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Bio::FeatureIO::bed.3pm

NAME

Bio::FeatureIO::bed - read/write features from UCSC BED format

SYNOPSIS

   my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
   for my $feat ($in->next_feature) {
     # do something with $feat (a Bio::SeqFeature::Annotated object)
   }
 
   my $out = Bio::FeatureIO(-format=>'bed');
   for my $feat ($seq->get_seqFeatures) {
     $out->write_feature($feat);
   }
 
 

DESCRIPTION

See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.

Currently for read and write only the first 6 fields (chr, start, end, name, score, strand) are supported.

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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Allen Day

Email allenday@ucla.edu

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

APPENDIX

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

_initialize

  Title   : _initialize
  Function: initializes BED for reading/writing
  Args    : all optional:
            name          description
            ----------------------------------------------------------
            -name         the name for the BED track, stored in header
                          name defaults to localtime()
            -description  the description for the BED track, stored in
                          header.  defaults to localtime().
            -use_score    whether or not the score attribute of
                          features should be used when rendering them.
                          the higher the score the darker the color.
                          defaults to 0 (false)
 
 

use_score

  Title   : use_score
  Usage   : $obj->use_score($newval)
  Function: should score be used to adjust feature color when rendering?  set to true if so.
  Example : 
  Returns : value of use_score (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

name

  Title   : name
  Usage   : $obj->name($newval)
  Function: name of BED track
  Example : 
  Returns : value of name (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

description

  Title   : description
  Usage   : $obj->description($newval)
  Function: description of BED track
  Example : 
  Returns : value of description (a scalar)
  Args    : on set, new value (a scalar or undef, optional)