Bio::Location::Simple - Implementation of a Simple Location on a Sequence
use Bio::Location::Simple; my $location = Bio::Location::Simple->new(-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'.
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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) Note : If start is set but end is undefined, this now assumes that start is the same as end but throws a warning (i.e. it assumes this is a possible error). If start is undefined, this now throws an exception.
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 = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none
Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.