Bio::Map::Contig man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::Map::Contig(3)   User Contributed Perl Documentation  Bio::Map::Contig(3)

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\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";

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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-22		   Bio::Map::Contig(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net