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Bio::Seq::Quality.3pm

NAME

Bio::Seq::Quality - Implementation of sequence with residue quality and trace values

SYNOPSIS

   use Bio::Seq::Quality;
 
 

   # input can be space delimited string or array ref
   my $qual = '0 1 2 3 4 5 6 7 8 9 11 12';
   my $trace = '0 5 10 15 20 25 30 35 40 45 50 55';
 
 

   my $seq = Bio::Seq::Quality->new
       ( -qual => $qual,
         -trace_indices => $trace,
         -seq =>  'atcgatcgatcg',
         -id  => 'human_id',
         -accession_number => 'S000012',
         -verbose => -1   # to silence deprecated methods
   );
 
 

   my $quals = $seq->qual; # array ref
   my $traces = $seq->trace;  # array ref
 
 

   my $quals = $seq->qual_text; # string
   my $traces = $seq->trace_text; # string
 
 

   # get sub values
   $quals = $seq->subqual(2, 3);  # array ref
   $traces = $seq->subtrace(2, 3); # array ref
   $quals = $seq->subqual_text(2, 3); # string
   $quals = $seq->subtrace_text(2, 3); # string
 
 

   # set sub values 
   $seq->subqual(2, 3, "9 9");
   $seq->subtrace(2, 3, "9 9");
 
 

DESCRIPTION

This object stores base quality values together with the sequence string.

It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality module using Bio::Seq::MetaI.

The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods to store and retrieve information that have extensions to retrieve values as a scalar (e.g. qual_text() ), or get or set subvalues (e.g. subqual() ). See Bio::Seq::MetaI for more details.

All the functional code is in Bio::Seq::Meta::Array.

There deprecated methods that are included for compatibility with Bio::Seq::SeqWithQuality. These will print a warning unless verbosity of the object is set to be less than zero.

Differences from Bio::Seq::SeqWithQuality

It is not possible to fully follow the interface of Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality object is a composite of two independent objects: a Bio::PrimarySeq object and Bio::Seq::PrimaryQual object. Both of these objects can be created separately and merged into Bio::Seq::SeqWithQuality.

This implementation is based on Bio::Seq::Meta::Array that is a subclass of Bio::PrimarySeq that stores any number of meta information in unnamed arrays.

Here we assume that two meta sets, called 'qual' and 'trace_indices' are attached to a sequence. (But there is nothing that prevents you to add as many named meta sets as you need using normal meta() methods).

qual() is an alias to meta(), qualat($loc) is an alias to submeta($loc,$loc).

trace_indices() in Bio::Seq::SeqWithQuality has been abbreviated to trace() and is an alias to named_meta('trace').

You can create an object without passing any arguments to the constructor (Bio::Seq::SeqWithQuality fails without alphabet). It will warn about not being able to set alphabet unless you set verbosity of the object to a negative value.

After the latest rewrite, the meta information sets (quality and trace) no longer cover all the residues automatically. Methods to check the length of meta information (quality_length, trace_length)and to see if the ends are flushed to the sequence have been added (quality_is_flush, trace_is_flush). To force the old functinality, set force_flush to true.

qual_obj() and seq_obj() methods do not exist!

Finally, there is only one set of descriptors (primary_id, display_id, accession_number) for the object.

SEE ALSO

Bio::Seq::MetaI, Bio::Seq::Meta::Array

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
 
 

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

CONTRIBUTORS

Chad Matsalla, 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   : $metaseq = Bio::Seq::Quality->new
                 ( -qual => '0 1 2 3 4 5 6 7 8 9 11 12',
                   -trace => '0 5 10 15 20 25 30 35 40 45 50 55',
                   -seq =>  'atcgatcgatcg',
                   -id  => 'human_id',
                   -accession_number => 'S000012',
                 );
  Function: Constructor for Bio::Seq::Quality class.
            Note that you can provide an empty quality and trace strings.
  Returns : a new Bio::Seq::Quality object
 
 

qual

  Title   : qual
  Usage   : $qual_values  = $obj->qual($values_string);
  Function:
 
 

            Get and set method for the meta data starting from residue
            position one. Since it is dependent on the length of the
            sequence, it needs to be manipulated after the sequence.
 
 

            The length of the returned value always matches the length
            of the sequence.
 
 

  Returns : reference to an array of meta data
  Args    : new value, string or array ref or Bio::Seq::PrimaryQual, optional
 
 

qual_text

  Title   : qual_text
  Usage   : $qual_values  = $obj->qual_text($values_arrayref);
  Function: Variant of meta() and qual()  guarantied to return a string
            representation  of meta data. For details, see L<meta>.
  Returns : a string
  Args    : new value, optional
 
 

subqual

  Title   : subqual
  Usage   : $subset_of_qual_values = $obj->subqual(10, 20, $value_string);
            $subset_of_qual_values = $obj->subqual(10, undef, $value_string);
  Function:
 
 

            Get and set method for meta data for subsequences.
 
 

            Numbering starts from 1 and the number is inclusive, ie 1-2
            are the first two residue of the sequence. Start cannot be
            larger than end but can be equal.
 
 

            If the second argument is missing the returned values
            should extend to the end of the sequence.
 
 

  Returns : A reference to an array
  Args    : integer, start position
            integer, end position, optional when a third argument present
            new value, optional
 
 

subqual_text

  Title   : subqual_text
  Usage   : $meta_values  = $obj->subqual_text(20, $value_string);
  Function: Variant of subqual() returning a stringified
            representation  of meta data. For details, see L<Bio::Seq::MetaI>.
  Returns : a string
  Args    : new value, optional
 
 

quality_length

  Title   : quality_length()
  Usage   : $qual_len  = $obj->quality_length();
  Function: return the number of elements in the quality array
  Returns : integer
  Args    : -
 
 

quality_is_flush

  Title   : quality_is_flush
  Usage   : $quality_is_flush  = $obj->quality_is_flush()
  Function: Boolean to tell if the trace length equals the sequence length.
            Returns true if force_flush() is set.
  Returns : boolean 1 or 0
  Args    : none
 
 

trace

  Title   : trace
  Usage   : $trace_values  = $obj->trace($values_string);
  Function:
 
 

            Get and set method for the meta data starting from residue
            position one. Since it is dependent on the length of the
            sequence, it needs to be manipulated after the sequence.
 
 

            The length of the returned value always matches the length
            of the sequence.
 
 

  Returns : reference to an array of meta data
  Args    : new value, string or array ref, optional
 
 

trace_text

  Title   : trace_text
  Usage   : $trace_values  = $obj->trace_text($values_arrayref);
  Function: Variant of meta() and trace()  guarantied to return a string
            representation  of meta data. For details, see L<meta>.
  Returns : a string
  Args    : new value, optional
 
 

subtrace

  Title   : subtrace
  Usage   : $subset_of_trace_values = $obj->subtrace(10, 20, $value_string);
            $subset_of_trace_values = $obj->subtrace(10, undef, $value_string);
  Function:
 
 

            Get and set method for meta data for subsequences.
 
 

            Numbering starts from 1 and the number is inclusive, ie 1-2
            are the first two residue of the sequence. Start cannot be
            larger than end but can be equal.
 
 

            If the second argument is missing the returned values
            should extend to the end of the sequence.
 
 

  Returns : A reference to an array
  Args    : integer, start position
            integer, end position, optional when a third argument present
            new value, optional
 
 

subtrace_text

  Title   : subtrace_text
  Usage   : $meta_values  = $obj->subtrace_text(20, $value_string);
  Function: Variant of subtrace() returning a stringified
            representation  of meta data. For details, see L<Bio::Seq::MetaI>.
  Returns : a string
  Args    : new value, optional
 
 

trace_length

  Title   : trace_length()
  Usage   : $trace_len  = $obj->trace_length();
  Function: return the number of elements in the trace set
  Returns : integer
  Args    : -
 
 

trace_is_flush

  Title   : trace_is_flush
  Usage   : $trace_is_flush  = $obj->trace_is_flush()
  Function: Boolean to tell if the trace length equals the sequence length.
            Returns true if force_flush() is set.
  Returns : boolean 1 or 0
  Args    : none