Bio::Seq
SeqWithQuality
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Summary
Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::PrimarySeq;
use Bio::Seq::PrimaryQual;
# 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.
Methods
Methods description
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. |
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. |
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. |
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. |
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. |
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(). |
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 |
Title : alphabet();
Usage : $molecule_type = $obj->alphabet();
Function: Get the molecule type from the PrimarySeq object.
Returns : What what PrimarySeq says the type of the sequence is.
Args : None. |
Title : baseat($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. |
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. |
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 |
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. |
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. |
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
Notes : Arguments:
-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?) |
Title : primary_id()
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
way the implementaiton can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the SeqWithQuality
object.
Returns : A string. (the value of primary_id)
Args : If a scalar is provided, it is set as the new primary_id for
the SeqWithQuality object. |
Title : qual()
Usage : @quality_values = @{$obj->qual()}; _or_
$obj->qual("10 10 20 40 50");
Function: Returns the quality as imbedded in the PrimaryQual object
within the SeqWithQuality object.
Returns : A reference to an array containing the quality values in the
PrimaryQual object.
Args : If a scalar is provided, the SeqWithQuality object will
attempt to set that as the quality for the imbedded PrimaryQual
object. Otherwise, the value of qual() for the PrimaryQual
object is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you a strong
board with which to flagellate yourself. |
Title : qual_obj($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. |
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. |
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. |
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. |
Title : set_common_descriptors()
Usage : $self->set_common_descriptors();
Function: Compare the descriptors (id,accession_number,display_id,
primary_id, desc) for the PrimarySeq and PrimaryQual objects
within the SeqWithQuality object. If they match, make that
descriptor the descriptor for the SeqWithQuality object.
Returns : Nothing.
Args : None. |
Title : sub_trace_index($start,$end)
Usage : @trace_indices = @{$obj->sub_trace_index(10,20);
Function: returns the trace index values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be e_trace_index.
Returns : A reference to an array.
Args : a start position and an end position |
Title : subqual($start,$end)
Usage : @qualities = @{$obj->subqual(10,20);
Function: returns the quality values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be equal.
Returns : A reference to an array.
Args : a start position and an end position |
Title : subseq($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. |
Title : to_string()
Usage : $quality = $obj->to_string();
Function: Return a textual representation of what the object contains.
For this module, this function will return:
qual
seq
display_id
accession_number
primary_id
desc
id
length_sequence
length_quality
Returns : A scalar.
Args : None. |
Title : trace_index_at($position)
Usage : $trace_index = $obj->trace_index_at(10);
Function: Return the trace_index value at the given location, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be etrace_index_.
Returns : A scalar.
Args : A position. |
Title : trace_indices()
Usage : @trace_indice_values = @{$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. |
Methods code
sub _common_accession_number
{ my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
my $acc = $self->{seq_ref}->accession_number();
return if (!$acc);
return $acc if ($acc eq $self->{qual_ref}->accession_number());
} | 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());
} | sub _common_display_id
{ my $self = shift;
$self->common_id(); } | 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());
} | 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 $self->{qual_ref}->primary_id());
} | sub _set_descriptors
{ my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_;
my ($c_id,$c_acc,$c_pid,$c_desc);
if (!$self->display_id()) {
if ($c_id = $self->_common_id() ) { $self->display_id($c_id); }
else {
if ($self->{seq_ref}) {
$self->display_id($self->{seq_ref}->id());
}
elsif ($self->{qual_ref}) {
$self->display_id($self->{qual_ref}->id());
}
}
}
if ($acc) { $self->accession_number($acc); }
elsif ($c_acc = $self->_common_accession_number() ) { $self->accession_number($c_acc); }
if ($pid) { $self->primary_id($pid); }
elsif ($c_pid = $self->_common_primary_id() ) { $self->primary_id($c_pid); }
if ($desc) { $self->desc($desc); }
elsif ($c_desc = $self->_common_desc() ) { $self->desc($c_desc); }} | 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;} | sub alphabet
{ my $self = shift;
return $self->{seq_ref}->alphabet();} | sub baseat
{ my ($self,$val) = @_;
return $self->{seq_ref}->subseq($val,$val);} | sub desc
{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'desc'} = $value;
}
return $obj->{'desc'}; } | sub display_id
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'display_id'} = $value;
}
return $obj->{'display_id'};} | sub id
{ my ($self,$value) = @_;
if (!$self) { $self->throw("no value for self in $value"); }
if( defined $value ) {
return $self->display_id($value);
}
return $self->display_id();} | sub length
{ my $self = shift;
if (!$self->{seq_ref}) {
unless ($self->{supress_warnings} == 1) {
$self->warn("Can't find {seq_ref} here in length().");
}
return;
}
if (!$self->{qual_ref}) {
unless ($self->{supress_warnings} == 1) {
$self->warn("Can't find {qual_ref} here in length().");
}
return;
}
my $seql = $self->{seq_ref}->length();
if ($seql != $self->{qual_ref}->length()) {
unless ($self->{supress_warnings} == 1) {
$self->warn("Sequence length (".$seql.") is different from quality length (".$self->{qual_ref}->length().") in the SeqWithQuality object. This can only lead to problems later.");
}
$self->{'length'} = "DIFFERENT";
}
else {
$self->{'length'} = $seql;
}
return $self->{'length'};} | sub new
{ my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->{supress_warnings} = 1;
my($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet,$trace_indices) =
$self->_rearrange([qw(
QUAL
SEQ
DISPLAY_ID
ACCESSION_NUMBER
PRIMARY_ID
DESC
ID
ALPHABET
TRACE_INDICES
)],
@args);
if ( defined $id && defined $given_id ) {
if( $id ne $given_id ) {
$self->throw("Provided both id and display_id constructor functions. [$id] [$given_id]");
}
}
if( defined $given_id ) {
$self->display_id($given_id);
$id = $given_id;
}
if (!$seq) {
my $id;
unless ($self->{supress_warnings} == 1) {
$self->warn("You did not provide sequence information during the construction of a Bio::Seq::SeqWithQuality object. Sequence components for this object will be empty.");
}
if (!$alphabet) {
$self->throw("If you want me to create a PrimarySeq object for your empty sequence <boggle> you must specify a -alphabet to satisfy the constructor requirements for a Bio::PrimarySeq object with no sequence. Read the POD for it, luke.");
}
$self->{seq_ref} = Bio::PrimarySeq->new
(
-seq => "",
-accession_number => $acc,
-primary_id => $pid,
-desc => $desc,
-display_id => $id,
-alphabet => $alphabet
);
}
elsif (ref($seq) eq "Bio::PrimarySeq" ) {
$self->{seq_ref} = $seq;
}
else {
my $seqobj = Bio::PrimarySeq->new
(
-seq => $seq,
-accession_number => $acc,
-primary_id => $pid,
-desc => $desc,
-display_id => $id,
);
$self->{seq_ref} = $seqobj;
}
if (!$qual) {
$self->{qual_ref} = Bio::Seq::PrimaryQual->new
(
-qual => "",
-accession_number => $acc,
-primary_id => $pid,
-desc => $desc,
-display_id => $id,
);
}
elsif (ref($qual) eq "Bio::Seq::PrimaryQual") {
$self->{qual_ref} = $qual;
}
else {
my $qualobj = Bio::Seq::PrimaryQual->new
(
-qual => $qual,
-accession_number => $acc,
-primary_id => $pid,
-desc => $desc,
-display_id => $id,
-trace_indices => $trace_indices
);
$self->{qual_ref} = $qualobj;
}
$self->_set_descriptors($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet);
$self->length();
return $self;} | sub primary_id
{ my ($obj,$value) = @_;
if ($value) {
$obj->{'primary_id'} = $value;
}
return $obj->{'primary_id'};} | sub qual
{ my ($self,$value) = @_;
if( defined $value) {
$self->{qual_ref}->qual($value);
$self->length();
}
return $self->{qual_ref}->qual();} | sub qual_obj
{ my ($self,$value) = @_;
if (defined($value)) {
if (ref($value) eq "Bio::Seq::PrimaryQual") {
$self->{qual_ref} = $value;
$self->debug("You successfully changed the PrimaryQual object within a SeqWithQuality object. ID's for the SeqWithQuality object may now not be what you expect. Use something like set_common_descriptors() to fix them if you care,");
}
else {
$self->debug("You tried to change the PrimaryQual object within a SeqWithQuality object but you passed a reference to an object that was not a Bio::Seq::PrimaryQual object. Thus your change failed. Sorry.\n");
}
}
return $self->{qual_ref};} | sub qualat
{ my ($self,$val) = @_;
return $self->{qual_ref}->qualat($val);} | sub seq
{ my ($self,$value) = @_;
if( defined $value) {
$self->{seq_ref}->seq($value);
$self->length();
}
return $self->{seq_ref}->seq();} | sub seq_obj
{ my ($self,$value) = @_;
if( defined $value) {
if (ref($value) eq "Bio::PrimarySeq") {
$self->debug("You successfully changed the PrimarySeq object within a SeqWithQuality object. ID's for the SeqWithQuality object may now not be what you expect. Use something like set_common_descriptors() to fix them if you care,");
} else {
$self->debug("You tried to change the PrimarySeq object within a SeqWithQuality object but you passed a reference to an object that was not a Bio::PrimarySeq object. Thus your change failed. Sorry.\n");
}
}
return $self->{seq_ref};} | sub set_common_descriptors
{ my $self = shift;
return if ($self->{seq_ref} || $self->{qual_ref});
&_common_id();
&_common_display_id();
&_common_accession_number();
&_common_primary_id();
&_common_desc();} | sub sub_trace_index
{ my ($self,@args) = @_;
return $self->{qual_ref}->sub_trace_index(@args);} | sub subqual
{ my ($self,@args) = @_;
return $self->{qual_ref}->subqual(@args);} | sub subseq
{ my ($self,@args) = @_;
return $self->{seq_ref}->subseq(@args);} | sub to_string
{ my ($self,$out,$result) = shift;
$out = "qual: ".join(',',@{$self->qual()})."\n";
foreach (qw(seq display_id accession_number primary_id desc id)) {
$result = $self->$_();
if (!$result) { $result = "<unset>"; }
$out .= "$_: $result\n";
}
return $out;
}
1;} | sub trace_index_at
{ my ($self,$val) = @_;
return $self->{qual_ref}->trace_index_at($val);} | sub trace_indices
{ my ($self,$value) = @_;
if( defined $value) {
$self->{qual_ref}->trace_indices($value);
$self->length();
}
return $self->{qual_ref}->trace_indices();} | General documentation
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
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/
| AUTHOR - Chad Matsalla | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _