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Bio::Map::PositionWithSequence.3pm

NAME

Bio::Map::PositionWithSequence - A position with a sequence.

SYNOPSIS

     use Bio::Map::PositionWithSequence;
     
     my $pos = Bio::Map::PositionWithSequence->new(-map => $map, 
                                 -element => $element,
                                 -start => 0,
                                 -seq => 'ATGC');
 
 

DESCRIPTION

Have a position with a sequence, eg. define what the binding site sequence of a certain transcription factor binding site is by modelling it as one of these objects with the -element assigned to a Bio::Map::TranscriptionFactor instance.

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 - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

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

new

  Title   : new
  Usage   : my $obj = Bio::Map::PositionWithSequence->new();
  Function: Builds a new Bio::Map::PositionWithSequence object 
  Returns : Bio::Map::PositionWithSequence
  Args    : -map      => Bio::Map::GeneMap object
            -element  => Bio::Map::Gene object
            -relative => Bio::Map::GeneRelative object
            -seq      => string, length of this string will set the length
                         of this position's range
 
            * If this position has no range, or if a single value can describe
              the range *
            -value => scalar             : something that describes the single
                                           point position or range of this
                                           Position, most likely an int
 
            * Or if this position has a range, at least two of *
            -start => int                : value of the start co-ordinate
            -end => int                  : value of the end co-ordinate
            -length => int               : length of the range
 
 

seq

  Title   : seq
  Usage   : my $string = $obj->seq();
  Function: Get/set the sequence as a string of letters.
  Returns : scalar
  Args    : Optionally on set the new value (a string). An optional second
            argument presets the alphabet (otherwise it will be guessed).