Raw content of Bio::Seq::SequenceTrace
<![CDATA[# $Id: SequenceTrace.pm,v 1.1.2.1 2003/03/25 12:32:16 heikki Exp $
#
# BioPerl module for Bio::Seq::SeqWithQuality
#
# 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://bio.perl.org/MailList.html - About the mailing lists
=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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Chad Matsalla
Email bioinformatics@dieselwurks.com
=head1 CONTRIBUTORS
Jason Stajich, jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Seq::SequenceTrace;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Seq::QualI;
use Bio::PrimarySeqI;
use Bio::PrimarySeq;
use Bio::Seq::PrimaryQual;
use Bio::Seq::TraceI;
@ISA = qw(Bio::Root::Root Bio::Seq::SeqWithQuality Bio::Seq::TraceI);
=head2 new()
Title : new()
Usage : $st = Bio::Seq::SequenceTrace->new
( -sequencewithquality => Bio::Seq::SequenceWithQuality,
-trace_a => \@trace_values_for_a_channel,
-trace_t => \@trace_values_for_t_channel,
-trace_g => \@trace_values_for_g_channel,
-trace_c => \@trace_values_for_c_channel,
-trace_indices => '0 5 10 15 20 25 30 35'
);
Function: Returns a new Bio::Seq::SequenceTrace object from basic
constructors.
Returns : a new Bio::Seq::SequenceTrace object
Arguments: I think that these are all describes in the usage above.
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
# default: turn OFF the warnings
$self->{supress_warnings} = 1;
my($sequence_with_quality,$trace_indices,$trace_a,$trace_t,
$trace_g,$trace_c) =
$self->_rearrange([qw(
SEQUENCEWITHQUALITY
TRACE_INDICES
TRACE_A
TRACE_T
TRACE_G)], @args);
# first, deal with the sequence and quality information
if ($sequence_with_quality && ref($sequence_with_quality) eq "Bio::Seq::SeqWithQuality") {
$self->{swq} = $sequence_with_quality;
}
else {
$self->throw("A Bio::Seq::SequenceTrace object must be created with a
Bio::Seq::SeqWithQuality object.");
}
$self->{trace_a} = $trace_a ? $trace_a : undef;
$self->{trace_t} = $trace_t ? $trace_t : undef;
$self->{trace_g} = $trace_g ? $trace_g : undef;
$self->{trace_c} = $trace_c ? $trace_c : undef;
$self->{trace_indices} = $trace_indices ? $trace_indices : undef;
return $self;
}
=head2 trace($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) = @_;
$base_channel =~ tr/A-Z/a-z/;
if (length($base_channel) > 1 && $base_channel !~ /a|t|g|c/) {
$self->throw("The base channel must be a, t, g, or c");
}
if ( $values && ref($values) eq "ARRAY") {
$self->{trace_$base_channel} = $values;
}
elsif ($values) {
$self->warn("You tried to change the traces for the $base_channel but
the values you wave were not a reference to an array.");
}
return $self->{trace_$base_channel};
}
=head2 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.
=cut
sub trace_indices {
my ($self,$trace_indices)= @_;
if ($trace_indices) { $self->{trace_indices} = $trace_indices; }
return $self->{trace_indices};
}
=head2 _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.
=cut
#'
sub _common_id {
my $self = shift;
return if (!$self->{seq_ref} || !$self->{qual_ref});
my $sid = $self->{seq_ref}->display_id();
return if (!$sid);
return if (!$self->{qual_ref}->display_id());
return $sid if ($sid eq $self->{qual_ref}->display_id());
# should this become a warning?
# print("ids $sid and $self->{qual_ref}->display_id() do not match. Bummer.\n");
}
=head2 _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.
=cut
#'
sub _common_display_id {
my $self = shift;
$self->common_id();
}
=head2 _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.
=cut
#'
sub _common_accession_number {
my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
my $acc = $self->{seq_ref}->accession_number();
# if (!$acc) { print("the seqref has no acc.\n"); }
return if (!$acc);
# if ($acc eq $self->{qual_ref}->accession_number()) { print("$acc matches ".$self->{qual_ref}->accession_number()."\n"); }
return $acc if ($acc eq $self->{qual_ref}->accession_number());
# should this become a warning?
# print("accession numbers $acc and $self->{qual_ref}->accession_number() do not match. Bummer.\n");
}
=head2 _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.
=cut
#'
sub _common_primary_id {
my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
my $pid = $self->{seq_ref}->primary_id();
return if (!$pid);
return $pid if ($pid eq $self->{qual_ref}->primary_id());
# should this become a warning?
# print("primary_ids $pid and $self->{qual_ref}->primary_id() do not match. Bummer.\n");
}
=head2 _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.
=cut
#'
sub _common_desc {
my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
my $des = $self->{seq_ref}->desc();
return if (!$des);
return $des if ($des eq $self->{qual_ref}->desc());
# should this become a warning?
# print("descriptions $des and $self->{qual_ref}->desc() do not match. Bummer.\n");
}
=head2 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.
=cut
sub set_common_descriptors {
my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
&_common_id();
&_common_display_id();
&_common_accession_number();
&_common_primary_id();
&_common_desc();
}
=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->{seq_ref}->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 $seq->id() maps to this function, mainly for
legacy/convience issues.
This method sets the display_id for the SeqWithQuality object.
Returns : A string
Args : If a scalar is provided, it is set as the new display_id for
the SeqWithQuality object.
Status : Virtual
=cut
sub display_id {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'display_id'} = $value;
}
return $obj->{'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 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
=cut
sub accession_number {
my( $obj, $acc ) = @_;
if (defined $acc) {
$obj->{'accession_number'} = $acc;
} else {
$acc = $obj->{'accession_number'};
$acc = 'unknown' unless defined $acc;
}
return $acc;
}
=head2 primary_id()
Title : primary_id()
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
way the implementaiton can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the SeqWithQuality
object.
Returns : A string. (the value of primary_id)
Args : If a scalar is provided, it is set as the new primary_id for
the SeqWithQuality object.
=cut
sub primary_id {
my ($obj,$value) = @_;
if ($value) {
$obj->{'primary_id'} = $value;
}
return $obj->{'primary_id'};
}
=head2 desc()
Title : desc()
Usage : $qual->desc($newval); _or_
$description = $qual->desc();
Function: Get/set description text for this SeqWithQuality object.
Returns : A string. (the value of desc)
Args : If a scalar is provided, it is set as the new desc for the
SeqWithQuality object.
=cut
sub desc {
# a mechanism to set the disc for the SeqWithQuality object.
# probably will be used most often by set_common_features()
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'desc'} = $value;
}
return $obj->{'desc'};
}
=head2 id()
Title : id()
Usage : $id = $qual->id();
Function: Return the ID of the quality. This should normally be (and
actually is in the implementation provided here) just a synonym
for display_id().
Returns : A string. (the value of id)
Args : If a scalar is provided, it is set as the new id for the
SeqWithQuality object.
=cut
sub id {
my ($self,$value) = @_;
if (!$self) { $self->throw("no value for self in $value"); }
if( defined $value ) {
return $self->display_id($value);
}
return $self->display_id();
}
=head2 seq
Title : seq()
Usage : $string = $obj->seq(); _or_
$obj->seq("atctatcatca");
Function: Returns the sequence that is contained in the imbedded in the
PrimarySeq object within the SeqWithQuality object
Returns : A scalar (the seq() value for the imbedded PrimarySeq object.)
Args : If a scalar is provided, the SeqWithQuality object will
attempt to set that as the sequence for the imbedded PrimarySeq
object. Otherwise, the value of seq() for the PrimarySeq object
is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you rope to
hang yourself with. Tie it to a strong device and use a good
knot.
=cut
sub seq {
my ($self,$value) = @_;
if( defined $value) {
$self->{seq_ref}->seq($value);
$self->length();
}
return $self->{seq_ref}->seq();
}
=head2 qual()
Title : qual()
Usage : @quality_values = @{$obj->qual()}; _or_
$obj->qual("10 10 20 40 50");
Function: Returns the quality as imbedded in the PrimaryQual object
within the SeqWithQuality object.
Returns : A reference to an array containing the quality values in the
PrimaryQual object.
Args : If a scalar is provided, the SeqWithQuality object will
attempt to set that as the quality for the imbedded PrimaryQual
object. Otherwise, the value of qual() for the PrimaryQual
object is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you a strong
board with which to flagellate yourself.
=cut
sub qual {
my ($self,$value) = @_;
if( defined $value) {
$self->{qual_ref}->qual($value);
# update the lengths
$self->length();
}
return $self->{qual_ref}->qual();
}
=head2 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.
=cut
sub length {
my $self = shift;
# what do I return here? Whew. Ambiguity...
########
}
=head2 qual_obj
Title : qual_obj($different_obj)
Usage : $qualobj = $seqWqual->qual_obj(); _or_
$qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj);
Function: Get the 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.
=cut
sub qual_obj {
my ($self,$value) = @_;
return $self->{swq}->qual_obj($value);
}
=head2 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.
=cut
sub seq_obj {
my ($self,$value) = @_;
return $self->{swq}->seq_obj($value);
}
=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 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().
=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_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 $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be e_trace_index.
Returns : A reference to an array.
Args : a start position and an end position
=cut
sub sub_trace_index {
my ($self,$start,$end) = @_;
if( $start > $end ){
$self->throw("in sub_trace_index, start [$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--;
$end--;
my @sub_trace_index_array = @{$self->{trace_indices}}[$start..$end];
# return substr $self->seq(), $start, ($end-$start);
return \@sub_trace_index_array;
}
=head2 trace_index_at($position)
Title : trace_index_at($position)
Usage : $trace_index = $obj->trace_index_at(10);
Function: Return the trace_index value at the given location, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be etrace_index_.
Returns : A scalar.
Args : A position.
=cut
sub trace_index_at {
my ($self,$val) = @_;
my @trace_index_at = @{$self->sub_trace_index($val,$val)};
if (scalar(@trace_index_at) == 1) {
return $trace_index_at[0];
}
else {
$self->throw("AAAH! trace_index_at provided more then one quality.");
}
}
1;
]]>