Bio::LocatableSeq - A Sequence object with start/end points on it
Give standard usage here
# a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inheriets off RangeI, so range operations possible $locseq->overlaps($seqfeature);
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The locatable sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this.
It is, to be honest, not well integrated with the rest of bioperl, for example, the trunc() function does not return a LocatableSeq object, as some might have thought. There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : start Usage : $obj->start($newval) Function: Returns : value of start Args : newvalue (optional)
Title : end Usage : $obj->end($newval) Function: Returns : value of end Args : newvalue (optional)
Title : strand Usage : $obj->strand($newval) Function: Returns : value of strand Args : newvalue (optional)
Title : get_nse Usage : Function: Example : Returns : Args :
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.