Bio::LiveSeq::SeqI(3pm)

NAME

Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq

SYNOPSIS

  # documentation needed

DESCRIPTION

This class implements BioPerl PrimarySeqI interface for Live Seq objects.

One of the main difference in LiveSequence compared to traditional "string" sequences is that coordinate systems are flexible. Typically gene nucleotide numbering starts from 1 at the first character of the initiator codon (A in ATG). This means that negative positions are possible and common!

Secondly, the sequence manipulation methods do not return a new sequence object but change the current object. The current status can be written out to BioPerl sequence objects.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Joseph A.L. Insana

Email: [email protected], [email protected]

APPENDIX

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

Some note on the terminology/notation of method names:
label: a unique pointer to a single nucleotide
position: the position of a nucleotide according to a particular coordinate
system (e.g. counting downstream from a particular label taken as
number 1)
base: the one letter code for a nucleotide (i.e.: "a" "t" "c" "g")

       a base is the "value" that an "element" of a "chain" can assume
         (see documentation on the Chain datastructure if interested)

seq

 Title   : seq
 Usage   : $string    = $obj->seq()
 Function: Returns the complete sequence of an object as a string of letters.
           Suggested cases are upper case for proteins and lower case for
           DNA sequence (IUPAC standard),
 Returns : a string

all_labels

 Title   : all_labels
 Usage   : @labels = $obj->all_labels()
 Function: all the labels of every nucleotide an object is composed of
 Returns : an array of labels
 Args    : none

labelsubseq

  Title   : labelsubseq
  Usage   : $dna->labelsubseq();
          : $dna->labelsubseq($startlabel);
          : $dna->labelsubseq($startlabel,$length);
          : $dna->labelsubseq($startlabel,undef,$endlabel);
  e.g.    : $dna->labelsubseq(4,undef,8);
  Function: prints the sequence as string. The difference between labelsubseq
            and normal subseq is that it uses /labels/ as arguments, instead
            than positions. This allows for faster and more efficient lookup,
            skipping the (usually) lengthy conversion of positions into labels.
            This is especially useful for manipulating with high power
            LiveSeq objects, knowing the labels and exploiting their
            usefulness.
  Returns : a string
  Errorcode -1
  Args    : without arguments it returns the entire sequence
            with a startlabel it returns the sequence downstream that label
            if a length is specified, it returns only that number of bases
            if an endlabel is specified, it overrides the length argument
             and prints instead up to that label (included)
  Defaults: $startlabel defaults to the beginning of the entire sequence
            $endlabel defaults to the end of the entire sequence

subseq

 Title   : subseq
 Usage   : $substring = $obj->subseq(10,40);
         : $substring = $obj->subseq(10,undef,4);
 Function: returns the subseq from start to end, where the first base
           is 1 and the number is inclusive, ie 1-2 are the first two
           bases of the sequence
           Start cannot be larger than end but can be equal.
           Allows for negative numbers $obj->subseq(-10,-1). By
           definition, there is no 0!
                       -5  -1 1   5
                gctagcgcccaac atggctcgctg
           This allows one to retrieve sequences upstream from given position.
           The precedence is from left to right: if END is given LENGTH is
           ignored.
 Examples: $obj->subseq(-10,undef,10) returns 10 elements before position 1
           $obj->subseq(4,8) returns elements from the 4th to the 8th, inclusive
 Returns : a string
 Errorcode: -1
 Args    : start,  integer, defaults to start of the sequence
           end,    integer, '' or undef, defaults to end of the sequence
           length, integer, '' or undef
           an optional strand (1 or -1) 4th argument
            if strand argument is not given, it will default to the object
            argument. This argument is useful when a call is issued from a child
            of a parent object containing the subseq method

length

  Title   : length
  Usage   : $seq->length();
  Function: returns the number of nucleotides (or the number of aminoacids)
            in the entire sequence
  Returns : an integer
  Errorcode -1
  Args    : none

display_id

 Title   : display_id
 Usage   : $id_string = $obj->display_id();
 Function: returns the display id, alias the common name of the object
           The semantics of this is that it is the most likely string
           to be used as an identifier of the sequence, and likely to
           have "human" readability.  The id is equivalent to the ID
           field of the GenBank/EMBL databanks and the id field of the
           Swissprot/sptrembl database. In fasta format, the >(\S+) is
           presumed to be the id, though some people overload the id
           to embed other information.
 See also: accession_number
 Returns : a string
 Args    : none

accession_number

 Title   : accession_number
 Usage   : $unique_biological_key = $obj->accession_number;
 Function: Returns the unique biological id for a sequence, commonly
           called the accession_number.
           Notice that primary_id() provides the unique id for the
           implementation, allowing multiple objects to have the same accession
           number in a particular implementation.
           For objects with no accession_number this method returns "unknown".
 Returns : a string
 Args    : none

primary_id

 Title   : primary_id
 Usage   : $unique_implementation_key = $obj->primary_id;
 Function: Returns the unique id for this object in this
           implementation. This allows implementations to manage their own
           object ids in a way the implementation can control. Clients can
           expect one id to map to one object.
           For sequences with no primary_id, this method returns
           a stringified memory location.
 Returns : A string
 Args    : None

change

 Title   : change
 Usage   : $substring = $obj->change('AA', 10);
 Function: changes, modifies, mutates the LiveSequence
 Examples:
        $obj->change('',   10);      delete nucleotide #10
        $obj->change('',   10, 2);   delete two nucleotides starting from #10
        $obj->change('G',  10);      change nuc #10 to 'G'
        $obj->change('GA', 10, 4);   replace #10 and 3 following with 'GA'
        $obj->change('GA', 10, 2));  is same as $obj->change('GA',  10);
        $obj->change('GA', 10, 0 );  insert 'GA' before nucleotide at #10
        $obj->change('GA', 10, 1);   GA inserted before #10, #10 deleted
        $obj->change('GATC', 10, 2); GATC inserted before #10, #10&#11 deleted
        $obj->change('GATC', 10, 6); GATC inserted before #10, #10-#15 deleted
 Returns : a string of deleted bases (if any) or 1 (everything OK)
 Errorcode: -1
 Args    : seq,    string, or '' ('' = undef = 0 = deletion)
           start,  integer
           length, integer (optional)

positionchange

 Title   : positionchange
 Function: Exactly like change. I.e. change() defaults to positionchange()

labelchange

 Title   : labelchange
 Function: Exactly like change but uses a /label/ instead than a position
           as second argument. This allows for multiple changes in a LiveSeq
           without the burden of recomputing positions. I.e. for a multiple
           change in two different points of the LiveSeq, the approach would
           be the following: fetch the correct labels out of the two different
           positions (method: label($position)) and then use the labelchange()
           method to modify the sequence using those labels instead than
           relying on the positions (that would have modified after the
           first change).

valid

  Title   : valid
  Usage   : $boolean = $obj->valid($label)
  Function: tests if a label exists inside the object
  Returns : boolean
  Args    : label

start

  Title   : start
  Usage   : $startlabel=$obj->start()
  Function: returns the label of the first nucleotide of the object (exon, CDS)
  Returns : label
  Args    : none

end

  Title   : end
  Usage   : $endlabel=$obj->end()
  Function: returns the label of the last nucleotide of the object (exon, CDS)
  Returns : label
  Args    : none

strand

  Title   : strand
  Usage   : $strand=$obj->strand()
            $obj->strand($strand)
  Function: gets or sets strand information, being 1 or -1 (forward or reverse)
  Returns : -1 or 1
  Args    : none OR -1 or 1

alphabet

 Title   : alphabet
 Usage   : if( $obj->alphabet eq 'dna' ) { /Do Something/ }
 Function: Returns the type of sequence being one of
           'dna', 'rna' or 'protein'. This is case sensitive.
 Returns : a string either 'dna','rna','protein'.
 Args    : none

coordinate_start

  Title   : coordinate_start
  Usage   : $coordstartlabel=$obj->coordinate_start()
          : $coordstartlabel=$obj->coordinate_start($label)
  Function: returns and optionally sets the first label of the coordinate
            system used
            For some objects only labels inside the object or in frame (for
            Translation objects) will be allowed to get set as coordinate start
  Returns : label. It returns 0 if label not found.
  Errorcode -1
  Args    : an optional reference $label that is position 1

label

  Title   : label
  Usage   : $seq->label($position)
          : $seq->label($position,$firstlabel)
  Examples: $nextlabel=$seq->label(2,$label) -> retrieves the following label
          : $prevlabel=$seq->label(-1,$label) -> retrieves the preceding label
  Function: returns the label of the nucleotide at $position from current
            coordinate start
  Returns : a label. It returns 0 if label not found.
  Errorcode -1
  Args    : a position,
            an optional reference $firstlabel that is to be used as position 1
            an optional strand (1 or -1) argument
             if strand argument is not given, it will default to the object
             argument. This argument is useful when a call is issued from a child
             of a parent object containing the subseq method

position

  Title   : position
  Usage   : $seq->position($label)
          : $seq->position($label,$firstlabel)
  Function: returns the position of nucleotide at $label
  Returns : the position of the label from current coordinate start
  Errorcode 0
  Args    : a label pointing to a certain nucleotide (e.g. start of exon)
            an optional "firstlabel" as reference to count from
            an optional strand (1 or -1) argument
             if strand argument is not given, it will default to the object
             argument. This argument is useful when a call is issued from a child
             of a parent object containing the subseq method

follows

  Title   : follows
  Usage   : $seq->follows($firstlabel,$secondlabel)
          : $seq->follows($firstlabel,$secondlabel,$strand)
  Function: checks if SECONDlabel follows FIRSTlabel, undependent of the strand
            i.e. it checks downstream for forward strand and
            upstream for reverse strand
  Returns : 1 or 0
  Errorcode -1
  Args    : two labels
            an optional strand (1 or -1) argument
             if strand argument is not given, it will default to the object
             argument. This argument is useful when a call is issued from a child
             of a parent object containing the subseq method

gene

 Title   : gene
 Usage   : my $gene=$obj->gene;
 Function: Gets or sets the reference to the LiveSeq::Gene object.
           Objects that are features of a LiveSeq Gene will have this
           attribute set automatically.
 Returns : reference to an object of class Gene
 Note    : if Gene object is not set, this method will return 0;
 Args    : none or reference to object of class Bio::LiveSeq::Gene

obj_valid

 Title   : obj_valid
 Usage   : if ($obj->obj_valid) {do something;}
 Function: Checks if start and end labels are still valid for the ojbect,
           i.e. tests if the LiveSeq object is still valid
 Returns : boolean
 Args    : none

name

 Title   : name
 Usage   : $name = $obj->name;
         : $name = $obj->name("ABCD");
 Function: Returns or sets the name of the object.
           If there is no name, it will return "unknown";
 Returns : A string
 Args    : None

desc

 Title   : desc
 Usage   : $desc = $obj->desc;
         : $desc = $obj->desc("ABCD");
 Function: Returns or sets the description of the object.
           If there is no description, it will return "unknown";
 Returns : A string
 Args    : None

source

 Title   : source
 Usage   : $name = $obj->source;
         : $name = $obj->source("Homo sapiens");
 Function: Returns or sets the organism that is source of the object.
           If there is no source, it will return "unknown";
 Returns : A string
 Args    : None