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bio::liveseq::seqi(3pm) [debian man page]

Bio::LiveSeq::SeqI(3pm) 				User Contributed Perl Documentation				   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. 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://redmine.open-bio.org/projects/bioperl/ 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 perl v5.14.2 2012-03-02 Bio::LiveSeq::SeqI(3pm)
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