Bio::FeatureIO::bed(3) read/write features from UCSC BED format


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) {


See <>.

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


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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:

AUTHOR - Allen Day

Email [email protected]


Sendu Bala, [email protected]


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


 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)


 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)


 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)


 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)