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://github.com/bioperl/bioperl-live/issues

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"