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Bio::Seq::SequenceTrace.3pm

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"