Mercurial > repos > mahtabm > ensembl
diff variant_effect_predictor/Bio/Seq/SeqWithQuality.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/Seq/SeqWithQuality.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,916 @@ +# $Id: SeqWithQuality.pm,v 1.17 2002/12/19 22:02:38 matsallac Exp $ +# +# BioPerl module for Bio::Seq::QualI +# +# Cared for by Chad Matsalla <bioinformatics@dieselwurks.com +# +# Copyright Chad Matsalla +# +# You may distribute this module under the same terms as perl itself + +# POD documentation - main docs before the code + +=head1 NAME + +Bio::Seq::SeqWithQuality - Bioperl object packaging a sequence with its quality + +=head1 SYNOPSIS + + use Bio::PrimarySeq; + use Bio::Seq::PrimaryQual; + + # make from memory + my $qual = Bio::Seq::SeqWithQuality->new + ( -qual => '10 20 30 40 50 50 20 10', + -seq => 'ATCGATCG', + -id => 'human_id', + -accession_number => 'AL000012', + ); + + # make from objects + # first, make a PrimarySeq object + my $seqobj = Bio::PrimarySeq->new + ( -seq => 'atcgatcg', + -id => 'GeneFragment-12', + -accession_number => 'X78121', + -alphabet => 'dna' + ); + + # now make a PrimaryQual object + my $qualobj = Bio::Seq::PrimaryQual->new + ( -qual => '10 20 30 40 50 50 20 10', + -id => 'GeneFragment-12', + -accession_number => 'X78121', + -alphabet => 'dna' + ); + + # now make the SeqWithQuality object + my $swqobj = Bio::Seq::SeqWithQuality->new + ( -seq => $seqobj, + -qual => $qualobj + ); + # done! + + $swqobj->id(); # the id of the SeqWithQuality object + # may not match the the id of the sequence or + # of the quality (check the pod, luke) + $swqobj->seq(); # the sequence of the SeqWithQuality object + $swqobj->qual(); # the quality of the SeqWithQuality object + + # to get out parts of the sequence. + + print "Sequence ", $seqobj->id(), " with accession ", + $seqobj->accession, " and desc ", $seqobj->desc, "\n"; + + $string2 = $seqobj->subseq(1,40); + +=head1 DESCRIPTION + +This object stores base quality values together with the sequence string. + +=head1 FEEDBACK + +=head2 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://bio.perl.org/MailList.html - About the mailing lists + +=head2 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 email +or the web: + + bioperl-bugs@bio.perl.org + http://bugzilla.bioperl.org/ + +=head1 AUTHOR - Chad Matsalla + +Email bioinformatics@dieselwurks.com + +=head1 CONTRIBUTORS + +Jason Stajich, jason@bioperl.org + +=head1 APPENDIX + +The rest of the documentation details each of the object methods. +Internal methods are usually preceded with a _ + +=cut + + +package Bio::Seq::SeqWithQuality; + +use vars qw(@ISA); + +use strict; +use Bio::Root::Root; +use Bio::Seq::QualI; +use Bio::PrimarySeqI; +use Bio::PrimarySeq; +use Bio::Seq::PrimaryQual; + +@ISA = qw(Bio::Root::Root Bio::PrimarySeqI Bio::Seq::QualI); + +=head2 new() + + Title : new() + Usage : $qual = Bio::Seq::SeqWithQuality ->new + ( -qual => '10 20 30 40 50 50 20 10', + -seq => 'ATCGATCG', + -id => 'human_id', + -accession_number => 'AL000012', + -trace_indices => '0 5 10 15 20 25 30 35' + ); + Function: Returns a new Bio::Seq::SeqWithQual object from basic + constructors. + Returns : a new Bio::Seq::PrimaryQual object + Notes : Arguments: + -qual can be a quality string (see Bio::Seq::PrimaryQual for more + information on this) or a reference to a Bio::Seq::PrimaryQual + object. + -seq can be a sequence string (see Bio::PrimarySeq for more + information on this) or a reference to a Bio::PrimaryQual object. + -seq, -id, -accession_number, -primary_id, -desc, -id behave like + this: + 1. if they are provided on construction of the + Bio::Seq::SeqWithQuality they will be set as the descriptors for + the object unless changed by one of the following mechanisms: + a) $obj->set_common_descriptors() is used and both the -seq and + the -qual object have the same descriptors. These common + descriptors will then become the descriptors for the + Bio::Seq::SeqWithQual object. + b) the descriptors are manually set using the seq(), id(), + desc(), or accession_number(), primary_id(), + 2. if no descriptors are provided, the new() constructor will see + if the descriptor used in the PrimarySeq and in the + PrimaryQual objects match. If they do, they will become + the descriptors for the SeqWithQuality object. + + To eliminate ambiguity, I strongly suggest you set the + descriptors manually on construction of the object. Really. + -trace_indices : a space_delimited list of trace indices + (where would the peaks be drawn if this list of qualities + was to be plotted?) + +=cut + +sub new { + my ($class, @args) = @_; + my $self = $class->SUPER::new(@args); + # default: turn OFF the warnings + $self->{supress_warnings} = 1; + my($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet,$trace_indices) = + $self->_rearrange([qw( + QUAL + SEQ + DISPLAY_ID + ACCESSION_NUMBER + PRIMARY_ID + DESC + ID + ALPHABET + TRACE_INDICES + )], + @args); + # first, deal with the sequence and quality information + if ( defined $id && defined $given_id ) { + if( $id ne $given_id ) { + $self->throw("Provided both id and display_id constructor functions. [$id] [$given_id]"); + } + } + if( defined $given_id ) { + $self->display_id($given_id); + $id = $given_id; + } + if (!$seq) { + my $id; + unless ($self->{supress_warnings} == 1) { + $self->warn("You did not provide sequence information during the construction of a Bio::Seq::SeqWithQuality object. Sequence components for this object will be empty."); + } + if (!$alphabet) { + $self->throw("If you want me to create a PrimarySeq object for your empty sequence <boggle> you must specify a -alphabet to satisfy the constructor requirements for a Bio::PrimarySeq object with no sequence. Read the POD for it, luke."); + } + $self->{seq_ref} = Bio::PrimarySeq->new + ( + -seq => "", + -accession_number => $acc, + -primary_id => $pid, + -desc => $desc, + -display_id => $id, + -alphabet => $alphabet + ); + } + elsif (ref($seq) eq "Bio::PrimarySeq" ) { + $self->{seq_ref} = $seq; + } + + else { + my $seqobj = Bio::PrimarySeq->new + ( + -seq => $seq, + -accession_number => $acc, + -primary_id => $pid, + -desc => $desc, + -display_id => $id, + ); + $self->{seq_ref} = $seqobj; + } + + if (!$qual) { + $self->{qual_ref} = Bio::Seq::PrimaryQual->new + ( + -qual => "", + -accession_number => $acc, + -primary_id => $pid, + -desc => $desc, + -display_id => $id, + ); + } + elsif (ref($qual) eq "Bio::Seq::PrimaryQual") { + $self->{qual_ref} = $qual; + } + else { + my $qualobj = Bio::Seq::PrimaryQual->new + ( + -qual => $qual, + -accession_number => $acc, + -primary_id => $pid, + -desc => $desc, + -display_id => $id, + -trace_indices => $trace_indices + ); + $self->{qual_ref} = $qualobj; + } + + # now try to set the descriptors for this object + $self->_set_descriptors($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet); + $self->length(); + + return $self; +} + +=head2 _common_id() + + Title : _common_id() + Usage : $common_id = $self->_common_id(); + Function: Compare the display_id of {qual_ref} and {seq_ref}. + Returns : Nothing if they don't match. If they do return + {seq_ref}->display_id() + Args : None. + +=cut + +#' +sub _common_id { + my $self = shift; + return if (!$self->{seq_ref} || !$self->{qual_ref}); + my $sid = $self->{seq_ref}->display_id(); + return if (!$sid); + return if (!$self->{qual_ref}->display_id()); + return $sid if ($sid eq $self->{qual_ref}->display_id()); + # should this become a warning? + # print("ids $sid and $self->{qual_ref}->display_id() do not match. Bummer.\n"); +} + +=head2 _common_display_id() + + Title : _common_id() + Usage : $common_id = $self->_common_display_id(); + Function: Compare the display_id of {qual_ref} and {seq_ref}. + Returns : Nothing if they don't match. If they do return + {seq_ref}->display_id() + Args : None. + +=cut + +#' +sub _common_display_id { + my $self = shift; + $self->common_id(); +} + +=head2 _common_accession_number() + + Title : _common_accession_number() + Usage : $common_id = $self->_common_accession_number(); + Function: Compare the accession_number() of {qual_ref} and {seq_ref}. + Returns : Nothing if they don't match. If they do return + {seq_ref}->accession_number() + Args : None. + +=cut + +#' +sub _common_accession_number { + my $self = shift; + return if ($self->{seq_ref} || $self->{qual_ref}); + my $acc = $self->{seq_ref}->accession_number(); + # if (!$acc) { print("the seqref has no acc.\n"); } + return if (!$acc); + # if ($acc eq $self->{qual_ref}->accession_number()) { print("$acc matches ".$self->{qual_ref}->accession_number()."\n"); } + return $acc if ($acc eq $self->{qual_ref}->accession_number()); + # should this become a warning? + # print("accession numbers $acc and $self->{qual_ref}->accession_number() do not match. Bummer.\n"); +} + +=head2 _common_primary_id() + + Title : _common_primary_id() + Usage : $common_primard_id = $self->_common_primary_id(); + Function: Compare the primary_id of {qual_ref} and {seq_ref}. + Returns : Nothing if they don't match. If they do return + {seq_ref}->primary_id() + Args : None. + +=cut + +#' +sub _common_primary_id { + my $self = shift; + return if ($self->{seq_ref} || $self->{qual_ref}); + my $pid = $self->{seq_ref}->primary_id(); + return if (!$pid); + return $pid if ($pid eq $self->{qual_ref}->primary_id()); + # should this become a warning? + # print("primary_ids $pid and $self->{qual_ref}->primary_id() do not match. Bummer.\n"); + +} + +=head2 _common_desc() + + Title : _common_desc() + Usage : $common_desc = $self->_common_desc(); + Function: Compare the desc of {qual_ref} and {seq_ref}. + Returns : Nothing if they don't match. If they do return + {seq_ref}->desc() + Args : None. + +=cut + +#' +sub _common_desc { + my $self = shift; + return if ($self->{seq_ref} || $self->{qual_ref}); + my $des = $self->{seq_ref}->desc(); + return if (!$des); + return $des if ($des eq $self->{qual_ref}->desc()); + # should this become a warning? + # print("descriptions $des and $self->{qual_ref}->desc() do not match. Bummer.\n"); + +} + +=head2 set_common_descriptors() + + Title : set_common_descriptors() + Usage : $self->set_common_descriptors(); + Function: Compare the descriptors (id,accession_number,display_id, + primary_id, desc) for the PrimarySeq and PrimaryQual objects + within the SeqWithQuality object. If they match, make that + descriptor the descriptor for the SeqWithQuality object. + Returns : Nothing. + Args : None. + +=cut + +sub set_common_descriptors { + my $self = shift; + return if ($self->{seq_ref} || $self->{qual_ref}); + &_common_id(); + &_common_display_id(); + &_common_accession_number(); + &_common_primary_id(); + &_common_desc(); +} + +=head2 alphabet() + + Title : alphabet(); + Usage : $molecule_type = $obj->alphabet(); + Function: Get the molecule type from the PrimarySeq object. + Returns : What what PrimarySeq says the type of the sequence is. + Args : None. + +=cut + +sub alphabet { + my $self = shift; + return $self->{seq_ref}->alphabet(); +} + +=head2 display_id() + + Title : display_id() + Usage : $id_string = $obj->display_id(); + Function: Returns the display id, aka the common name of the Quality + object. + The semantics of this is that it is the most likely string to be + used as an identifier of the quality sequence, and likely to have + "human" readability. The id is equivalent to the ID field of the + GenBank/EMBL databanks and the id field of the Swissprot/sptrembl + database. In fasta format, the >(\S+) is presumed to be the id, + though some people overload the id to embed other information. + Bioperl does not use any embedded information in the ID field, + and people are encouraged to use other mechanisms (accession + field for example, or extending the sequence object) to solve + this. Notice that $seq->id() maps to this function, mainly for + legacy/convience issues. + This method sets the display_id for the SeqWithQuality object. + Returns : A string + Args : If a scalar is provided, it is set as the new display_id for + the SeqWithQuality object. + Status : Virtual + +=cut + +sub display_id { + my ($obj,$value) = @_; + if( defined $value) { + $obj->{'display_id'} = $value; + } + return $obj->{'display_id'}; + +} + +=head2 accession_number() + + Title : accession_number() + Usage : $unique_biological_key = $obj->accession_number(); + Function: Returns the unique biological id for a sequence, commonly + called the accession_number. For sequences from established + databases, the implementors should try to use the correct + accession number. Notice that primary_id() provides the unique id + for the implemetation, allowing multiple objects to have the same + accession number in a particular implementation. For sequences + with no accession number, this method should return "unknown". + This method sets the accession_number for the SeqWithQuality + object. + Returns : A string (the value of accession_number) + Args : If a scalar is provided, it is set as the new accession_number + for the SeqWithQuality object. + Status : Virtual + + +=cut + +sub accession_number { + my( $obj, $acc ) = @_; + + if (defined $acc) { + $obj->{'accession_number'} = $acc; + } else { + $acc = $obj->{'accession_number'}; + $acc = 'unknown' unless defined $acc; + } + return $acc; +} + +=head2 primary_id() + + Title : primary_id() + Usage : $unique_implementation_key = $obj->primary_id(); + Function: Returns the unique id for this object in this implementation. + This allows implementations to manage their own object ids in a + way the implementaiton can control clients can expect one id to + map to one object. For sequences with no accession number, this + method should return a stringified memory location. + This method sets the primary_id for the SeqWithQuality + object. + Returns : A string. (the value of primary_id) + Args : If a scalar is provided, it is set as the new primary_id for + the SeqWithQuality object. + +=cut + +sub primary_id { + my ($obj,$value) = @_; + if ($value) { + $obj->{'primary_id'} = $value; + } + return $obj->{'primary_id'}; + +} + +=head2 desc() + + Title : desc() + Usage : $qual->desc($newval); _or_ + $description = $qual->desc(); + Function: Get/set description text for this SeqWithQuality object. + Returns : A string. (the value of desc) + Args : If a scalar is provided, it is set as the new desc for the + SeqWithQuality object. + +=cut + +sub desc { + # a mechanism to set the disc for the SeqWithQuality object. + # probably will be used most often by set_common_features() + my ($obj,$value) = @_; + if( defined $value) { + $obj->{'desc'} = $value; + } + return $obj->{'desc'}; +} + +=head2 id() + + Title : id() + Usage : $id = $qual->id(); + Function: Return the ID of the quality. This should normally be (and + actually is in the implementation provided here) just a synonym + for display_id(). + Returns : A string. (the value of id) + Args : If a scalar is provided, it is set as the new id for the + SeqWithQuality object. + +=cut + +sub id { + my ($self,$value) = @_; + if (!$self) { $self->throw("no value for self in $value"); } + if( defined $value ) { + return $self->display_id($value); + } + return $self->display_id(); +} + +=head2 seq + + Title : seq() + Usage : $string = $obj->seq(); _or_ + $obj->seq("atctatcatca"); + Function: Returns the sequence that is contained in the imbedded in the + PrimarySeq object within the SeqWithQuality object + Returns : A scalar (the seq() value for the imbedded PrimarySeq object.) + Args : If a scalar is provided, the SeqWithQuality object will + attempt to set that as the sequence for the imbedded PrimarySeq + object. Otherwise, the value of seq() for the PrimarySeq object + is returned. + Notes : This is probably not a good idea because you then should call + length() to make sure that the sequence and quality are of the + same length. Even then, how can you make sure that this sequence + belongs with that quality? I provided this to give you rope to + hang yourself with. Tie it to a strong device and use a good + knot. + +=cut + +sub seq { + my ($self,$value) = @_; + if( defined $value) { + $self->{seq_ref}->seq($value); + $self->length(); + } + return $self->{seq_ref}->seq(); +} + +=head2 qual() + + Title : qual() + Usage : @quality_values = @{$obj->qual()}; _or_ + $obj->qual("10 10 20 40 50"); + Function: Returns the quality as imbedded in the PrimaryQual object + within the SeqWithQuality object. + Returns : A reference to an array containing the quality values in the + PrimaryQual object. + Args : If a scalar is provided, the SeqWithQuality object will + attempt to set that as the quality for the imbedded PrimaryQual + object. Otherwise, the value of qual() for the PrimaryQual + object is returned. + Notes : This is probably not a good idea because you then should call + length() to make sure that the sequence and quality are of the + same length. Even then, how can you make sure that this sequence + belongs with that quality? I provided this to give you a strong + board with which to flagellate yourself. + +=cut + +sub qual { + my ($self,$value) = @_; + + if( defined $value) { + $self->{qual_ref}->qual($value); + # update the lengths + $self->length(); + } + return $self->{qual_ref}->qual(); +} + + + +=head2 trace_indices() + + Title : trace_indices() + Usage : @trace_indice_values = @{$obj->trace_indices()}; _or_ + $obj->trace_indices("10 10 20 40 50"); + Function: Returns the trace_indices as imbedded in the Primaryqual object + within the SeqWithQualiity object. + Returns : A reference to an array containing the trace_indice values in the + PrimaryQual object. + Args : If a scalar is provided, the SeqWithuQuality object will + attempt to set that as the trace_indices for the imbedded PrimaryQual + object. Otherwise, the value of trace_indices() for the PrimaryQual + object is returned. + Notes : This is probably not a good idea because you then should call + length() to make sure that the sequence and trace_indices are of the + same length. Even then, how can you make sure that this sequence + belongs with that trace_indicex? I provided this to give you a strong + board with which to flagellate yourself. + +=cut + +sub trace_indices { + my ($self,$value) = @_; + + if( defined $value) { + $self->{qual_ref}->trace_indices($value); + # update the lengths + $self->length(); + } + return $self->{qual_ref}->trace_indices(); +} + + + + +=head2 length() + + Title : length() + Usage : $length = $seqWqual->length(); + Function: Get the length of the SeqWithQuality sequence/quality. + Returns : Returns the length of the sequence and quality if they are + both the same. Returns "DIFFERENT" if they differ. + Args : None. + +=cut + +sub length { + my $self = shift; + if (!$self->{seq_ref}) { + unless ($self->{supress_warnings} == 1) { + $self->warn("Can't find {seq_ref} here in length()."); + } + return; + } + if (!$self->{qual_ref}) { + unless ($self->{supress_warnings} == 1) { + $self->warn("Can't find {qual_ref} here in length()."); + } + return; + } + my $seql = $self->{seq_ref}->length(); + + if ($seql != $self->{qual_ref}->length()) { + unless ($self->{supress_warnings} == 1) { + $self->warn("Sequence length (".$seql.") is different from quality length (".$self->{qual_ref}->length().") in the SeqWithQuality object. This can only lead to problems later."); + } + $self->{'length'} = "DIFFERENT"; + } + else { + $self->{'length'} = $seql; + } + return $self->{'length'}; +} + + +=head2 qual_obj + + Title : qual_obj($different_obj) + Usage : $qualobj = $seqWqual->qual_obj(); _or_ + $qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj); + Function: Get the PrimaryQual object that is imbedded in the + SeqWithQuality object or if a reference to a PrimaryQual object + is provided, set this as the PrimaryQual object imbedded in the + SeqWithQuality object. + Returns : A reference to a Bio::Seq::SeqWithQuality object. + +=cut + +sub qual_obj { + my ($self,$value) = @_; + if (defined($value)) { + if (ref($value) eq "Bio::Seq::PrimaryQual") { + $self->{qual_ref} = $value; + + $self->debug("You successfully changed the PrimaryQual object within a SeqWithQuality object. ID's for the SeqWithQuality object may now not be what you expect. Use something like set_common_descriptors() to fix them if you care,"); + } + else { + $self->debug("You tried to change the PrimaryQual object within a SeqWithQuality object but you passed a reference to an object that was not a Bio::Seq::PrimaryQual object. Thus your change failed. Sorry.\n"); + } + } + return $self->{qual_ref}; +} + + +=head2 seq_obj + + Title : seq_obj() + Usage : $seqobj = $seqWqual->qual_obj(); _or_ + $seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj); + Function: Get the PrimarySeq object that is imbedded in the + SeqWithQuality object or if a reference to a PrimarySeq object is + provided, set this as the PrimarySeq object imbedded in the + SeqWithQuality object. + Returns : A reference to a Bio::PrimarySeq object. + +=cut + +sub seq_obj { + my ($self,$value) = @_; + if( defined $value) { + if (ref($value) eq "Bio::PrimarySeq") { + $self->debug("You successfully changed the PrimarySeq object within a SeqWithQuality object. ID's for the SeqWithQuality object may now not be what you expect. Use something like set_common_descriptors() to fix them if you care,"); + } else { + $self->debug("You tried to change the PrimarySeq object within a SeqWithQuality object but you passed a reference to an object that was not a Bio::PrimarySeq object. Thus your change failed. Sorry.\n"); + } + } + return $self->{seq_ref}; +} + +=head2 _set_descriptors + + Title : _set_descriptors() + Usage : $seqWqual->_qual_obj($qual,$seq,$id,$acc,$pid,$desc,$given_id, + $alphabet); + Function: Set the descriptors for the SeqWithQuality object. Try to + match the descriptors in the PrimarySeq object and in the + PrimaryQual object if descriptors were not provided with + construction. + Returns : Nothing. + Args : $qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet as found + in the new() method. + Notes : Really only intended to be called by the new() method. If + you want to invoke a similar function try + set_common_descriptors(). + +=cut + + +sub _set_descriptors { + my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_; + my ($c_id,$c_acc,$c_pid,$c_desc); + if (!$self->display_id()) { + if ($c_id = $self->_common_id() ) { $self->display_id($c_id); } + else { + if ($self->{seq_ref}) { + # print("Using seq_ref to set id to ".$self->{seq_ref}->display_id()."\n"); + # ::dumpValue($self->{seq_ref}); + $self->display_id($self->{seq_ref}->id()); + } + elsif ($self->{qual_ref}) { + $self->display_id($self->{qual_ref}->id()); + } + } + } + if ($acc) { $self->accession_number($acc); } + elsif ($c_acc = $self->_common_accession_number() ) { $self->accession_number($c_acc); } + if ($pid) { $self->primary_id($pid); } + elsif ($c_pid = $self->_common_primary_id() ) { $self->primary_id($c_pid); } + if ($desc) { $self->desc($desc); } + elsif ($c_desc = $self->_common_desc() ) { $self->desc($c_desc); } +} + +=head2 subseq($start,$end) + + Title : subseq($start,$end) + Usage : $subsequence = $obj->subseq($start,$end); + Function: Returns the subseq from start to end, where the first base + is 1 and the number is inclusive, ie 1-2 are the first two + bases of the sequence. + Returns : A string. + Args : Two positions. + +=cut + +sub subseq { + my ($self,@args) = @_; + # does a single value work? + return $self->{seq_ref}->subseq(@args); +} + +=head2 baseat($position) + + Title : baseat($position) + Usage : $base_at_position_6 = $obj->baseat("6"); + Function: Returns a single base at the given position, where the first + base is 1 and the number is inclusive, ie 1-2 are the first two + bases of the sequence. + Returns : A scalar. + Args : A position. + +=cut + +sub baseat { + my ($self,$val) = @_; + return $self->{seq_ref}->subseq($val,$val); +} + +=head2 subqual($start,$end) + + Title : subqual($start,$end) + Usage : @qualities = @{$obj->subqual(10,20); + Function: returns the quality values from $start to $end, where the + first value is 1 and the number is inclusive, ie 1-2 are the + first two bases of the sequence. Start cannot be larger than + end but can be equal. + Returns : A reference to an array. + Args : a start position and an end position + +=cut + +sub subqual { + my ($self,@args) = @_; + return $self->{qual_ref}->subqual(@args); +} + +=head2 qualat($position) + + Title : qualat($position) + Usage : $quality = $obj->qualat(10); + Function: Return the quality value at the given location, where the + first value is 1 and the number is inclusive, ie 1-2 are the + first two bases of the sequence. Start cannot be larger than + end but can be equal. + Returns : A scalar. + Args : A position. + +=cut + +sub qualat { + my ($self,$val) = @_; + return $self->{qual_ref}->qualat($val); +} + +=head2 sub_trace_index($start,$end) + + Title : sub_trace_index($start,$end) + Usage : @trace_indices = @{$obj->sub_trace_index(10,20); + Function: returns the trace index values from $start to $end, where the + first value is 1 and the number is inclusive, ie 1-2 are the + first two bases of the sequence. Start cannot be larger than + end but can be e_trace_index. + Returns : A reference to an array. + Args : a start position and an end position + +=cut + +sub sub_trace_index { + my ($self,@args) = @_; + return $self->{qual_ref}->sub_trace_index(@args); +} + +=head2 trace_index_at($position) + + Title : trace_index_at($position) + Usage : $trace_index = $obj->trace_index_at(10); + Function: Return the trace_index value at the given location, where the + first value is 1 and the number is inclusive, ie 1-2 are the + first two bases of the sequence. Start cannot be larger than + end but can be etrace_index_. + Returns : A scalar. + Args : A position. + +=cut + +sub trace_index_at { + my ($self,$val) = @_; + return $self->{qual_ref}->trace_index_at($val); +} + +=head2 to_string() + + Title : to_string() + Usage : $quality = $obj->to_string(); + Function: Return a textual representation of what the object contains. + For this module, this function will return: + qual + seq + display_id + accession_number + primary_id + desc + id + length_sequence + length_quality + Returns : A scalar. + Args : None. + +=cut + +sub to_string { + my ($self,$out,$result) = shift; + $out = "qual: ".join(',',@{$self->qual()})."\n"; + foreach (qw(seq display_id accession_number primary_id desc id)) { + $result = $self->$_(); + if (!$result) { $result = "<unset>"; } + $out .= "$_: $result\n"; + } + return $out; +} +1;