| Bio::Map::PositionWithSequence(3pm) | User Contributed Perl Documentation | Bio::Map::PositionWithSequence(3pm) |
Bio::Map::PositionWithSequence - A position with a sequence.
use Bio::Map::PositionWithSequence;
my $pos = Bio::Map::PositionWithSequence->new(-map => $map,
-element => $element,
-start => 0,
-seq => 'ATGC');
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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).
| 2018-10-27 | perl v5.26.2 |