Bio::Seq::Quality - Implementation of sequence with residue quality and trace values
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");
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.
Bio::Seq::MetaI, Bio::Seq::Meta::Array
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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.
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
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
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
Title : quality_length() Usage : $qual_len = $obj->quality_length(); Function: return the number of elements in the quality array Returns : integer Args : -
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
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
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
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
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
Title : trace_length() Usage : $trace_len = $obj->trace_length(); Function: return the number of elements in the trace set Returns : integer Args : -
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
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
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.
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.
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
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
I think this method needs a better name! count_high_quality_bases? or sum_clear_ranges?
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
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.
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
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.