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\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 consistent 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 separating 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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

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 position
 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