Bio::Map::Contig(3pm) User Contributed Perl Documentation Bio::Map::Contig(3pm)
NAME
Bio::Map::Contig - A MapI implementation handling the contigs of a Physical Map (such as FPC)
SYNOPSIS
# 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 " +++$marker
";
}
# find the group of this contig
print "Group: ",$ctgobj->group(),"
";
# find the range of this contig
print "RANGE: start:",$ctgobj->range()->start()," end: ",
$ctgobj->range()->end(),"
";
# find the position of this contig in $group (chromosome)
print "Position in Group $group"," = ",$ctgobj->position($group),"
";
DESCRIPTION
This is an implementation of 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 tailored to work for FPC physical maps, but could probably be used for others as well (with the appropriate MapIO
module).
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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Gaurav Gupta
Email gaurav@genome.arizona.edu
CONTRIBUTORS
Sendu Bala bix@sendu.me.uk
PROJECT LEADERS
Jamie Hatfield jamie@genome.arizona.edu Dr. Cari Soderlund cari@genome.arizona.edu
PROJECT DESCRIPTION
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.genome.arizona.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $clone = Bio::Map::Contig->new
(
-name => $name,
-chr_remark => $cremark,
-user_remark => $uremark,
-trace_remark => $tremark,
-group => $group,
-subgroup=> $subgroup,
-anchor => $anchor,
-markers => \%markers,
-clones => \%clones,
-position => $pos
-range => Bio::Range->new(-start =>$s,-end=>$e),
);
Function: Initialize a new Bio::Map::Contig object
Most people will not use this directly but get Markers
through L<Bio::MapIO::fpc>
Returns : L<Bio::Map::Contig> object
Args : ( -name => name string,
-chr_remark => chr remark string,
-user_remark => userremark string,
-trace_remark => tremark string,
-group => group string,
-subgroup=> subgroup string,
-anchor => boolean if this is anchored or not,
-markers => hashref of contained markers,
-clones => hashref of contained clones,
-position => position
-range => L<Bio::Range>
Modifier methods
All methods present in Bio::Map::SimpleMap 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.
chr_remark
Title : chr_remark
Usage : my $chrremark = $contigobj->chr_remark();
Function: Get/set the group remark for this contig
Returns : scalar representing the current group_remark of this contig
Args : none to get, OR string to set
user_remark
Title : user_remark
Usage : my $userremark = $contigobj->user_remark();
Function: Get/set the user remark for this contig
Returns : scalar representing the current user_remark of this contig
Args : none to get, OR string to set
trace_remark
Title : trace_remark
Usage : my $traceremark = $contigobj->trace_remark();
Function: Get/set the trace remark for this contig
Returns : scalar representing the current trace_remark of this contig
Args : none to get, OR string to set
range
Title : range
Usage : my $range = $contigobj->range();
Function: Get/set 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 to get, OR Bio::Range to set
position
Title : position
Usage : $ctgpos = $contigobj->position();
Function: Get/set the position of the contig in the group
Returns : scalar representing the position of the contig in the group
Args : none to get, OR string to set
anchor
Title : anchor
Usage : $ctganchor = $contig->anchor();
Function: Get/set the anchor value for this Contig (True | False)
Returns : scalar representing the anchor (1 | 0) for this contig
Args : none to get, OR string to set
group
Title : group
Usage : $groupno = $contigobj->group();
Function: Get/set 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
subgroup
Title : subgroup
Usage : $subgroup = $contig->subgroup();
Function: Get/set 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
each_cloneid
Title : each_cloneid
Usage : my @clones = $map->each_cloneid();
Function: retrieves all the clone ids in a map unordered
Returns : list of strings (ids)
Args : none
*** This only supplies the ids set with the set_clones method ***
*** It has nothing to do with actual Bio::Map::MappableI objects ***
each_markerid
Title : each_markerid
Usage : my @markers = $map->each_markerid();
Function: retrieves all the marker ids in a map unordered
Returns : list of strings (ids)
Args : none
*** This only supplies the ids set with the set_markers method ***
*** It has nothing to do with actual Bio::Map::MarkerI objects ***
set_clones
Title : set_clones
Usage : $marker->set_clones(\%clones)
Function: Set the clones hashref
Returns : None
Args : Hashref of clone ids
*** This only sets a hash of ids ***
*** It has nothing to do with actual Bio::Map::MappableI objects ***
set_markers
Title : markers
Usage : $obj->set_markers($newval)
Function: Set list of Markers (hashref)
Returns : None
Args : Hashref of marker ids
*** This only sets a hash of ids ***
*** It has nothing to do with actual Bio::Map::MarkerI objects ***
perl v5.14.2 2012-03-02 Bio::Map::Contig(3pm)