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: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
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 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