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"); $seq->subtrace(2, 3, "9 9");
This object stores base quality values together with the sequence string.
It is a reimplementation of Chad Matsalla's Bio::Seq::SeqWithQuality module using Bio::Seq::MetaI.
The implementation is based on Bio::Seq::Meta::Array. qual() and trace() are base methods to store and retrieve information that have extensions to retrieve values as a scalar (e.g. qual_text() ), or get or set subvalues (e.g. subqual() ). See Bio::Seq::MetaI for more details.
All the functional code is in Bio::Seq::Meta::Array.
There deprecated methods that are included for compatibility with Bio::Seq::SeqWithQuality. These will print a warning unless verbosity of the object is set to be less than zero.
It is not possible to fully follow the interface of Bio::Seq::SeqWithQuality since internally a Bio::Seq::SeqWithQuality object is a composite of two independent objects: a Bio::PrimarySeq object and Bio::Seq::PrimaryQual object. Both of these objects can be created separately and merged into Bio::Seq::SeqWithQuality.
This implementation is based on Bio::Seq::Meta::Array that is a subclass of Bio::PrimarySeq that stores any number of meta information in unnamed arrays.
Here we assume that two meta sets, called 'qual' and 'trace_indices' are attached to a sequence. (But there is nothing that prevents you to add as many named meta sets as you need using normal meta() methods).
qual() is an alias to meta(), qualat($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.
Bio::Seq::MetaI, Bio::Seq::Meta::Array
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
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/
Email heikki-at-bioperl-dot-org
Chad Matsalla, bioinformatics@dieselwurks.com
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
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.