Bio::Map::CytoPosition(3pm)				User Contributed Perl Documentation			       Bio::Map::CytoPosition(3pm)

NAME

       Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes

SYNOPSIS

	 $m1 = Bio::Map::CytoPosition->new ( '-id' => 'A1',
					      '-value' => '2q1-3'
						    );
	 $m2 = Bio::Map::CytoPosition->new ( '-id' => 'A2',
					      '-value' => '2q2'
						    );

	 if ($m1->cytorange->overlaps($m2->cytorange)) {
	     print "Makers overlap
";
	 }

DESCRIPTION

       CytoPosition is marker (Bio::Map::MarkerI compliant) with a location in a cytogenetic map. See Bio::Map::MarkerI for more information.

       Cytogenetic locations are names of bands visible in stained mitotic eucaryotic chromosomes. The naming follows strict rules which are
       consistant at least in higher vertebates, e.g. mammals. The chromosome name preceds the band names.

       The shorter arm of the chromosome is called 'p' ('petit') and usually drawn pointing up. The lower arm is called 'q' ('queue'). The bands
       are named from the region separting these, a centromere (cen), towards the tips or telomeric regions (ter) counting from 1 upwards.
       Depending of the resolution used the bands are identified with one or more digit. The first digit determines the major band and subsequent
       digits sub bands: p1 band can be divided into subbands p11, p12 and 13 and p11 can furter be divided into subbands p11.1 and p11.2. The dot
       after second digit makes it easier to read the values. A region between ands is given from the centromere outwards towards the telomere
       (e.g. 2p2-5 or 3p21-35) or from a band in the p arm to a band in the q arm.

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

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

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 _

   cytorange
	Title	: cytorange
	Usage	: my $range = $obj->cytorange();
	Function:
		   Converts cytogenetic location set by value method into
		   an integer range. The chromosome number determines the
		   "millions" in the values.  Human X and Y chromosome
		   symbols are represented by values 100 and 101.

		   The localization within chromosomes are converted into
		   values between the range of 0 and 200,000:

		   pter 		   cen			     qter
		   |------------------------|-------------------------|
		   0			 100,000		   200,000

		   The values between -100,000 through 0 for centromere to
		   100,000 would have reflected the band numbering better but
		   use of positive integers was chosen since the
		   transformation is very easy. These values are not metric.

		   Each band defines a range in a chromosome. A band string
		   is converted into a range by padding it with lower and and
		   higher end digits (for q arm: '0' and '9') to the length
		   of five. The arm and chromosome values are added to these:
		   e.g. 21000 & 21999 (band 21) + 100,000 (q arm) + 2,000,000
		   (chromosome 2) => 2q21 : 2,121,000 .. 2,121,999. Note that
		   this notation breaks down if there is a band or a subband
		   using digit 9 in its name!  This is not the case in human
		   karyotype.

		   The full algorithm used for bands:

		   if arm is 'q' then
		      pad char for start is '0', for end '9'
		      range is chromosome + 100,000 + padded range start or end
		   elsif arm is 'p' then
		      pad char for start is '9', for end '0'
		      range is chromosome + 100,000 - padded range start or end

	Returns : Bio::Range object or undef
	Args	: none

   range2value
	Title	: range2value
	Usage	: my $value = $obj->range2value($range);
	Function: Sets and returns the value string based on start and end values of
		  the Bio::Range object passes as an argument.
	Returns : string or false
	Args	: Bio::Range object

   value
	Title	: value
	Usage	: my $pos = $position->value;
	Function: Get/Set the value for this postion
	Returns : scalar, value
	Args	: none to get, OR scalar to set

   numeric
	Title	: numeric
	Usage	: my $num = $position->numeric;
	Function: Read-only method that is guarantied to return a numeric
		  representation of the start of this position.
	Returns : int (the start of the range)
	Args	: optional Bio::RangeI object

   chr
	Title	: chr
	Usage	: my $mychr = $position->chr();
	Function: Get/Set method for the chromosome string of the location.
	Returns : chromosome value
	Args	: none to get, OR scalar to set

perl v5.14.2							    2012-03-02					       Bio::Map::CytoPosition(3pm)