Bio::Seq::PrimaryQual - Bioperl lightweight Quality Object 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); 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.

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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

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/ Email bioinformatics@dieselwurks.com 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: 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.

validate_qual($qualstring)
Title : validate_qual($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)
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

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($position)
Title : qualat($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.

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.