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Bio::Map::CytoPositionUser Contributed Perl DocumentaBio::Map::CytoPosition(3)

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\n";
	 }

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

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 v5.24.1			  2017-07-08	     Bio::Map::CytoPosition(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Heikki Lehvaslaiho | CONTRIBUTORS | APPENDIX

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