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03 Feb 2021 05:15:14 UTC
- Distribution: BioPerl
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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.
Module Install Instructions
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm BioPerl
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.