Re^2: Bioperl + perl modules

I have progressed slightly since my post. Here is my newer code below, it doesn't print any warnings or errors, I am having a problem in the loop starting foreach $key ( $ac->get_all_annotation_keys() ) {

. How can I tell whether $ac variable has a value? If I print it out, it looks like a hash.

                                                                      
+                        
my $seqio = $gb->get_Stream_by_id(['13474692']);
#print $gb->get_Stream_by_id(['13474692']);
                                                                      
+                        
                                                                      
+                        
  while( my $seq = $seqio->next_seq ) {
      print "seq is  ", $seq->display_id, "\n";
      my @f=$seq->get_SeqFeatures; #This gives you the annotation of t
+he retrieved sequence object
                                                                      
+                        
      foreach my $feat (@f) {
                                                                      
+                        
       print "Feature ",$feat->primary_tag," starts ",$feat->start," e
+nds ",
       $feat->end," strand ",$feat->strand,"\n";
                                                                      
+                        
       # features retain link to underlying sequence object
       #print "Feature sequence is ",$feat->seq->seq(),"\n";
                                                                      
+                        
       my $ac=$feat->annotation();
                                                                      
+                        
        # HOW CAN I TELL IF $ac HAS A VALUE
        print "GETS TO HERE\n";
                                                                      
+                        
           foreach $key ( $ac->get_all_annotation_keys() ) {
                print "DOESN'T GET TO HERE\n";
               @values = $ac->get_Annotations($key);
               foreach $value ( @values ) {
                # value is an Bio::AnnotationI, and defines a "as_text
+" method
                print "Annotation ",$key," stringified value ",$value-
+>as_text,"\n";
                                                                      
+                        
                # also defined hash_tree method, which allows data ori
+entated
                # access into this object
                $hash = $value->hash_tree();
               }
           }
                                                                      
+                        
                                                                      
+                        
       next unless ($ac->get_Annotations('coded_by'));
       my @coded=$ac->get_Annotations('coded_by');
       foreach my $location (@coded) {
         print $location->value, " is the location that codes this pro
+tein\n";
       }
      }
  }
[download]

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Re^3: Bioperl + perl modules by Joost (Canon) on Jun 27, 2005 at 10:35 UTC
`foreach $key ( $ac->get_all_annotation_keys() ) {` [download] if $ac is not a valid object of the right type, that code would throw an error: note that you are not indexing a hash here, you're calling an object method. see perltoot for more information on the perl OO system. If you want to know what data is stored in a perl variable or object, an easy way to see that is to use the standard Data::Dumper module: `use Data::Dumper; # ... print '$ac: ',Dumper($ac); foreach $key ( $ac->get_all_annotation_keys() ) print '$key: ',Dumper($key); }` [download] That should probably give you some indication of what these objects contain. Note that object can store data in such a way that Data::Dumper doesn't know how to get at it, but it's a start anyway. "What should it profit a man, if he should win a flame war, yet lose his cool?"	[reply] [d/l] [select]

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Re^3: Bioperl + perl modules
by Joost (Canon) on Jun 27, 2005 at 10:35 UTC

foreach $key ( $ac->get_all_annotation_keys() ) {
[download]

not

perltoot

If you want to know what data is stored in a perl variable or object, an easy way to see that is to use the standard Data::Dumper module:

use Data::Dumper;

# ...

print '$ac: ',Dumper($ac);
foreach $key ( $ac->get_all_annotation_keys() ) 
   print '$key: ',Dumper($key);
}
[download]

That should probably give you some indication of what these objects contain. Note that object can store data in such a way that Data::Dumper doesn't know how to get at it, but it's a start anyway.

"What should it profit a man, if he should win a flame war, yet lose his cool?"

[reply]
[d/l]
[select]