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)