Mailing Lists¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

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¶

  https://github.com/bioperl/bioperl-live/issues

version¶

 Title   : version
 Usage   : my $version = $map->version();
 Function: Get/set the version of the program used to
           generate this map
 Returns : scalar representing the version
 Args    : none to get, OR string to set

modification_user¶

 Title   : modification_user
 Usage   : my $modification_user = $map->modification_user();
 Function: Get/set the name of the user who last modified this map
 Returns : scalar representing the username
 Args    : none to get, OR string to set

group_type¶

 Title   : group_type
 Usage   : $map->group_type($grptype);
               my $grptype = $map->group_type();
 Function: Get/set the group type of this map
 Returns : scalar representing the group type
 Args    : none to get, OR string to set

group_abbr¶

 Title   : group_abbr
 Usage   : $map->group_abbr($grpabbr);
               my $grpabbr = $map->group_abbr();
 Function: get/set the group abbrev of this map
 Returns : string representing the group abbrev
 Args    : none to get, OR string to set

core_exists¶

 Title   : core_exists
 Usage   : my $core_exists = $map->core_exists();
 Function: Get/set if the FPC file is accompanied by COR file
 Returns : boolean
 Args    : none to get, OR 1|0 to set

each_cloneid¶

 Title   : each_cloneid
 Usage   : my @clones = $map->each_cloneid();
 Function: returns an array of clone names
 Returns : list of clone names
 Args    : none

get_cloneobj¶

 Title   : get_cloneobj
 Usage   : my $cloneobj = $map->get_cloneobj('CLONEA');
 Function: returns an object of the clone given in the argument
 Returns : object of the clone
 Args    : scalar representing the clone name

each_markerid¶

 Title   : each_markerid
 Usage   : my @markers = $map->each_markerid();
 Function: returns list of marker names
 Returns : list of marker names
 Args    : none

get_markerobj¶

 Title   : get_markerobj
 Usage   : my $markerobj = $map->get_markerobj('MARKERA');
 Function: returns an object of the marker given in the argument
 Returns : object of the marker
 Args    : scalar representing the marker name

each_contigid¶

 Title   : each_contigid
 Usage   : my @contigs = $map->each_contigid();
 Function: returns a list of contigs (numbers)
 Returns : list of contigs
 Args    : none

get_contigobj¶

 Title   : get_contigobj
 Usage   : my $contigobj = $map->get_contigobj('CONTIG1');
 Function: returns an object of the contig given in the argument
 Returns : object of the contig
 Args    : scalar representing the contig number

matching_bands¶

 Title   : matching_bands
 Usage   : $self->matching_bands('cloneA','cloneB',[$tol]);
 Function: given two clones [and tolerence], this method calculates how many
           matching bands do they have.
           (this method is ported directly from FPC)
 Returns : scalar representing the number of matching bands
 Args    : names of the clones ('cloneA', 'cloneB') [Default tolerence=7]

coincidence_score¶

 Title   : coincidence_score
 Usage   : $self->coincidence_score('cloneA','cloneB'[,$tol,$gellen]);
 Function: given two clones [,tolerence and gellen], this method calculates
           the Sulston Coincidence score.
           (this method is ported directly from FPC)
 Returns : scalar representing the Sulston coincidence score.
 Args    : names of the clones ('cloneA', 'cloneB')
           [Default tol=7 gellen=3300.0]

print_contiglist¶

 Title   : print_contiglist
 Usage   : $map->print_contiglist([showall]); #[Default 0]
 Function: prints the list of contigs, markers that hit the contig, the
           global position and whether the marker is a placement (P) or
           a Framework (F) marker.
 Returns : none
 Args    : [showall] [Default 0], 1 includes all the discrepant markers

print_markerlist¶

 Title    : print_markerlist
 Usage    : $map->print_markerlist();
 Function : prints the marker list; contig and corresponding number of
            clones for each marker.
 Returns  : none
 Args     : none

print_gffstyle¶

 Title    : print_gffstyle
 Usage    : $map->print_gffstyle([style]);
 Function : prints GFF; either Contigwise (default) or Groupwise
 Returns  : none
 Args     : [style] default = 0 contigwise, else
                              1 groupwise (chromosome-wise).

_calc_markerposition¶

 Title   : _calc_markerposition
 Usage   : $map->_calc_markerposition();
 Function: Calculates the position of the marker in the contig
 Returns : none
 Args    : none

_calc_contigposition¶

 Title   : _calc_contigposition
 Usage   : $map->_calc_contigposition();
 Function: calculates the position of the contig in the group
 Returns : none
 Args    : none

_calc_contiggroup¶

 Title   : _calc_contiggroup
 Usage   : $map->_calc_contiggroup();
 Function: calculates the group of the contig
 Returns : none
 Args    : none

_set<Type>Ref¶

 Title   : _set<Type>Ref
 Usage   : These are used for initializing the reference of the hash in
           Bio::MapIO (fpc.pm) to the corresponding hash in Bio::Map
           (physical.pm). Should be used only from Bio::MapIO System.
               $map->setCloneRef(\%_clones);
               $map->setMarkerRef(\%_markers);
               $map->setContigRef(\%_contigs);
 Function: sets the hash references to the corresponding hashes
 Returns : none
 Args    : reference of the hash.