Bio::Map::contig - A MapI implementation handling a the contigs of a Physical Map (such as FPC)
## get the contig object of $contig from the Bio::Map::physical
my $ctgobj = $physical->get_contigobj($contig);
## acquire all the markers that lie in this contig
foreach my $marker ($ctgobj->each_markerid()) {
print " +++$marker\n";
}
## find the group of this contig
print "Group: ",$ctgobj->group(),"\n";
## find the range of this contig
print "RANGE: start:",$ctgobj->range()->start(),"\tend: ",
$ctgobj->range()->end(),"\n";
## find the position of this contig in $group (chromosome)
print "Position in Group $group"," = ",$ctgobj->position($group),"\n";
This is an implementation of a Bio::Map::MapI. It handles the essential storage of name, species, type, and units as well as in memory representation of the elements of a map.
Bio::Map::contig has been taylored to work for FPC physical maps, but could probably be used for others as well (with the appropriate MapIO module).
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 list. Your participation is much appreciated.
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Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:
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Email will@agcol.arizona.edu
The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of Arizona.
This work was funded by USDA-IFAFS grant #11180 titled ``Web Resources for the Computation and Display of Physical Mapping Data''.
For more information on this project, please refer: http://www.agcol.arizona.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
These methods let you get and set the member variables
All methods present in the Bio::Map::SimpleMap manpage are implemented by this class. Most of the methods are inherited from SimpleMap. The following methods have been modified to reflect the needs of physical maps.
Title : chr_remark Usage : my $chrremark = $contigobj->chr_remark(); Function: get the group remark for this contig Returns : scalar representing the current group_remark of this contig Args : none
Title : user_remark Usage : my $userremark = $contigobj->user_remark(); Function: get the user remark for this contig Returns : scalar representing the current user_remark of this contig Args : none
Title : trace_remark Usage : my $traceremark = $contigobj->trace_remark(); Function: get the trace remark for this contig Returns : scalar representing the current trace_remark of this contig Args : none
Title : range
Usage : my $range = $contigobj->range();
Function: get the range for this Contig
Returns : Bio::Range representing the current range of this contig,
start and end of the contig can be thus found using:
my $start = $contigobj->range()->start();
my $end = $contigobj->range()->end();
Args : none
Title : position Usage : $ctgpos = $contigobj->position(); Function: get the position of the contig in the group Returns : scalar representing the position of the contig in the group Args : none
Title : anchor Usage : $ctganchor = $contig->anchor(); Function: get the anchor value for this Contig (True | False) Returns : scalar representing the anchor (1 | 0) for this contig Args : none
Title : group
Usage : $groupno = $contigobj->group();
Function: get the group number for this contig
this is a generic term, used for Linkage-Groups
as well as for Chromosomes.
Returns : scalar representing the group number of this contig
Args : none
Title : subgroup
Usage : $subgroup = $contig->subgroup();
Function: get the subgroup for this contig. This is a
generic term: subgroup here could represent subgroup
of a Chromosome or of a Linkage Group.
the user must take care of which subgroup he/she is querying
for.
Returns : A scalar representing the subgroup of this contig
Args : none
Title : each_<element>id
Usage : my @clones = $map->each_cloneid();
my @markers = $map->each_markerid();
Function: retrieves all the elements in a map unordered
Returns : list of Bio::Map::MappableI ids (names)
Args : type of elements you want (clones, markers)