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Bio::LocatableSeq.3pm

NAME

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.

SYNOPSIS

     use Bio::LocatableSeq;
     my $seq = new Bio::LocatableSeq(-seq => "CAGT-GGT",
                                     -id  => "seq1",
                                     -start => 1,
                                     -end   => 7);
 
 

DESCRIPTION

     # a normal sequence object
     $locseq->seq();
     $locseq->id();
 
 

     # has start,end points
     $locseq->start();
     $locseq->end();
 
 

     # inherits off RangeI, so range operations possible
 
 

FEEDBACK

Mailing Lists

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
 
 

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.

Reporting Bugs

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/
 
 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

start

  Title   : start
  Usage   : $obj->start($newval)
  Function:
  Returns : value of start
  Args    : newvalue (optional)
 
 

end

  Title   : end
  Usage   : $obj->end($newval)
  Function:
  Returns : value of end
  Args    : newvalue (optional)
 
 

strand

  Title   : strand
  Usage   : $obj->strand($newval)
  Function:
  Returns : value of strand
  Args    : newvalue (optional)
 
 

get_nse

  Title   : get_nse
  Usage   :
  Function: read-only name of form id/start-end
  Example :
  Returns :
  Args    :
 
 

no_gap

  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)
 
 

column_from_residue_number

  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)
 
 

location_from_column

  Title   : location_from_column
  Usage   : $loc = $ali->location_from_column($column_number)
  Function:
 
 

            This function gives the residue number 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 sequence:
 
 

              Seq/91-97 .AC..DEF.G.
 
 

            location_from_column( 3 ) position 93
            location_from_column( 2 ) position 92^93
            location_from_column(10 ) position 97^98
            location_from_column( 1 ) position undef
 
 

            An exact position returns a Bio::Location::Simple object
            where where location_type() returns 'EXACT', if a position
            is between bases location_type() returns 'IN-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 undef
  Args    : A column number
  Throws  : If column is not within the sequence
 
 

See Bio::Location::Simple for more.

revcom

  Title   : revcom
  Usage   : $rev = $seq->revcom()
  Function: Produces a new Bio::LocatableSeq object which
            has the reversed complement of the sequence. For protein
            sequences this throws an exception of "Sequence is a
            protein. Cannot revcom"
 
 

  Returns : A new Bio::LocatableSeq object
  Args    : none
 
 

trunc

  Title   : trunc
  Usage   : $subseq = $myseq->trunc(10,100);
  Function: Provides a truncation of a sequence,
 
 

  Example :
  Returns : a fresh Bio::PrimarySeqI implementing object
  Args    : Two integers denoting first and last columns of the
            sequence to be included into sub-sequence.