Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality.
       Deprecated class, use Bio::Seq::Quality instead!

SYNOPSIS

           use Bio::PrimarySeq;
           use Bio::Seq::PrimaryQual;
           use Bio::Seq::SeqWithQuality;

           # make from memory
           my $qual = Bio::Seq::SeqWithQuality->new
           ( -qual => '10 20 30 40 50 50 20 10',
             -seq => 'ATCGATCG',
             -id  => 'human_id',
             -accession_number => 'AL000012',
           );

           # make from objects
           # first, make a PrimarySeq object
           my $seqobj = Bio::PrimarySeq->new
           ( -seq => 'atcgatcg',
             -id  => 'GeneFragment-12',
             -accession_number => 'X78121',
             -alphabet => 'dna'
           );

           # now make a PrimaryQual object
           my $qualobj = Bio::Seq::PrimaryQual->new
           ( -qual => '10 20 30 40 50 50 20 10',
             -id  => 'GeneFragment-12',
             -accession_number => 'X78121',
             -alphabet => 'dna'
           );

           # now make the SeqWithQuality object
           my $swqobj = Bio::Seq::SeqWithQuality->new
           ( -seq  => $seqobj,
             -qual => $qualobj
           );
           # done!

           $swqobj->id(); # the id of the SeqWithQuality object
           # may not match the the id of the sequence or
           # of the quality (check the pod, luke)
           $swqobj->seq(); # the sequence of the SeqWithQuality object
           $swqobj->qual(); # the quality of the SeqWithQuality object

           # to get out parts of the sequence.

           print "Sequence ", $seqobj->id(), " with accession ",
           $seqobj->accession, " and desc ", $seqobj->desc, "\n";

           $string2 = $seqobj->subseq(1,40);

DESCRIPTION

       This object stores base quality values together with the sequence string.

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 - Chad Matsalla

       Email bioinformatics@dieselwurks.com

CONTRIBUTORS

       Jason Stajich, jason@bioperl.org

APPENDIX

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

   new()
        Title   : new()
        Usage   : $qual = Bio::Seq::SeqWithQuality ->new
                    ( -qual => '10 20 30 40 50 50 20 10',
                      -seq => 'ATCGATCG',
                      -id  => 'human_id',
                      -accession_number => 'AL000012',
                      -trace_indices    => '0 5 10 15 20 25 30 35'
                    );
        Function: Returns a new Bio::Seq::SeqWithQual object from basic
                  constructors.
        Returns : a new Bio::Seq::PrimaryQual object
        Args    : -qual can be a quality string (see Bio::Seq::PrimaryQual for more
                   information on this) or a reference to a Bio::Seq::PrimaryQual
                   object.
                  -seq can be a sequence string (see Bio::PrimarySeq for more
                   information on this) or a reference to a Bio::PrimaryQual object.
                  -seq, -id, -accession_number, -primary_id, -desc, -id behave like
                   this:
                    1. if they are provided on construction of the
                        Bio::Seq::SeqWithQuality they will be set as the descriptors for
                        the object unless changed by one of the following mechanisms:
                     a) $obj->set_common_descriptors() is used and both the -seq and
                        the -qual object have the same descriptors. These common
                        descriptors will then become the descriptors for the
                        Bio::Seq::SeqWithQual object.
                     b) the descriptors are manually set using the seq(), id(),
                        desc(), or accession_number(), primary_id(),
                    2. if no descriptors are provided, the new() constructor will see
                       if the descriptor used in the PrimarySeq and in the
                       PrimaryQual objects match. If they do, they will become
                       the descriptors for the SeqWithQuality object.
                    To eliminate ambiguity, I strongly suggest you set the
                    descriptors manually on construction of the object. Really.
                  -trace_indices : a space_delimited list of trace indices
                   (where would the peaks be drawn if this list of qualities
                   was to be plotted?)

   _common_id()
        Title   : _common_id()
        Usage   : $common_id = $self->_common_id();
        Function: Compare the display_id of {qual_ref} and {seq_ref}.
        Returns : Nothing if they don't match. If they do return {seq_ref}->display_id()
        Args    : None.

   _common_display_id()
        Title   : _common_id()
        Usage   : $common_id = $self->_common_display_id();
        Function: Compare the display_id of {qual_ref} and {seq_ref}.
        Returns : Nothing if they don't match. If they do return {seq_ref}->display_id()
        Args    : None.

   _common_accession_number()
        Title   : _common_accession_number()
        Usage   : $common_id = $self->_common_accession_number();
        Function: Compare the accession_number() of {qual_ref} and {seq_ref}.
        Returns : Nothing if they don't match. If they do return {seq_ref}->accession_number()
        Args    : None.

   _common_primary_id()
        Title   : _common_primary_id()
        Usage   : $common_primard_id = $self->_common_primary_id();
        Function: Compare the primary_id of {qual_ref} and {seq_ref}.
        Returns : Nothing if they don't match. If they do return {seq_ref}->primary_id()
        Args    : None.

   _common_desc()
        Title   : _common_desc()
        Usage   : $common_desc = $self->_common_desc();
        Function: Compare the desc of {qual_ref} and {seq_ref}.
        Returns : Nothing if they don't match. If they do return {seq_ref}->desc()
        Args    : None.

   set_common_descriptors()
        Title   : set_common_descriptors()
        Usage   : $self->set_common_descriptors();
        Function: Compare the descriptors (id,accession_number,display_id,
                  primary_id, desc) for the PrimarySeq and PrimaryQual objects
                  within the SeqWithQuality object. If they match, make that
                  descriptor the descriptor for the SeqWithQuality object.
        Returns : Nothing.
        Args    : None.

   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 SeqWithQuality object.
        Returns : A string
        Args    : If a scalar is provided, it is set as the new display_id for
                  the SeqWithQuality 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 SeqWithQuality
                  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 SeqWithQuality 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 SeqWithQuality 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 SeqWithQuality object.

   desc()
        Title   : desc()
        Usage   : $qual->desc($newval); _or_
                  $description = $qual->desc();
        Function: Get/set description text for this SeqWithQuality object.
        Returns : A string. (the value of desc)
        Args    : If a scalar is provided, it is set as the new desc for the
                  SeqWithQuality 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
                  SeqWithQuality 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 SeqWithQuality object
        Returns : A scalar (the seq() value for the imbedded PrimarySeq object.)
        Args    : If a scalar is provided, the SeqWithQuality 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 SeqWithQuality object.
        Returns : A reference to an array containing the quality values in the
                  PrimaryQual object.
        Args    : If a scalar is provided, the SeqWithQuality 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.

   trace_indices()
        Title   : trace_indices()
        Usage   : @trace_indice_values  = @{$obj->trace_indices()}; _or_
                  $obj->trace_indices("10 10 20 40 50");
        Function: Returns the trace_indices as imbedded in the Primaryqual object
                  within the SeqWithQualiity object.
        Returns : A reference to an array containing the trace_indice values in the
                  PrimaryQual object.
        Args    : If a scalar is provided, the SeqWithuQuality object will
                  attempt to set that as the trace_indices for the imbedded PrimaryQual
                  object. Otherwise, the value of trace_indices() 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 trace_indices are of the
                  same length. Even then, how can you make sure that this sequence
                  belongs with that trace_indicex? 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 SeqWithQuality sequence/quality.
        Returns : Returns the length of the sequence and quality if they are
                  both the same. Returns "DIFFERENT" if they differ.
        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 PrimaryQual object that is imbedded in the
                  SeqWithQuality object or if a reference to a PrimaryQual object
                  is provided, set this as the PrimaryQual object imbedded in the
                  SeqWithQuality object.
        Returns : A reference to a Bio::Seq::SeqWithQuality object.

   seq_obj
        Title   : seq_obj()
        Usage   : $seqobj = $seqWqual->qual_obj(); _or_
                  $seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj);
        Function: Get the PrimarySeq object that is imbedded in the
                  SeqWithQuality object or if a reference to a PrimarySeq object is
                  provided, set this as the PrimarySeq object imbedded in the
                  SeqWithQuality 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 SeqWithQuality 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_trace_index($start,$end)
        Title   : sub_trace_index($start,$end)
        Usage   : @trace_indices = @{$obj->sub_trace_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 bases of the sequence. Start cannot be larger than
                  end but can be e_trace_index.
        Returns : A reference to an array.
        Args    : a start position and an end position

   trace_index_at($position)
        Title   : trace_index_at($position)
        Usage   : $trace_index = $obj->trace_index_at(10);
        Function: Return the trace_index 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 etrace_index_.
        Returns : A scalar.
        Args    : A position.

   to_string()
        Title   : to_string()
        Usage   : $quality = $obj->to_string();
        Function: Return a textual representation of what the object contains.
                  For this module, this function will return:
                       qual
                       seq
                       display_id
                       accession_number
                       primary_id
                       desc
                       id
                       length_sequence
                       length_quality
        Returns : A scalar.
        Args    : None.