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.\" ========================================================================
.\"
.IX Title "Bio::Map::CytoPosition 3pm"
.TH Bio::Map::CytoPosition 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Map::CytoPosition \- Marker class with cytogenetic band storing attributes
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&  $m1 = Bio::Map::CytoPosition\->new ( \*(Aq\-id\*(Aq => \*(AqA1\*(Aq,
\&                                       \*(Aq\-value\*(Aq => \*(Aq2q1\-3\*(Aq
\&                                             );
\&  $m2 = Bio::Map::CytoPosition\->new ( \*(Aq\-id\*(Aq => \*(AqA2\*(Aq,
\&                                       \*(Aq\-value\*(Aq => \*(Aq2q2\*(Aq
\&                                             );
\&
\&  if ($m1\->cytorange\->overlaps($m2\->cytorange)) {
\&      print "Makers overlap\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
CytoPosition is marker (Bio::Map::MarkerI compliant) with a location in a
cytogenetic map. See Bio::Map::MarkerI for more information.
.PP
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.
.PP
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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Sendu Bala  bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "cytorange"
.IX Subsection "cytorange"
.Vb 7
\& 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: \*(Aq0\*(Aq and \*(Aq9\*(Aq) 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 \*(Aqq\*(Aq then
\&               pad char for start is \*(Aq0\*(Aq, for end \*(Aq9\*(Aq
\&               range is chromosome + 100,000 + padded range start or end
\&            elsif arm is \*(Aqp\*(Aq then
\&               pad char for start is \*(Aq9\*(Aq, for end \*(Aq0\*(Aq
\&               range is chromosome + 100,000 \- padded range start or end
\&
\& Returns : Bio::Range object or undef
\& Args    : none
.Ve
.SS "range2value"
.IX Subsection "range2value"
.Vb 6
\& 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
.Ve
.SS "value"
.IX Subsection "value"
.Vb 5
\& 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
.Ve
.SS "numeric"
.IX Subsection "numeric"
.Vb 6
\& 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
.Ve
.SS "chr"
.IX Subsection "chr"
.Vb 5
\& 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
.Ve