#
# BioPerl module for Bio::Seq::SequenceTrace
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chad Matsalla <bioinformatics@dieselwurks.com
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
=head1 SYNOPSIS
# example code here
=head1 DESCRIPTION
This object stores a sequence with its trace.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 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 _
=cut
package Bio::Seq::SequenceTrace;
use strict;
use Bio::Seq::QualI;
use Bio::PrimarySeqI;
use Bio::PrimarySeq;
use Bio::Seq::PrimaryQual;
use base qw(Bio::Root::Root Bio::Seq::Quality Bio::Seq::TraceI);
=head2 new()
Title : new()
Usage : $st = Bio::Seq::SequenceTrace->new
( -swq => Bio::Seq::SequenceWithQuality,
-trace_a => \@trace_values_for_a_channel,
-trace_t => \@trace_values_for_t_channel,
-trace_g => \@trace_values_for_g_channel,
-trace_c => \@trace_values_for_c_channel,
-accuracy_a => \@a_accuracies,
-accuracy_t => \@t_accuracies,
-accuracy_g => \@g_accuracies,
-accuracy_c => \@c_accuracies,
-peak_indices => '0 5 10 15 20 25 30 35'
);
Function: Returns a new Bio::Seq::SequenceTrace object from basic
constructors.
Returns : a new Bio::Seq::SequenceTrace object
Arguments: I think that these are all describes in the usage above.
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# default: turn OFF the warnings
$self->{supress_warnings} = 1;
my($swq,$peak_indices,$trace_a,$trace_t,
$trace_g,$trace_c,$acc_a,$acc_t,$acc_g,$acc_c) =
$self->_rearrange([qw(
SWQ
PEAK_INDICES
TRACE_A
TRACE_T
TRACE_G
TRACE_C
ACCURACY_A
ACCURACY_T
ACCURACY_G
ACCURACY_C )], @args);
# first, deal with the sequence and quality information
if ($swq && ref($swq) eq "Bio::Seq::Quality") {
$self->{swq} = $swq;
}
else {
$self->throw("A Bio::Seq::SequenceTrace object must be created with a
Bio::Seq::Quality object. You provided this type of object: "
.ref($swq));
}
if (!$acc_a) {
# this means that you probably did not provide traces and accuracies
# and that they need to be synthesized
$self->set_accuracies();
}
else {
$self->accuracies('a',$acc_a);
$self->accuracies('t',$acc_t);
$self->accuracies('g',$acc_g);
$self->accuracies('c',$acc_c);
}
if (!$trace_a) {
$self->_synthesize_traces();
}
else {
$self->trace('a',$trace_a);
$self->trace('t',$trace_t);
$self->trace('g',$trace_g);
$self->trace('c',$trace_c);
$self->peak_indices($peak_indices);
}
$self->id($self->seq_obj->id);
return $self;
}
sub swq_obj {
my $self = shift;
$self->warn('swq_obj() is deprecated: use seq_obj()');
return $self->{swq};
}
=head2 trace($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?
- $base must be one of "A","T","G","C"
\@new_values : a reference to an array of values containing trace
data for this base
=cut
sub trace {
my ($self,$base_channel,$values) = @_;
if (!$base_channel) {
$self->throw('You must provide a valid base channel (atgc) to use trace()');
}
$base_channel =~ tr/A-Z/a-z/;
if ($base_channel !~ /[acgt]/) {
$self->throw('You must provide a valid base channel (atgc) to use trace()');
}
if ($values) {
if (ref($values) eq "ARRAY") {
$self->{trace}->{$base_channel} = $values;
}
else {
my @trace = split(' ',$values);
$self->{trace}->{$base_channel} = \@trace;
}
}
if ($self->{trace}->{$base_channel}) {
return $self->{trace}->{$base_channel};
}
else {
return;
}
}
=head2 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.
=cut
sub peak_indices {
my ($self,$peak_indices)= @_;
if ($peak_indices) {
if (ref($peak_indices) eq "ARRAY") {
$self->{peak_indices} = $peak_indices;
}
else {
my @indices = split(' ',$peak_indices);
$self->{peak_indices} = \@indices;
}
}
if (!$self->{peak_indices}) {
my @temp = ();
$self->{peak_indices} = \@temp;
}
return $self->{peak_indices};
}
=head2 _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".
=cut
sub _reset_peak_indices {
my $self = shift;
my $length = $self->length();
my $subtractive = $self->peak_index_at(1);
my ($original,$new);
$self->peak_index_at(1,"null");
for (my $counter=2; $counter<= $length; $counter++) {
my $original = $self->peak_index_at($counter);
$new = $original - $subtractive;
$self->peak_index_at($counter,$new);
}
return;
}
=head2 peak_index_at($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.
=cut
sub peak_index_at {
my ($self,$position,$value)= @_;
if ($value) {
if ($value eq "null") {
$self->peak_indices->[$position-1] = "0";
}
else {
$self->peak_indices->[$position-1] = $value;
}
}
return $self->peak_indices()->[$position-1];
}
=head2 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.
=cut
sub alphabet {
my $self = shift;
return $self->{swq}->alphabet;
}
=head2 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 $seq->id() maps to this function, mainly for
legacy/convience issues.
This method sets the display_id for the Quality object.
Returns : A string
Args : If a scalar is provided, it is set as the new display_id for
the Quality object.
Status : Virtual
=cut
sub display_id {
my ($self,$value) = @_;
if( defined $value) {
$self->{swq}->display_id($value);
}
return $self->{swq}->display_id();
}
=head2 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 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
=cut
sub accession_number {
my( $self, $acc ) = @_;
if (defined $acc) {
$self->{swq}->accession_number($acc);
} else {
$acc = $self->{swq}->accession_number();
$acc = 'unknown' unless defined $acc;
}
return $acc;
}
=head2 primary_id()
Title : primary_id()
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
way the implementaiton can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the Quality
object.
Returns : A string. (the value of primary_id)
Args : If a scalar is provided, it is set as the new primary_id for
the Quality object.
=cut
sub primary_id {
my ($self,$value) = @_;
if ($value) {
$self->{swq}->primary_id($value);
}
return $self->{swq}->primary_id();
}
=head2 desc()
Title : desc()
Usage : $qual->desc($newval); _or_
$description = $qual->desc();
Function: Get/set description text for this Quality object.
Returns : A string. (the value of desc)
Args : If a scalar is provided, it is set as the new desc for the
Quality object.
=cut
sub desc {
# a mechanism to set the desc for the Quality object.
# probably will be used most often by set_common_features()
my ($self,$value) = @_;
if( defined $value) {
$self->{swq}->desc($value);
}
return $self->{swq}->desc();
}
=head2 id()
Title : id()
Usage : $id = $qual->id();
Function: Return the ID of the quality. This should normally be (and
actually is in the implementation provided here) just a synonym
for display_id().
Returns : A string. (the value of id)
Args : If a scalar is provided, it is set as the new id for the
Quality object.
=cut
sub id {
my ($self,$value) = @_;
if (!$self) { $self->throw("no value for self in $value"); }
if( defined $value ) {
$self->{swq}->display_id($value);
}
return $self->{swq}->display_id();
}
=head2 seq
Title : seq()
Usage : $string = $obj->seq(); _or_
$obj->seq("atctatcatca");
Function: Returns the sequence that is contained in the imbedded in the
PrimarySeq object within the Quality object
Returns : A scalar (the seq() value for the imbedded PrimarySeq object.)
Args : If a scalar is provided, the Quality object will
attempt to set that as the sequence for the imbedded PrimarySeq
object. Otherwise, the value of seq() for the PrimarySeq object
is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you rope to
hang yourself with. Tie it to a strong device and use a good
knot.
=cut
sub seq {
my ($self,$value) = @_;
if( defined $value) {
$self->{swq}->seq($value);
}
return $self->{swq}->seq();
}
=head2 qual()
Title : qual()
Usage : @quality_values = @{$obj->qual()}; _or_
$obj->qual("10 10 20 40 50");
Function: Returns the quality as imbedded in the PrimaryQual object
within the Quality object.
Returns : A reference to an array containing the quality values in the
PrimaryQual object.
Args : If a scalar is provided, the Quality object will
attempt to set that as the quality for the imbedded PrimaryQual
object. Otherwise, the value of qual() for the PrimaryQual
object is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you a strong
board with which to flagellate yourself.
=cut
sub qual {
my ($self,$value) = @_;
if( defined $value) {
$self->{swq}->qual($value);
}
return $self->{swq}->qual();
}
=head2 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.
=cut
sub length {
my $self = shift;
return $self->seq_obj->length;
}
=head2 qual_obj
Title : qual_obj($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 L<seq_obj>.
=cut
sub qual_obj {
my ($self,$value) = @_;
# return $self->{swq}->qual_obj($value);
return $self->{swq};
}
=head2 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.
=cut
sub seq_obj {
my ($self,$value) = @_;
return $self->{swq};
}
=head2 _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().
=cut
sub _set_descriptors {
my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_;
$self->{swq}->_seq_descriptors($qual,$seq,$id,$acc,$pid,
$desc,$given_id,$alphabet);
}
=head2 subseq($start,$end)
Title : subseq($start,$end)
Usage : $subsequence = $obj->subseq($start,$end);
Function: Returns the subseq from start to end, where the first base
is 1 and the number is inclusive, ie 1-2 are the first two
bases of the sequence.
Returns : A string.
Args : Two positions.
=cut
sub subseq {
my ($self,@args) = @_;
# does a single value work?
return $self->{swq}->subseq(@args);
}
=head2 baseat($position)
Title : baseat($position)
Usage : $base_at_position_6 = $obj->baseat("6");
Function: Returns a single base at the given position, where the first
base is 1 and the number is inclusive, ie 1-2 are the first two
bases of the sequence.
Returns : A scalar.
Args : A position.
=cut
sub baseat {
my ($self,$val) = @_;
return $self->{swq}->subseq($val,$val);
}
=head2 subqual($start,$end)
Title : subqual($start,$end)
Usage : @qualities = @{$obj->subqual(10,20);
Function: returns the quality values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be equal.
Returns : A reference to an array.
Args : a start position and an end position
=cut
sub subqual {
my ($self,@args) = @_;
return $self->{swq}->subqual(@args);
}
=head2 qualat($position)
Title : qualat($position)
Usage : $quality = $obj->qualat(10);
Function: Return the quality value at the given location, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be equal.
Returns : A scalar.
Args : A position.
=cut
sub qualat {
my ($self,$val) = @_;
return $self->{swq}->qualat($val);
}
=head2 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 $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two trace indices for this channel.
Returns : A reference to an array.
Args : a start position and an end position
=cut
sub sub_peak_index {
my ($self,$start,$end) = @_;
if( $start > $end ){
$self->throw("in sub_peak_index, start [$start] has to be greater than end [$end]");
}
if( $start <= 0 || $end > $self->length ) {
$self->throw("You have to have start positive and length less than the total length of sequence [$start:$end] Total ".$self->length."");
}
# remove one from start, and then length is end-start
$start--;
$end--;
my @sub_peak_index_array = @{$self->{peak_indices}}[$start..$end];
# return substr $self->seq(), $start, ($end-$start);
return \@sub_peak_index_array;
}
=head2 sub_trace($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 $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be e_peak_index.
Returns : A reference to an array.
Args : a start position and an end position
=cut
sub sub_trace {
my ($self,$base_channel,$start,$end) = @_;
if( $start > $end ){
$self->throw("in sub_trace, start [$start] has to be greater than end [$end]");
}
if( $start <= 0 || $end > $self->trace_length() ) {
$self->throw("You have to have start positive and length less than the total length of traces [$start:$end] Total ".$self->trace_length."");
}
# remove one from start, and then length is end-start
$start--;
$end--;
my @sub_peak_index_array = @{$self->trace($base_channel)}[$start..$end];
# return substr $self->seq(), $start, ($end-$start);
return \@sub_peak_index_array;
}
=head2 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
=cut
sub trace_length {
my $self = shift;
if ( !$self->trace('a') || !$self->trace('t') || !$self->trace('g') || !$self->trace('c') ) {
$self->warn("One or more of the trace channels are missing. Cannot give you a length.");
}
my $lengtha = scalar(@{$self->trace('a')});
my $lengtht = scalar(@{$self->trace('t')});
my $lengthg = scalar(@{$self->trace('g')});
my $lengthc = scalar(@{$self->trace('c')});
if (($lengtha == $lengtht) && ($lengtha == $lengthg) && ($lengtha == $lengthc) ) {
return $lengtha;
}
$self->warn("Not all of the trace indices are the same length".
" Here are their lengths: a: $lengtha t:$lengtht ".
" g: $lengthg c: $lengthc");
}
=head2 sub_trace_object($start,$end)
Title : sub_trace_object($start,$end)
Usage : $smaller_object = $object->sub_trace_object('1','100');
Function: Get a subset of the sequence, its quality, and its trace.
Returns : A reference to a Bio::Seq::SequenceTrace object
Args : a start position and an end position
Notes :
- the start and end position refer to the positions of _bases_.
- for example, to get a sub SequenceTrace for bases 5-10,
use this routine.
- you will get the bases, qualities, and the trace values
- you can then use this object to synthesize a new scf
using seqIO::scf.
=cut
sub sub_trace_object {
my ($self,$start,$end) = @_;
my ($start2,$end2);
my @subs = @{$self->sub_peak_index($start,$end)};
$start2 = shift(@subs);
$end2 = pop(@subs);
my $new_object = Bio::Seq::SequenceTrace->new(
-swq => Bio::Seq::Quality->new(
-seq => $self->subseq($start,$end),
-qual => $self->subqual($start,$end),
-id => $self->id()
),
-trace_a => $self->sub_trace('a',$start2,$end2),
-trace_t => $self->sub_trace('t',$start2,$end2),
-trace_g => $self->sub_trace('g',$start2,$end2),
-trace_c => $self->sub_trace('c',$start2,$end2),
-peak_indices => $self->sub_peak_index($start,$end)
);
$new_object->set_accuracies();
$new_object->_reset_peak_indices();
return $new_object;
}
=head2 _synthesize_traces()
Title : _synthesize_traces()
Usage : $obj->_synthesize_traces();
Function: Synthesize false traces for this object.
Returns : Nothing.
Args : None.
Notes : This method is intended to be invoked when this
object is created with a SWQ object- that is to say that
there is a sequence and a set of qualities but there was
no actual trace data.
=cut
sub _synthesize_traces {
my ($self) = shift;
$self->peak_indices(qw());
#ml my $version = 2;
# the user should be warned if traces already exist
#
#
#ml ( my $sequence = $self->seq() ) =~ tr/a-z/A-Z/;
#ml my @quals = @{$self->qual()};
#ml my $info;
# build the ramp for the first base.
# a ramp looks like this "1 4 13 29 51 71 80 71 51 29 13 4 1" times the quality score.
# REMEMBER: A C G T
# note to self-> smooth this thing out a bit later
my $ramp_data;
@{$ramp_data->{'ramp'}} = qw( 1 4 13 29 51 75 80 75 51 29 13 4 1 );
# the width of the ramp
$ramp_data->{'ramp_width'} = scalar(@{$ramp_data->{'ramp'}});
# how far should the peaks overlap?
$ramp_data->{'ramp_overlap'} = 1;
# where should the peaks be located?
$ramp_data->{'peak_at'} = 7;
$ramp_data->{'ramp_total_length'} =
$self->seq_obj()->length() * $ramp_data->{'ramp_width'}
- $self->seq_obj()->length() * $ramp_data->{'ramp_overlap'};
my $pos;
my $total_length = $ramp_data->{ramp_total_length};
$self->initialize_traces("0",$total_length+2);
# now populate them
my ($current_base,$place_base_at,$peak_quality,$ramp_counter,$current_ramp,$ramp_position);
#ml my $sequence_length = $self->length();
my $half_ramp = int($ramp_data->{'ramp_width'}/2);
for ($pos = 0; $pos<$self->length();$pos++) {
$current_base = uc $self->seq_obj()->subseq($pos+1,$pos+1);
# print("Synthesizing the ramp for $current_base\n");
my $all_bases = "ATGC";
$peak_quality = $self->qual_obj()->qualat($pos+1);
# where should the peak for this base be placed? Modeled after a mktrace scf
$place_base_at = ($pos * $ramp_data->{'ramp_width'}) -
($pos * $ramp_data->{'ramp_overlap'}) -
$half_ramp + $ramp_data->{'ramp_width'} - 1;
# print("Placing this base at this position: $place_base_at\n");
push @{$self->peak_indices()},$place_base_at;
$ramp_position = $place_base_at - $half_ramp;
if ($current_base =~ "N" ) {
$current_base = "A";
}
for ($current_ramp = 0; $current_ramp < $ramp_data->{'ramp_width'}; $current_ramp++) {
# print("Placing a trace value here: $current_base ".($ramp_position+$current_ramp+1)." ".$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]."\n");
$self->trace_value_at($current_base,$ramp_position+$current_ramp+1,$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]);
}
$self->peak_index_at($pos+1,
$place_base_at+1
);
#ml my $other_bases = $self->_get_other_bases($current_base);
# foreach ( split('',$other_bases) ) {
# push @{$self->{'text'}->{"v3_base_accuracy"}->{$_}},0;
#}
}
}
=head2 _dump_traces($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.
=cut
#'
sub _dump_traces {
my ($self) = @_;
my (@sA,@sT,@sG,@sC);
print ("Count\ta\tc\tg\tt\n");
my $length = $self->trace_length();
for (my $curr=1; $curr <= $length; $curr++) {
print(($curr-1)."\t".$self->trace_value_at('a',$curr).
"\t".$self->trace_value_at('c',$curr).
"\t".$self->trace_value_at('g',$curr).
"\t".$self->trace_value_at('t',$curr)."\n");
}
return;
}
=head2 _initialize_traces()
Title : _initialize_traces()
Usage : $trace_object->_initialize_traces();
Function: Creates empty arrays to hold synthetic trace values.
Returns : Nothing.
Args : None.
=cut
sub initialize_traces {
my ($self,$value,$length) = @_;
foreach (qw(a t g c)) {
my @temp;
for (my $count=0; $count<$length; $count++) {
$temp[$count] = $value;
}
$self->trace($_,\@temp);
}
}
=head2 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 ( < $trace_object->trace_length() )
=cut
sub trace_value_at {
my ($self,$channel,$position,$value) = @_;
if ($value) {
$self->trace($channel)->[$position] = $value;
}
return $self->sub_trace($channel,($position),($position))->[0];
}
sub _deprecated_get_scf_version_2_base_structure {
# this sub is deprecated- check inside SeqIO::scf
my $self = shift;
my (@structure,$current);
my $length = $self->length();
for ($current=1; $current <= $self->length() ; $current++) {
my $base_here = $self->seq_obj()->subseq($current,$current);
$base_here = lc($base_here);
my $probabilities;
$probabilities->{$base_here} = $self->qual_obj()->qualat($current);
my $other_bases = "atgc";
my $empty = "";
$other_bases =~ s/$base_here/$empty/e;
foreach ( split('',$other_bases) ) {
$probabilities->{$_} = "0";
}
@structure = (
@structure,
$self->peak_index_at($current),
$probabilities->{'a'},
$probabilities->{'t'},
$probabilities->{'g'},
$probabilities->{'c'}
);
}
return \@structure;
}
sub _deprecated_get_scf_version_3_base_structure {
my $self = shift;
my $structure;
$structure = join('',$self->peak_indices());
return $structure;
}
=head2 accuracies($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 ( < $trace_object->trace_length() )
=cut
sub accuracies {
my ($self,$channel,$value) = @_;
if ($value) {
if (ref($value) eq "ARRAY") {
$self->{accuracies}->{$channel} = $value;
}
else {
my @acc = split(' ',$value);
$self->{accuracies}->{$channel} = \@acc;
}
}
return $self->{accuracies}->{$channel};
}
=head2 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.
=cut
sub set_accuracies {
my $self = shift;
my $count = 0;
my $length = $self->length();
for ($count=1; $count <= $length; $count++) {
my $base_here = $self->seq_obj()->subseq($count,$count);
my $qual_here = $self->qual_obj()->qualat($count);
$self->accuracy_at($base_here,$count,$qual_here);
my $other_bases = $self->_get_other_bases($base_here);
foreach (split('',$other_bases)) {
$self->accuracy_at($_,$count,"null");
}
}
}
=head2 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.
=cut
sub scf_dump {
my $self = shift;
my $count;
for ($count=1;$count<=$self->length();$count++) {
my $base_here = lc($self->seq_obj()->subseq($count,$count));
print($base_here." ".sprintf("%05d",$self->peak_index_at($count))."\t");
foreach (sort qw(a c g t)) {
print(sprintf("%03d",$self->accuracy_at($_,$count))."\t");
}
print("\n");
}
$self->_dump_traces();
}
=head2 _get_other_bases($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 : $obj->_get_other_bases("a") returns "tgc"
=cut
sub _get_other_bases {
my ($self,$this_base) = @_;
$this_base = lc($this_base);
my $all_bases = "atgc";
my $empty = "";
$all_bases =~ s/$this_base/$empty/e;
return $all_bases;
}
=head2 accuracy_at($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 : $obj->_get_other_bases("a") returns "tgc"
=cut
sub accuracy_at {
my ($self,$base,$position,$value) = @_;
$base = lc($base);
if ($value) {
if ($value eq "null") {
$self->{accuracies}->{$base}->[$position-1] = "0";
}
else {
$self->{accuracies}->{$base}->[$position-1] = $value;
}
}
return $self->{accuracies}->{$base}->[$position-1];
}
1;