Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Seq::TraceI(3)   User Contributed Perl Documentation  Bio::Seq::TraceI(3)

NAME
       Bio::Seq::TraceI	- Interface definition for a Bio::Seq::Trace

SYNOPSIS
	   # get a Bio::Seq::Qual compliant object somehow
		 $st = &get_object_somehow();

	   # to	test this is a seq object
		 $st->isa("Bio::Seq::TraceI")
		      || $obj->throw("$obj does	not implement the Bio::Seq::TraceI interface");

		 # set the trace for T to be @trace_points
	    my $arrayref = $st->trace("T",\@trace_points);
		 # get the trace points	for "C"
	    my $arrayref = $st->trace("C");
		 # get a subtrace for "G" from 10 to 100
	    $arrayref =	$st->subtrace("G",10,100);
		 # what	is the trace value for "A" at position 355?
	    my $trace_calue = $st->traceat("A",355);
		 # create a false trace	for "A"	with $accuracy
	    $arrayref =	$st->false_trace("A",Bio::Seq::Quality,	$accuracy);
		 # does	this trace have	entries	for each base?
	    $bool = $st->is_complete();
		 # how many entries are	there in this trace?
	    $length = $st->length();

DESCRIPTION
       This object defines an abstract interface to basic trace	information.
       This information	may have come from an ABI- or scf- formatted file or
       may have	been made up.

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

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

Implementation Specific	Functions
       These functions are the ones that a specific implementation must
       define.

   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

   subtrace($base,$start,$end)
	Title	: subtrace($base,$start,$end)
	Usage	: @subset_of_traces = @{$obj->subtrace("A",10,40)};
	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 trace values	of this	base. Start cannot be larger than end but can
	       be equal.
	Returns	: A reference to an array.
	Args	: $base: "A","T","G" or	"C"
		 $start: a start position
		 $end  : an end	position

   can_call_new()
	Title	: can_call_new()
	Usage	: if( $obj->can_call_new ) {
		    $newobj = $obj->new( %param	);
		}
	Function: can_call_new returns 1 or 0 depending	on whether an
	       implementation allows new constructor to	be called. If a	new
	       constructor is allowed, then it should take the followed	hashed
	       constructor list.
		  $myobject->new( -qual	=> $quality_as_string,
				  -display_id  => $id,
				  -accession_number => $accession,
				  );
	Example	:
	Returns	: 1 or 0
	Args	:

   traceat($channel,$position)
	Title	: qualat($channel,$position)
	Usage	: $trace = $obj->traceat(500);
	Function: Return the trace 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 base and a position.

   length()
	Title	: length()
	Usage	: $length = $obj->length("A");
	Function: Return the length of the array holding the trace values for the "A"
	    channel. A check should be done to make sure that this Trace object
	    is_complete() before doing this to prevent hazardous results.
	Returns	: A scalar (the	number of elements in the quality array).
	Args	: If used, get the traces from that channel. Default to	"A"

   trace_indices($new_indices)
	Title	: trace_indices($new_indices)
	Usage	: $indices = $obj->trace_indices($new_indices);
	Function: Return the trace iindex points for this object.
	Returns	: A scalar
	Args	: If used, the trace indices will be set to the	provided value.

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chad Matsalla | APPENDIX | Implementation Specific Functions

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

home | help