Bio::LocatableSeq - A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
use Bio::LocatableSeq; my $seq = new Bio::LocatableSeq(-seq => "CAGT-GGT", -id => "seq1", -start => 1, -end => 7);
# a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inheriets off RangeI, so range operations possible
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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:
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: read-only name of form id/start-end Example : Returns : Args :
Title : no_gaps Usage :$self->no_gaps('.') Function: Gets number of gaps in the sequence. The count excludes leading or trailing gap characters. Valid bioperl sequence characters are [A-Za-z\-\.\*]. Of these, '.' and '-' are counted as gap characters unless an optional argument specifies one of them. Returns : number of internal gaps in the sequnce. Args : a gap character (optional)
Title : column_from_residue_number Usage : $col = $seq->column_from_residue_number($resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence. For example, for the sequence Seq1/91-97 AC..DEF.GH column_from_residue_number(94) returns 5. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Returns : A column number for the position of the given residue in the given sequence (1 = first column) Args : A residue number in the whole sequence (not just that segment of it in the alignment)
Title : location_from_column Usage : $loc = $ali->location_from_column( $seq_number, $column_number) Function: This function gives the residue number in the sequence with the given name for a given position in the alignment (i.e. column number) of the given. Gaps complicate this process and force the output to be a L<Bio::Range> where values can be undefined. For example, for the alignment Seq1/91-97 AC..DEF.G. Seq2/1-9 .CYHDEFKGK location_from_column( Seq1/91-97, 3 ) position 93 location_from_column( Seq1/91-97, 2 ) position 92^93 location_from_column( Seq1/91-97, 10) position 97^98 location_from_column( Seq2/1-9, 1 ) position undef An exact position returns a Bio::Location::Simple object, a position between bases returns a Bio::Location::Fuzzy object where loc_type() returns 'BETWEEN'. Column before the first residue returns undef. Note that if the position is after the last residue in the alignment, that there is no guarantee that the original sequence has residues after that position. An exception is thrown if the column number is not within the sequence. Returns : Bio::Location::Simple or Bio::Location::Fuzzy object or undef Args : A column number Throws : If column is not within the sequence