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Bio::Seq::SeqWithQualiUser)Contributed Perl DocumenBio::Seq::SeqWithQuality(3)

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.

perl v5.14.1			  2011-07-22	   Bio::Seq::SeqWithQuality(3)
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