--- name: "Bio::Map::Clone" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.2-3" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Map::Clone" --- # Bio::Map::Clone(3pm) An central map object representing a clone ## NAME Bio::Map::Clone - An central map object representing a clone ## SYNOPSIS ``` # get the clone object of $clone from the Bio::Map::Clone my $cloneobj = $physical->get_cloneobj($clone); # acquire all the markers that hit this clone foreach my $marker ($cloneobj->each_markerid()) { print " +++$marker\n"; } ``` See Bio::Map::Position and Bio::Map::PositionI for more information. ## DESCRIPTION This object handles the notion of a clone. This clone will have a name and a position in a map. This object is intended to be used by a map parser like fpc.pm. ## 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://github.com/bioperl/bioperl-live/issues ``` ## 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::Clone->new ( -name => $clone, -markers => \@markers, -contig => $contig, -type => $type, -bands => $bands, -gel => $gel, -group => $group, -remark => $remark, -fpnumber=> $fp_number, -sequencetype => $seq_type, -sequencestatus=> $seq_status, -fpcremark => $fpc_remark, -matche => \@ematch, -matcha => \@amatch, -matchp => \@pmatch, -range => Bio::Range->new(-start => $startrange, -end => $endrange) ); Function: Initialize a new Bio::Map::Clone object Most people will not use this directly but get Clones through L Returns : L object Args : -name => marker name string, -markers => array ref of markers, -contig => contig name string, -type => type string, -bands => band string, -gel => gel string, -group => group name string, -remark => remark string, -fpnumber=> FP number string, -sequencetype => seq type string, -sequencestatus=> seq status string, -fpcremark => FPC remark, -matche => array ref, -matcha => array ref, -matchp => array ref, -range => L object, ``` ## Access Methods These methods let you get and set the member variables ### name ``` Title : name Usage : my $name = $cloneobj->name(); Function: Get/set the name for this Clone Returns : scalar representing the current name of this clone Args : none to get, OR string to set ``` ### type ``` Title : type Usage : my $type = $cloneobj->type(); Function: Get/set the type for this clone Returns : scalar representing the current type of this clone Args : none to get, OR string to set ``` ### range ``` Title : range Usage : my $range = $cloneobj->range(); Function: Get/set the range of the contig that this clone covers 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 ``` ### match ``` Title : match Usage : @eclone = $cloneobj->match('exact'); @aclone = $cloneobj->match('approximate'); @pclone = $cloneobj->match('pseudo'); Function: get all matching clones Returns : list Args : scalar representing the type of clone to be queried. ``` ### each\_match ``` Title : each_match Function: Synonym of the match() method. ``` ### set\_match ``` Title : set_match Usage : $clone->set_match($type,$values); Function: Set the Matches per type Returns : None Args : type (one of 'exact' 'approx' 'pseudo') array ref of match values ``` ### gel ``` Title : gel Usage : $clonegel = $cloneobj->gel(); Function: Get/set the gel number for this clone Returns : scalar representing the gel number of this clone Args : none to get, OR string to set ``` ### remark ``` Title : remark Usage : $cloneremark = $cloneobj->remark(); Function: Get/set the remark for this clone Returns : scalar representing the current remark of this clone Args : none to get, OR string to set ``` ### fp\_number ``` Title : fp_number Usage : $clonefpnumber = $cloneobj->fp_number(); Function: Get/set the fp number for this clone Returns : scalar representing the fp number of this clone Args : none to get, OR string to set ``` ### sequence\_type ``` Title : sequence_type Usage : $cloneseqtype = $cloneobj->sequence_type(); Function: Get/set the sequence type for this clone Returns : scalar representing the sequence type of this clone Args : none to get, OR string to set ``` ### sequence\_status ``` Title : sequence_status Usage : $cloneseqstatus = $cloneobj->sequence_status(); Function: Get/set the sequence status for this clone Returns : scalar representing the sequence status of this clone Args : none to get, OR string to set ``` ### fpc\_remark ``` Title : fpc_remark Usage : $clonefpcremark = $cloneobj->fpc_remark(); Function: Get/set the fpc remark for this clone Returns : scalar representing the fpc remark of this clone Args : none to get, OR string to set ``` ### bands ``` Title : bands Usage : @clonebands = $cloneobj->bands(); Function: Get/set the bands for this clone Returns : liat representing the band of this clone, if readcor = 1 while creating the MapIO object and the .cor exists Args : none to get, OR string to set ``` ### group ``` Title : group Usage : $cloneobj->group($chrno); Function: Get/set the group number for this clone. This is a generic term, used for Linkage-Groups as well as for Chromosomes. Returns : scalar representing the group number of this clone Args : none to get, OR string to set ``` ### contigid ``` Title : contigid Usage : my $ctg = $cloneobj->contigid(); Function: Get/set the contig this clone belongs to Returns : scalar representing the contig Args : none to get, OR string to set ``` ### each\_markerid ``` Title : each_markerid Usage : @markers = $cloneobj->each_markerid(); Function: retrieves all the elements 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\_markers ``` Title : markers Usage : $obj->set_markers($newval) Function: Set list of Marker ids (arrayref) Returns : None Args : arrayref of strings (ids) *** This only sets a list of ids *** *** It has nothing to do with actual Bio::Map::MarkerI objects *** ```