Provided by: libbio-perl-perl_1.7.2-3_all bug

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.

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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 implementation, 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 implementation 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"