NAME
Bio::LiveSeq::SeqI - Abstract sequence interface class for LiveSeq
SYNOPSIS
# documentation neededDESCRIPTION
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
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bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing listsReporting 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 email or the web:
bioperl-bugs@bioperl.org
http://bio.perl.org/bioperl-bugs/AUTHOR - Joseph A.L. Insana
Email: Insana@ebi.ac.uk, jinsana@gmx.net
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom 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 stringall_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 : nonelabelsubseq
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 expecially 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 sequencesubseq
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 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 methodlength
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 : nonedisplay_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 : noneaccession_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 : noneprimary_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 : Nonechange
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 : labelstart
Title : start
Usage : $startlabel=$obj->start()
Function: returns the label of the first nucleotide of the object (exon, CDS)
Returns : label
Args : noneend
Title : end
Usage : $endlabel=$obj->end()
Function: returns the label of the last nucleotide of the object (exon, CDS)
Returns : label
Args : nonestrand
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 1moltype
Title : moltype
Usage : if( $obj->moltype 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
Note : "circular dna" is set as dnacoordinate_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 1label
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 methodposition
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 methodfollows
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 methodtranslate
Title : translate
Usage : $protein_seq = $obj->translate
Function: Provides the translation of the DNA sequence
using full IUPAC ambiguities in DNA/RNA and amino acid codes.
The resulting translation is identical to EMBL/TREMBL database
translations.
Returns : a string
Args : character for terminator (optional) defaults to '*'
character for unknown amino acid (optional) defaults to 'X'
frame (optional) valid values 0, 1, 3, defaults to 0
codon table id (optional) defaults to 1translate_string
Title : translate_string
Usage : $protein_seq = $obj->translate_string("attcgtgttgatcgatta");
Function: Like translate, but can be used to translate subsequences after
having retrieved them as string.
Args : 1st argument is a string. Optional following arguments: like in
the translate methodgene
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::Geneobj_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 : nonename
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 : Nonedescription
Title : description
Usage : $description = $obj->description;
: $description = $obj->description("ABCD");
Function: Returns or sets the description of the object.
If there is no description, it will return "unknown";
Returns : A string
Args : Nonesource
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 : Noneverbose
Title : verbose
Usage : $self->verbose(0)
Function: Sets verbose level for how ->warn behaves
-1 = silent: no warning
0 = reduced: minimal warnings
1 = default: all warnings
2 = extended: all warnings + stack trace dump
3 = paranoid: a warning becomes a throw and the program dies
Note: a quick way to set all LiveSeq objects at the same verbosity
level is to change the DNA level object, since they all look to
that one if their verbosity_level attribute is not set.
But the method offers fine tuning possibility by changing the
verbose level of each object in a different way.
So for example, after $loader= and $gene= have been retrieved
by a program, the command $gene->verbose(0); would
set the default verbosity level to 0 for all objects.
Returns : the current verbosity level
Args : -1,0,1,2 or 3warn
Title : warn
Usage : $object->warn("Warning message",$ignorable);
Function: Places a warning. What happens now is down to the
verbosity of the object (value of $obj->verbose)
-1 = silent: no warning
0 = reduced: minimal warnings
1 = default: all warnings
2 = extended: all warnings + stack trace dump
3 = paranoid: a warning becomes a throw and the program dies
If a second argument is given and is 1, then the warning becomes
a relatively ignorable one. I.e. it means that warning is one
the program can cope with, so at verbose level "0", it wouldn't
be printed. At verbose level >1 it will be printed with the rest.
Example : $obj->warn("Label not found");
Example : $obj->warn("Starting position not specified, using default start",1);
Returns : nothing
Args : string, booleanthrow
Title : throw
Usage : $obj->throw("throwing exception message")
Function: Throws an exception, which, if not caught with an eval brace
will print the error message, a stack trace dump, and die.
Returns : nothing
Args : A string giving a descriptive error messagestack_trace
Title : stack_trace
Usage : @stack_array_ref= $self->stack_trace
Function: gives an array to a reference of arrays with stack trace info
each coming from the caller(stack_number) call
Returns : array containing a reference of arrays
Args : none