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Bio::Seq::SequenceTracUser Contributed Perl DocumentBio::Seq::SequenceTrace(3)

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:

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

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 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"

perl v5.32.0			  2019-12-07	    Bio::Seq::SequenceTrace(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chad Matsalla

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Seq::SequenceTrace&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

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