::Writer::HitTableWriter->new( -columns => \@columns
 						       );
 my $out    = Bio::SearchIO->new( -format => 'blast',
@@ -83,9 +94,15 @@
 while ( my $blast = $in->next_result() ) {
   printf STDERR "\nReport %d: $blast\n", $in->result_count;
   
+  printf STDERR "query=%s, length=%d\n", $blast->query_name, $blast->query_length;
+
   if( $blast->hits ) {
-    $hit_count++;
-    $out->write_result($blast, $hit_count==1 );
+      print STDERR "# hits= ", $blast->num_hits, "\n";
+      $hit_count++;
+      my @hits= $blast->hits;
+      print STDERR "frac_aligned_query= ", $hits[0]->frac_aligned_query, "\n";
+
+      $out->write_result($blast, $hit_count==1 );
   }
   else {
     print STDERR "Hitless Blast Report ";