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BioPerl-1.7.8
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/ Bio::Seq::Quality

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.

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.

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

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 - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

CONTRIBUTORS

Chad Matsalla, bioinformatics at dieselwurks dot com

Dan Bolser, dan dot bolser at gmail 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   : $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

Setting quality values resets the clear range.

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

get_trace_graph


            

              
              
Title    : get_trace_graph
Usage    : @trace_values = $obj->get_trace_graph( -trace => 'a',
                                                  -scale => 100)
Function : Returns array of raw trace values for a trace file, or
           false if no trace data exists.  Requires a value for trace
           to get either the a, g, c or t trace information, and an
           optional value for scale, which rescales the data between
           0 and the provided value, a scale value of '0' performs no
           scaling
Returns  : Array or 0
Args     : string, trace to retrieve, one of a, g, c or t integer,
           scale, for scaling of trace between 0 and scale, or 0 for
           no scaling, optional

threshold


            

              
              
Title   : threshold
Usage   : $qual->threshold($value);
Function: Sets the quality threshold.
Returns : an integer
Args    : new value, optional

Value used by *clear_range* method below.

mask_below_threshold


            

              
              
Title   : mask_below_threshold
Usage   : $count = $obj->count_clear_ranges($threshold);
Function: Counts number of ranges in the sequence where quality
          values are above the threshold
Returns : count integer
Args    : threshold integer, optional

Set threshold first using method threshold.

count_clear_ranges


            

              
              
Title   : count_clear_ranges
Usage   : $count = $obj->count_clear_ranges($threshold);
Function: Counts number of ranges in the sequence where quality
          values are above the threshold
Returns : count integer
Args    : threshold integer, optional

Set threshold first using method threshold.

clear_ranges_length


            

              
              
Title   : clear_ranges_length
Usage   : $total_lenght = $obj->clear_ranges_length($threshold);
Function: Return number of residues with quality values above
          the threshold in all clear ranges
Returns : an integer
Args    : threshold, optional

Set threshold first using method threshold.

I think this method needs a better name! count_high_quality_bases? or sum_clear_ranges?

get_clear_range


            

              
              
Title   : get_clear_range
Usage   : $newqualobj = $obj->get_clear_range($threshold);
Function: Return longest subsequence that has quality values above
          the given threshold, or a default value of 13
Returns : a new Bio::Seq::Quality object
Args    : threshold, optional

Set threshold first using method threshold.

Note, this method could be implemented using some gaussian smoothing of the quality scores. Currently one base below the threshold is enough to end the clear range.

get_all_clean_ranges


            

              
              
Title   : get_all_clean_ranges
Usage   : @ranges = $obj->get_all_clean_ranges($minlength);
Function: Return all ranges where quality values are above
          the threshold. Original ordering.
Returns : an ordered array of new Bio::Seq::Quality objects
Args    : minimum length , optional

Set threshold first using method threshold.