Bio::Seq PrimaryQual
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Summary
Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object
Package variables
No package variables defined.
Inherit
Bio::Root::Root Bio::Seq::QualI
Synopsis
 use Bio::Seq::PrimaryQual;
# you can use either a space-delimited string for quality my $string_quals = "10 20 30 40 50 40 30 20 10"; my $qualobj = Bio::Seq::PrimaryQual->new( -qual => $string_quals, -id => 'QualityFragment-12', -accession_number => 'X78121', ); # _or_ you can use an array of quality values my @q2 = split/ /,$string_quals; $qualobj = Bio::Seq::PrimaryQual->new( -qual => \@q2, -primary_id => 'chads primary_id', -desc => 'chads desc', -accession_number => 'chads accession_number', -id => 'chads id' ); # to get the quality values out: my @quals = @{$qualobj->qual()}; # to give _new_ quality values my $newqualstring = "50 90 1000 20 12 0 0"; $qualobj->qual($newqualstring);
Description
This module provides a mechanism for storing quality
values. Much more useful as part of
Bio::Seq::SeqWithQuality where these quality values
are associated with the sequence information.
Methods
newDescriptionCode
qualDescriptionCode
seqDescriptionCode
validate_qualDescriptionCode
subqualDescriptionCode
display_idDescriptionCode
headerDescriptionCode
accession_numberDescriptionCode
primary_idDescriptionCode
descDescriptionCode
idDescriptionCode
lengthDescriptionCode
qualatDescriptionCode
to_stringDescriptionCode
to_string_automatic
No description
Code
Methods description
new()code    nextTop
 Title   : new()
Usage : $qual = Bio::Seq::PrimaryQual->new(
-qual => '10 20 30 40 50 50 20 10',
-id => 'human_id',
-accession_number => 'AL000012',
);
Function: Returns a new Bio::Seq::PrimaryQual object from basic constructors, being a string _or_ a reference to an array for the sequence and strings for id and accession_number. Note that you can provide an empty quality string. Returns : a new Bio::Seq::PrimaryQual object
qual()codeprevnextTop
 Title   : qual()
Usage : @quality_values = @{$obj->qual()};
Function: Returns the quality as a reference to an array containing the
quality values. The individual elements of the quality array are
not validated and can be any numeric value.
Returns : A reference to an array.
seq()codeprevnextTop
 Title    : seq()
Usager : $sequence = $obj->seq();
Function : Returns the quality numbers as a space-separated string.
Returns : Single string.
Args : None.
validate_qual($qualstring)codeprevnextTop
 Title   : validate_qual($qualstring)
Usage : print("Valid.") if { &validate_qual($self,$qualities); }
Function: Make sure that the quality, if it has length > 0, contains at
least one digit. Note that quality strings are parsed into arrays
using split/\d+/,$quality_string, so make sure that your quality
scalar looks like this if you want it to be parsed properly.
Returns : 1 for a valid sequence (WHY? Shouldn\'t it return 0? <boggle>)
Args : a scalar (any scalar, why PrimarySeq author?) and a scalar
containing the string to validate.
subqual($start,$end)codeprevnextTop
 Title   : subqual($start,$end)
Usage : @subset_of_quality_values = @{$obj->subqual(10,40)};
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
display_id()codeprevnextTop
 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
Returns : A string
Args : None
header()codeprevnextTop
 Title   : header()
Usage : $header = $obj->header();
Function: Get/set the header that the user wants printed for this
quality object.
Returns : A string
Args : None
accession_number()codeprevnextTop
 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".
Returns : A string
Args : None
primary_id()codeprevnextTop
 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.
Returns : A string
Args : None
desc()codeprevnextTop
 Title   : desc()
Usage : $qual->desc($newval);
$description = $qual->desc();
Function: Get/set description text for a qual object
Example :
Returns : Value of desc
Args : newvalue (optional)
id()codeprevnextTop
 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.
Args : None.
length()codeprevnextTop
 Title   : length()
Usage : $length = $qual->length();
Function: Return the length of the array holding the quality values.
Under most circumstances, this should match the number of quality
values but no validation is done when the PrimaryQual object is
constructed and non-digits could be put into this array. Is this
a bug? Just enough rope...
Returns : A scalar (the number of elements in the quality array).
Args : None.
qualat()codeprevnextTop
 Title   : qualat
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.
to_string()codeprevnextTop
 Title   : to_string()
Usage : $quality = $obj->to_string();
Function: Return a textual representation of what the object contains.
For this module, this function will return:
qual
display_id
accession_number
primary_id
desc
id
length
Returns : A scalar.
Args : None.
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    # default: turn ON the warnings (duh)
my($qual,$id,$acc,$pid,$desc,$given_id,$header) = $self->_rearrange([qw(QUAL DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID DESC ID HEADER )], @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 ) { $id = $given_id; } # note: the sequence string may be empty
$self->qual(defined($qual) ? $qual : []); $header && $self->header($header); $id && $self->display_id($id); $acc && $self->accession_number($acc); $pid && $self->primary_id($pid); $desc && $self->desc($desc); return $self;
}
qualdescriptionprevnextTop
sub qual {
    my ($self,$value) = @_;

    if( ! defined $value || length($value) == 0 ) { 
        $self->{'qual'} ||= [];
    } elsif( ref($value) =~ /ARRAY/i ) {
        # if the user passed in a reference to an array
$self->{'qual'} = $value; } elsif(! $self->validate_qual($value)){ $self->throw("Attempting to set the quality to [$value] which does not look healthy"); } else { $value =~ s/^\s+//; $self->{'qual'} = [split(/\s+/,$value)]; } return $self->{'qual'};
}
seqdescriptionprevnextTop
sub seq {
    return join ' ', @{ shift->qual };
}
validate_qualdescriptionprevnextTop
sub validate_qual {
    # how do I validate quality values?
# \d+\s+\d+..., I suppose
my ($self,$qualstr) = @_; # why the CORE?? -- (Because Bio::PrimarySeqI namespace has a
# length method, you have to qualify
# which length to use)
return 0 if (!defined $qualstr || CORE::length($qualstr) <= 0); return 1 if( $qualstr =~ /\d/); return 0;
}
subqualdescriptionprevnextTop
sub subqual {
    my ($self,$start,$end) = @_;

    if( $start > $end ){
        $self->throw("in subqual, start [$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--; $end--; my @sub_qual_array = @{$self->{qual}}[$start..$end]; # return substr $self->seq(), $start, ($end-$start);
return\@ sub_qual_array;
}
display_iddescriptionprevnextTop
sub display_id {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'display_id'} = $value;
    }
    return $obj->{'display_id'};
}
headerdescriptionprevnextTop
sub header {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'header'} = $value;
    }
    return $obj->{'header'};
}
accession_numberdescriptionprevnextTop
sub accession_number {
    my( $obj, $acc ) = @_;

    if (defined $acc) {
        $obj->{'accession_number'} = $acc;
    } else {
        $acc = $obj->{'accession_number'};
        $acc = 'unknown' unless defined $acc;
    }
    return $acc;
}
primary_iddescriptionprevnextTop
sub primary_id {
    my ($obj,$value) = @_;
    if( defined $value) {
        $obj->{'primary_id'} = $value;
    }
    return $obj->{'primary_id'};
}
descdescriptionprevnextTop
sub desc {
    my ($obj,$value) = @_;
    if( defined $value) {
        $obj->{'desc'} = $value;
    }
    return $obj->{'desc'};
}
iddescriptionprevnextTop
sub id {
    my ($self,$value) = @_;
    if( defined $value ) {
        return $self->display_id($value);
    }
    return $self->display_id();
}
lengthdescriptionprevnextTop
sub length {
    my $self = shift;
    if (ref($self->{qual}) ne "ARRAY") {
        $self->warn("{qual} is not an array here. Why? It appears to be ".ref($self->{qual})."(".$self->{qual}."). Good thing this can _never_ happen.");
    }
    return scalar(@{$self->{qual}});
}
qualatdescriptionprevnextTop
sub qualat {
    my ($self,$val) = @_;
    my @qualat = @{$self->subqual($val,$val)};
    if (scalar(@qualat) == 1) {
        return $qualat[0];
    } else {
        $self->throw("qualat() provided more than one quality.");
    }
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self,$out,$result) = shift;
    $out = "qual: ".join(',',@{$self->qual()});
    foreach (qw(display_id accession_number primary_id desc id length)) {
        $result = $self->$_();
        if (!$result) { $result = "<unset>"; }
        $out .= "$_: $result\n";
    }
    return $out;
}
to_string_automaticdescriptionprevnextTop
sub to_string_automatic {
    my ($self,$sub_result,$out) = shift;
    foreach (sort keys %$self) {
        print("Working on $_\n");
        eval { $self->$_(); };
        if ($@) { $sub_result = ref($_); }
        elsif (!($sub_result = $self->$_())) {
            $sub_result = "<unset>";
        }
        if (ref($sub_result) eq "ARRAY") {
            print("This thing ($_) is an array!\n");
            $sub_result = join(',',@$sub_result);
        }
        $out .= "$_: ".$sub_result."\n";
    }
    return $out;
} 

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics@dieselwurks.com
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _