/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Seq::PrimaryQual

NAME

Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object

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.

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 _

new()

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()

Title   : qual()
Usage   : @quality_values  = @{$obj->qual()};
Function: Get or set the quality as a reference to an array containing the
          quality values. An error is generated if the quality scores are
          invalid, see validate_qual().
Returns : A reference to an array.

seq()

Title    : seq()
Usager   : $sequence = $obj->seq();
Function : Returns the quality numbers as a space-separated string.
Returns  : Single string.
Args     : None.

validate_qual($qualstring)

Title   : validate_qual($qualstring)
Usage   : print("Valid.") if { &validate_qual($self, $quality_string); }
Function: Test that the given quality string is valid. It is expected to
          contain space-delimited numbers that can be parsed using split /\d+/.
          However, this validation takes shortcuts and only tests that the
          string contains characters valid in numbers: 0-9 . eE +-
          Note that empty quality strings are valid too.
Returns : 1 for a valid sequence, 0 otherwise
Args    : - Scalar containing the quality string to validate.
          - Boolean to optionally throw an error if validation failed

subqual($start,$end)

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()

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()

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()

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()

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()

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()

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()

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()

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()

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.