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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ Bio::LiveSeq::SeqI

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

bioperl-l@bioperl.org

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: Insana@ebi.ac.uk, jinsana@gmx.net

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
           argment. 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
          implemetation, 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