use Bio::Location::Simple; use Bio::Coordinate::Pair; my $match1 = Bio::Location::Simple->new (-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 ); my $match2 = Bio::Location::Simple->new (-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 ); my $pair = Bio::Coordinate::Pair->new(-in => $match1, -out => $match2 ); # location to match $pos = Bio::Location::Simple->new (-start => 25, -end => 25, -strand=> -1 ); # results are in a Bio::Coordinate::Result # they can be Matches and Gaps; are Bio::LocationIs $res = $pair->map($pos); $res->isa('Bio::Coordinate::Result'); $res->each_match == 1; $res->each_gap == 0; $res->each_Location == 1; $res->match->start == 5; $res->match->end == 5; $res->match->strand == -1; $res->match->seq_id eq 'peptide';
This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another.
The map() method returns Bio::Coordinate::Results with Bio::Coordinate::Result::Gaps. The calling code have to deal (process or ignore) them.
Title : in Usage : $obj->in('peptide'); Function: Set and read the input coordinate system. Example : Returns : value of input system Args : new value (optional), Bio::LocationI
Title : out Usage : $obj->out('peptide'); Function: Set and read the output coordinate system. Example : Returns : value of output system Args : new value (optional), Bio::LocationI
Title : swap Usage : $obj->swap; Function: Swap the direction of mapping; input <-> output Example : Returns : 1 Args :
Title : strand Usage : $obj->strand; Function: Get strand value for the pair Example : Returns : ( 1 | 0 | -1 ) Args :
Title : test Usage : $obj->test; Function: test that both components are of the same length Example : Returns : ( 1 | undef ) Args :
Title : map Usage : $newpos = $obj->map($pos); Function: Map the location from the input coordinate system to a new value in the output coordinate system. Example : Returns : new Bio::LocationI in the output coordinate system or undef Args : Bio::LocationI object
Title : _map Usage : $newpos = $obj->_map($simpleloc); Function: Internal method that does the actual mapping. Called multiple times by map() if the location to be mapped is a split location Example : Returns : new location in the output coordinate system or undef Args : Bio::Location::Simple
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.