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