Bio::Location::Simple - Implementation of a Simple Location on a Sequence
use Bio::Location::Simple; my $location = new Bio::Location::Simple(-start => 1, -end => 100, -strand => 1 ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; }
This is an implementation of Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'.
You can test the type of the location using length() function () or directly location_type() which can one of two values: 'EXACT' or 'IN-BETWEEN'.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Email heikki-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : start Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range Args : optionaly allows the start to be set : using $loc->start($start)
Title : end Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range Args : optionaly allows the end to be set : using $loc->end($start)
Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandedness (-1, 0, +1) Args : optionaly allows the strand to be set : using $loc->strand($strand)
Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none
Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no minimum starting point. Args : none
Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint. In this implementation this is exactly the same as min_start(). Returns : integer or undef if no maximum starting point. Args : none
Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^). Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none
Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : none
Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint In this implementation this is exactly the same as min_end(). Returns : integer or undef if no maximum ending point. Args : none
Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none
Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT' or 'IN-BETWEEN') Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^'
Title : is_remote Usage : $self->is_remote($newval) Function: Getset for is_remote value Returns : value of is_remote Args : newvalue (optional)
Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.