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::Quality 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 AT bioperl DOT 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 AT bioperl DOT 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 AT dieselwurks DOT 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 implementation, 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 implementation 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.