[Bioperl-l] accessing optional qualifiers within features?

[Hilmar Lapp]

Samuel Aparicio wrote:
> 
> Hi everyone
> I am wondering if there is a method in Bioperl which allows access to
> optional qualifiers with features in a genbank/embl entry. For example,
> being able to parse out
> the value of /note in the example below.
> 
>  repeat_region   1586..1760
>                      /note="L1M1 repeat: matches 5299..5484 of
> consensus"
> 

Bio::Seq has a method all_SeqFeatures(). For every element of the returned
array (a Bio::SeqFeatureI compliant object) you can call
has_tag("tag_name") and each_tag_value("tag_name") in order to query for
existence and retrieve the values associated with a tag. So,

foreach $feat ($seq->all_SeqFeatures()) {
	if(($feat->primary_tag() eq "repeat_region") &&
	   ($feat->has_tag("note")) {
		foreach $val ($feat->each_tag_value("note")) {
			print "note: $val\n";
		}
	}
}

Hope this helps. BTW the mentioned methods are documented in the perldoc
pages of their modules (Bio::Seq and Bio::SeqFeature::Generic).

	Hilmar
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Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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