Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::SeqFeature::ToolsUseraContributed)Bio::SeqFeature::Tools::FeatureNamer(3)

NAME
       Bio::SeqFeature::Tools::FeatureNamer - generates	unique persistent
       names for features

SYNOPSIS
	 use Bio::SeqIO;
	 use Bio::SeqFeature::Tools::FeatureNamer;

	 # first fetch a genbank SeqI object
	 $seqio	=
	   Bio::SeqIO->new(-file=>'AE003644.gbk',
			   -format=>'GenBank');
	 $seq =	$seqio->next_seq();

	 $namer	= Bio::SeqFeature::Tools::FeatureNamer->new;
	 my @features =	$seq->get_SeqFeatures;
	 foreach my $feature (@features) {
	   $namer->name_feature($feature) unless $feature->display_name;
	 }

DESCRIPTION
       This is a helper	class for providing names for SeqFeatures

       The Bio::SeqFeatureI class provides a display_name method. Typically
       the display_name	is not set when	parsing	formats	such as	genbank	-
       instead properties such as label, product or gene are set in a somewhat
       inconsistent manner.

       In addition, when generating subfeatures	(for example, exons that are
       subfeatures of a	transcript feature), it	is often desirable to name
       these subfeatures before	either exporting to another format or
       reporting to the	user.

       This module is intended to help given uniform display_names to features
       and their subfeatures.

TODO
       Currently the naming policy is hardcoded. It may	be desirable to	allow
       plugging	in variations on naming	policies; this could be	done either by
       subclassing, anonymous subroutines (closures) or	parameterization.
       Contact the author if you feel you have need for	a different naming
       policy

FEEDBACK
   Mailing Lists
       User feedback is	an integral part of the	evolution of this and other
       Bioperl modules.	Send your comments and suggestions preferably to the
       Bioperl mailing lists  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the	problem	with code and
       data examples if	at all possible.

   Reporting Bugs
       report bugs to the Bioperl bug tracking system to help us keep track
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Mungall
       Email:  cjm AT fruitfly DOT org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: $unflattener = Bio::SeqFeature::Tools::FeatureNamer->new();
	Function: constructor
	Example	:
	Returns	: a new	Bio::SeqFeature::Tools::FeatureNamer
	Args	: see below

   name_feature
	Title	: name_feature
	Usage	: $namer->name_feature($sf);
	Function: sets display_name
	Example	:
	Returns	:
	Args	: L<Bio::SeqFeatureI>

       This method calls generate_feature_name() and uses the returned value
       to set the display_name of the feature

   name_contained_features
	Title	: name_contained_features
	Usage	: $namer->name_contained_features($sf);
	Function: sets display_name for	all features contained by sf
	Example	:
	Returns	:
	Args	: L<Bio::SeqFeatureI>

       iterates	through	all subfeatures	of a certain feature (using
       get_all_SeqFeatures) and	names each subfeatures,	based on the generated
       name for	the holder feature

       A subfeature is named by	concatenating the generated name of the
       container feature with the type and a number.

       For example, if the containing feature is a gene	with display name dpp,
       subfeatures will	be named dpp-mRNA-1 dpp-mRNA2 dpp-exon1	dpp-exon2 etc

   generate_feature_name
	Title	: generate_feature_name
	Usage	: $name	= $namer->generate_feature_name($sf);
	Function: derives a sensible human readable name for a $sf
	Example	:
	Returns	: str
	Args	: L<Bio::SeqFeatureI>

       returns a generated name	(but does not actually set display_name).

       If display_name is already set, the method will return this

       Otherwise, the name will	depend on the property:

       label
       product
       gene
       locus_tag

       (in order of priority)

perl v5.24.1			  2017-Bio::SeqFeature::Tools::FeatureNamer(3)

NAME | SYNOPSIS | DESCRIPTION | TODO | FEEDBACK | AUTHOR - Chris Mungall | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::SeqFeature::Tools::FeatureNamer&sektion=3&manpath=FreeBSD+12.0-RELEASE+and+Ports>

home | help