Bio::Map::CytoPosition - Marker class with cytogenetic band storing attributes
$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"; }
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : cytorange Usage : $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 choosen 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 Example : Returns : Bio::Range object or undef Args : none
Title : range2value Usage : $obj->range2value(); Function: Sets and returns the value string based on start and end values of the Bio::Range object passes as an argument. Example : Returns : string or false Args : Bio::Range object
Title : value Usage : my $pos = $position->value; Function: Get/Set the value for this postion Returns : scalar, value Args : [optional] new value to set
Title : numeric Usage : my $num = $position->numeric; Function: Read-only method that is guarantied to return a numeric representation for this position. This instanse of the method can also be set, but you better know what you are doing. Returns : Bio::RangeI object Args : optional Bio::RangeI object
See Bio::RangeI for more information.
Title : chr Usage : my $mychr = $position->chr(); Function: Get/Set method for the chromosome string of the location. Returns : chromosome value Args : [optional] new chromosome value
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.