Bio::Seq::SeqWithQuality.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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

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.