Bio::Seq::SequenceTrace man page on Fedora

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Bio::Seq::SequenceTracUser Contributed Perl DocumentBio::Seq::SequenceTrace(3)

NAME
       Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its
       trace

SYNOPSIS
	 # example code here

DESCRIPTION
       This object stores a sequence with its trace.

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:

	 http://bugzilla.open-bio.org/

AUTHOR - Chad Matsalla
       Email bioinformatics@dieselwurks.com

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

   new()
	Title	: new()
	Usage	: $st = Bio::Seq::SequenceTrace->new
	    (	 -swq =>   Bio::Seq::SequenceWithQuality,
		 -trace_a  =>	\@trace_values_for_a_channel,
		 -trace_t  =>	\@trace_values_for_t_channel,
		 -trace_g  =>	\@trace_values_for_g_channel,
		 -trace_c  =>	\@trace_values_for_c_channel,
		 -accuracy_a	=>   \@a_accuracies,
		 -accuracy_t	=>   \@t_accuracies,
		 -accuracy_g	=>   \@g_accuracies,
		 -accuracy_c	=>   \@c_accuracies,
		 -peak_indices	  => '0 5 10 15 20 25 30 35'
	    );
	Function: Returns a new Bio::Seq::SequenceTrace object from basic
	       constructors.
	Returns : a new Bio::Seq::SequenceTrace object
       Arguments: I think that these are all describes in the usage above.

   trace($base,\@new_values)
	Title	: trace($base,\@new_values)
	Usage	: @trace_Values	 = @{$obj->trace($base,\@new_values)};
	Function: Returns the trace values as a reference to an array containing the
	    trace values. The individual elements of the trace array are not validated
	    and can be any numeric value.
	Returns : A reference to an array.
	Status	:
       Arguments: $base : which color channel would you like the trace values for?
		      - $base must be one of "A","T","G","C"
		 \@new_values : a reference to an array of values containing trace
		      data for this base

   peak_indices($new_indices)
	Title	: peak_indices($new_indices)
	Usage	: $indices = $obj->peak_indices($new_indices);
	Function: Return the trace index points for this object.
	Returns : A scalar
	Args	: If used, the trace indices will be set to the provided value.

   _reset_peak_indices()
	Title	: _rest_peak_indices()
	Usage	: $obj->_reset_peak_indices();
	Function: Reset the peak indices.
	Returns : Nothing.
	Args	: None.
	Notes	: When you create a sub_trace_object, the peak indices
	    will still be pointing to the apporpriate location _in the
	    original trace_. In order to fix this, the initial value must
	    be subtracted from each value here. ie. The first peak index
	    must be "1".

   peak_index_at($position)
	Title	: peak_index_at($position)
	Usage	: $peak_index = $obj->peak_index_at($postition);
	Function: Return the trace iindex point at this position
	Returns : A scalar
	Args	: If used, the trace index at this position will be
	    set to the provided value.

   alphabet()
	Title	: alphabet();
	Usage	: $molecule_type = $obj->alphabet();
	Function: Get the molecule type from the PrimarySeq object.
	Returns : What what PrimarySeq says the type of the sequence is.
	Args	: None.

   display_id()
	Title	: display_id()
	Usage	: $id_string = $obj->display_id();
	Function: Returns the display id, aka the common name of the Quality
	       object.
	       The semantics of this is that it is the most likely string to be
	       used as an identifier of the quality 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.
	       Bioperl does not use any embedded information in the ID field,
	       and people are encouraged to use other mechanisms (accession
	       field for example, or extending the sequence object) to solve
	       this. Notice that $seq->id() maps to this function, mainly for
	       legacy/convience issues.
	       This method sets the display_id for the Quality object.
	Returns : A string
	Args	: If a scalar is provided, it is set as the new display_id for
	       the Quality object.
	Status	: Virtual

   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. For sequences from established
	       databases, the implementors should try to use the correct
	       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 sequences
	       with no accession number, this method should return "unknown".
	       This method sets the accession_number for the Quality
	       object.
	Returns : A string (the value of accession_number)
	Args	: If a scalar is provided, it is set as the new accession_number
	       for the Quality object.
	Status	: Virtual

   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 implementaiton can control clients can expect one id to
	       map to one object. For sequences with no accession number, this
	       method should return a stringified memory location.
	       This method sets the primary_id for the Quality
	       object.
	Returns : A string. (the value of primary_id)
	Args	: If a scalar is provided, it is set as the new primary_id for
	       the Quality object.

   desc()
	Title	: desc()
	Usage	: $qual->desc($newval); _or_
		  $description = $qual->desc();
	Function: Get/set description text for this Quality object.
	Returns : A string. (the value of desc)
	Args	: If a scalar is provided, it is set as the new desc for the
		  Quality object.

   id()
	Title	: id()
	Usage	: $id = $qual->id();
	Function: Return the ID of the quality. This should normally be (and
	       actually is in the implementation provided here) just a synonym
	       for display_id().
	Returns : A string. (the value of id)
	Args	: If a scalar is provided, it is set as the new id for the
		  Quality object.

   seq
	Title	: seq()
	Usage	: $string    = $obj->seq(); _or_
	       $obj->seq("atctatcatca");
	Function: Returns the sequence that is contained in the imbedded in the
	       PrimarySeq object within the Quality object
	Returns : A scalar (the seq() value for the imbedded PrimarySeq object.)
	Args	: If a scalar is provided, the Quality object will
	       attempt to set that as the sequence for the imbedded PrimarySeq
	       object. Otherwise, the value of seq() for the PrimarySeq object
	       is returned.
	Notes	: This is probably not a good idea because you then should call
	       length() to make sure that the sequence and quality are of the
	       same length. Even then, how can you make sure that this sequence
	       belongs with that quality? I provided this to give you rope to
	       hang yourself with. Tie it to a strong device and use a good
	       knot.

   qual()
	Title	: qual()
	Usage	: @quality_values  = @{$obj->qual()}; _or_
	       $obj->qual("10 10 20 40 50");
	Function: Returns the quality as imbedded in the PrimaryQual object
	       within the Quality object.
	Returns : A reference to an array containing the quality values in the
	       PrimaryQual object.
	Args	: If a scalar is provided, the Quality object will
	       attempt to set that as the quality for the imbedded PrimaryQual
	       object. Otherwise, the value of qual() for the PrimaryQual
	       object is returned.
	Notes	: This is probably not a good idea because you then should call
	       length() to make sure that the sequence and quality are of the
	       same length. Even then, how can you make sure that this sequence
	       belongs with that quality? I provided this to give you a strong
	       board with which to flagellate yourself.

   length()
	Title	: length()
	Usage	: $length = $seqWqual->length();
	Function: Get the length of the Quality sequence/quality.
	Returns : Returns the length of the sequence and quality
	Args	: None.

   qual_obj
	Title	: qual_obj($different_obj)
	Usage	: $qualobj = $seqWqual->qual_obj(); _or_
	       $qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj);
	Function: Get the Qualilty object that is imbedded in the
	       Quality object or if a reference to a PrimaryQual object
	       is provided, set this as the PrimaryQual object imbedded in the
	       Quality object.
	Returns : A reference to a Bio::Seq::Quality object.

       Identical to seq_obj.

   seq_obj
	Title	: seq_obj()
	Usage	: $seqobj = $seqWqual->seq_obj(); _or_
	       $seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj);
	Function: Get the PrimarySeq object that is imbedded in the
	       Quality object or if a reference to a PrimarySeq object is
	       provided, set this as the PrimarySeq object imbedded in the
	       Quality object.
	Returns : A reference to a Bio::PrimarySeq object.

   _set_descriptors
	Title	: _set_descriptors()
	Usage	: $seqWqual->_qual_obj($qual,$seq,$id,$acc,$pid,$desc,$given_id,
	       $alphabet);
	Function: Set the descriptors for the Quality object. Try to
	       match the descriptors in the PrimarySeq object and in the
	       PrimaryQual object if descriptors were not provided with
	       construction.
	Returns : Nothing.
	Args	: $qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet as found
	       in the new() method.
	Notes	: Really only intended to be called by the new() method. If
	       you want to invoke a similar function try
	       set_common_descriptors().

   subseq($start,$end)
	Title	: subseq($start,$end)
	Usage	: $subsequence = $obj->subseq($start,$end);
	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.
	Returns : A string.
	Args	: Two positions.

   baseat($position)
	Title	: baseat($position)
	Usage	: $base_at_position_6 = $obj->baseat("6");
	Function: Returns a single base at the given position, where the first
	       base is 1 and the number is inclusive, ie 1-2 are the first two
	       bases of the sequence.
	Returns : A scalar.
	Args	: A position.

   subqual($start,$end)
	Title	: subqual($start,$end)
	Usage	: @qualities = @{$obj->subqual(10,20);
	Function: returns the quality values from $start to $end, where the
	       first value 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.
	Returns : A reference to an array.
	Args	: a start position and an end position

   qualat($position)
	Title	: qualat($position)
	Usage	: $quality = $obj->qualat(10);
	Function: Return the quality value at the given location, where the
	       first value 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.
	Returns : A scalar.
	Args	: A position.

   sub_peak_index($start,$end)
	Title	: sub_peak_index($start,$end)
	Usage	: @peak_indices = @{$obj->sub_peak_index(10,20);
	Function: returns the trace index values from $start to $end, where the
	       first value is 1 and the number is inclusive, ie 1-2 are the
	       first two trace indices for this channel.
	Returns : A reference to an array.
	Args	: a start position and an end position

   sub_trace($start,$end)
	Title	: sub_trace($base_channel,$start,$end)
	Usage	: @trace_values = @{$obj->sub_trace('a',10,20)};
	Function: returns the trace values from $start to $end, where the
	       first value 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 e_peak_index.
	Returns : A reference to an array.
	Args	: a start position and an end position

   trace_length()
	Title	: trace_length()
	Usage	: $trace_length = $obj->trace_length();
	Function: Return the length of the trace if all four traces (atgc)
	    are the same. Otherwise, throw an error.
	Returns : A scalar.
	Args	: none

   sub_trace_object($start,$end)
	Title	: sub_trace_object($start,$end)
	Usage	: $smaller_object = $object->sub_trace_object('1','100');
	Function: Get a subset of the sequence, its quality, and its trace.
	Returns : A reference to a Bio::Seq::SequenceTrace object
	Args	: a start position and an end position
	Notes	:
	    - the start and end position refer to the positions of _bases_.
	    - for example, to get a sub SequenceTrace for bases 5-10,
		 use this routine.
		 - you will get the bases, qualities, and the trace values
		 - you can then use this object to synthesize a new scf
		      using seqIO::scf.

   _synthesize_traces()
	Title	: _synthesize_traces()
	Usage	: $obj->_synthesize_traces();
	Function: Synthesize false traces for this object.
	Returns : Nothing.
	Args	: None.
	Notes	: This method is intended to be invoked when this
	    object is created with a SWQ object- that is to say that
	    there is a sequence and a set of qualities but there was
	    no actual trace data.

   _dump_traces($transformed)
	Title	: _dump_traces("transformed")
	Usage	: &_dump_traces($ra,$rc,$rg,$rt);
	Function: Used in debugging. Prints all traces one beside each other.
	Returns : Nothing.
	Args	: References to the arrays containing the traces for A,C,G,T.
	Notes	: Beats using dumpValue, I'll tell ya. Much better then using
		  join' ' too.
	    - if a scalar is included as an argument (any scalar), this
	    procedure will dump the _delta'd trace. If you don't know what
	    that means you should not be using this.

   _initialize_traces()
	Title	: _initialize_traces()
	Usage	: $trace_object->_initialize_traces();
	Function: Creates empty arrays to hold synthetic trace values.
	Returns : Nothing.
	Args	: None.

   trace_value_at($channel,$position)
	Title	: trace_value_at($channel,$position)
	Usage	: $value = $trace_object->trace_value_at($channel,$position);
	Function: What is the value of the trace for this base at this position?
	Returns : A scalar represnting the trace value here.
	Args	: a base channel (a,t,g,c)
		  a position ( < $trace_object->trace_length() )

   accuracies($channel,$position)
	Title	: trace_value_at($channel,$position)
	Usage	: $value = $trace_object->trace_value_at($channel,$position);
	Function: What is the value of the trace for this base at this position?
	Returns : A scalar representing the trace value here.
	Args	: a base channel (a,t,g,c)
		  a position ( < $trace_object->trace_length() )

   set_accuracies()
	Title	: set_sccuracies()
	Usage	: $trace_object->set_accuracies();
	Function: Take a sequence's quality and synthesize proper scf-style
	    base accuracies that can then be accessed with
	    accuracies("a") or something like it.
	Returns : Nothing.
	Args	: None.

   scf_dump()
	Title	: scf_dump()
	Usage	: $trace_object->scf_dump();
	Function: Prints out the contents of the structures representing
	    the SequenceTrace in a manner similar to io_lib's scf_dump.
	Returns : Nothing. Prints out the contents of the structures
	    used to represent the sequence and its trace.
	Args	: None.
	Notes	: Used in debugging, obviously.

   _get_other_bases($this_base)
	Title	: _get_other_bases($this_base)
	Usage	: $other_bases = $trace_object->_get_other_bases($this_base);
	Function: A utility routine to return bases other then the one provided.
	    I was doing this over and over so I put it here.
	Returns : Three of a,t,g and c.
	Args	: A base (atgc)
	Notes	: $obj->_get_other_bases("a") returns "tgc"

   accuracy_at($base,$position)
	Title	: accuracy_at($base,$position)
	Usage	: $accuracy = $trace_object->accuracy_at($base,$position);
	Function:
	Returns : Returns the accuracy of finding $base at $position.
	Args	: 1. a base channel (atgc) 2. a value to _set_ the accuracy
	Notes	: $obj->_get_other_bases("a") returns "tgc"

perl v5.14.1			  2011-07-22	    Bio::Seq::SequenceTrace(3)
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