Bio SeqUtils
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Summary
Bio::SeqUtils - Additional methods for PrimarySeq objects
Package variables
No package variables defined.
Included modules
Carp
Scalar::Util qw ( blessed )
Inherit
Bio::Root::Root
Synopsis
    use Bio::SeqUtils;
# get a Bio::PrimarySeqI compliant object, $seq, somehow
$util = Bio::SeqUtils->new();
$polypeptide_3char = $util->seq3($seq);
# or
$polypeptide_3char = Bio::SeqUtils->seq3($seq);
# set the sequence string (stored in one char code in the object) Bio::SeqUtils->seq3($seq, $polypeptide_3char); # translate a sequence in all six frames @seqs = Bio::SeqUtils->translate_6frames($seq); # inplace editing of the sequence Bio::SeqUtils->mutate($seq, Bio::LiveSeq::Mutation->new(-seq => 'c', -pos => 3 )); # mutate a sequence to desired similarity% $newseq = Bio::SeqUtils-> evolve ($seq, $similarity, $transition_transversion_rate); # concatenate two or more sequences with annotations and features, # the first sequence will be modified Bio::SeqUtils->cat(@seqs); my $catseq=$seqs[0]; # truncate a sequence, retaining features and adjusting their # coordinates if necessary my $truncseq = Bio::SeqUtils->trunc_with_features($seq, 100, 200); # reverse complement a sequence and its features my $revcomseq = Bio::SeqUtils->revcom_with_features($seq); # simulate cloning of a fragment into a vector. Cut the vector at # positions 1000 and 1100 (deleting postions 1001 to 1099) and # "ligate" a fragment into the sites. The fragment is # reverse-complemented in this example (option "flip"). # All features of the vector and fragment are preserved and # features that are affected by the deletion/insertion are # modified accordingly. # $vector and $fragment must be Bio::SeqI compliant objects my $new_molecule = Bio::Sequtils->ligate( -vector => $vector, -fragment => $fragment, -left => 1000, -right => 1100, -flip => 1 ); # delete a segment of a seqence (from pos 1000 to 1100, inclusive), # again preserving features and annotations my $new_molecule = Bio::SeqUtils->cut( $seq, 1000, 1100 ); # insert a fragment into a recipient between positions 1000 and # 1001. $recipient is a Bio::SeqI compliant object my $new_molecule = Bio::SeqUtils::PbrTools->insert( $recipient_seq, $fragment_seq, 1000 );
Description
This class is a holder of methods that work on Bio::PrimarySeqI-
compliant sequence objects, e.g. Bio::PrimarySeq and
Bio::Seq. These methods are not part of the Bio::PrimarySeqI
interface and should in general not be essential to the primary function
of sequence objects. If you are thinking of adding essential
functions, it might be better to create your own sequence class.
See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.
The methods take as their first argument a sequence object. It is
possible to use methods without first creating a SeqUtils object,
i.e. use it as an anonymous hash.
The first two methods, seq3() and seq3in(), give out or read in protein
sequences coded in three letter IUPAC amino acid codes.
The next two methods, translate_3frames() and translate_6frames(), wrap
around the standard translate method to give back an array of three
forward or all six frame translations.
The mutate() method mutates the sequence string with a mutation
description object.
The cat() method concatenates two or more sequences. The first sequence
is modified by addition of the remaining sequences. All annotations and
sequence features will be transferred.
The revcom_with_features() and trunc_with_features() methods are similar
to the revcom() and trunc() methods from Bio::Seq, but also adjust any
features associated with the sequence as appropriate.
There are also methods that simulate molecular cloning with rich
sequence objects.
The delete() method cuts a segment out of a sequence and re-joins the
left and right fragments (like splicing or digesting and re-ligating a
molecule). Positions (and types) of sequence features are adjusted
accordingly:
Features that span the deleted segment are converted to split featuress
to indicate the disruption. (Sub)Features that extend into the deleted
segment are truncated.
A new molecule is created and returned.
The insert() method inserts a fragment (which can be a rich Bio::Seq
object) into another sequence object adding all annotations and
features to the final product.
Features that span the insertion site are converted to split features
to indicate the disruption.
A new feature is added to indicate the inserted fragment itself.
A new molecule is created and returned.
The ligate() method simulates digesting a recipient (vector) and
ligating a fragment into it, which can also be flipped if needed. It
is simply a combination of a deletion and an insertion step and
returns a new molecule. The rules for modifying feature locations
outlined above are also used here, e.g. features that span the cut
sites are converted to split features with truncated sub-locations.
Methods
BEGIN Code
seq3DescriptionCode
seq3inDescriptionCode
translate_3framesDescriptionCode
translate_6framesDescriptionCode
valid_aaDescriptionCode
mutateDescriptionCode
catDescriptionCode
trunc_with_featuresDescriptionCode
deleteDescriptionCode
insertDescriptionCode
ligateDescriptionCode
_coord_adjust_deletionDescriptionCode
_coord_adjust_insertionDescriptionCode
_single_loc_object_from_collectionDescriptionCode
_location_objects_from_coordinate_listDescriptionCode
_new_seq_via_cloneDescriptionCode
_new_seq_from_oldDescriptionCode
_coord_adjustDescriptionCode
revcom_with_featuresDescriptionCode
_feature_revcomDescriptionCode
_coord_revcom
No description
Code
evolveDescriptionCode
_get_similarity
No description
Code
Methods description
seq3code    nextTop
 Title   : seq3
Usage : $string = Bio::SeqUtils->seq3($seq)
Function: Read only method that returns the amino acid sequence as a
string of three letter codes. alphabet has to be
'protein'. Output follows the IUPAC standard plus 'Ter' for
terminator. Any unknown character, including the default
unknown character 'X', is changed into 'Xaa'. A noncoded
aminoacid selenocystein is recognized (Sec, U).
Returns : A scalar Args : character used for stop in the protein sequence optional, defaults to '*' string used to separate the output amino acid codes, optional, defaults to ''
seq3incodeprevnextTop
 Title   : seq3in
Usage : $seq = Bio::SeqUtils->seq3in($seq, 'MetGlyTer')
Function: Method for changing of the sequence of a
Bio::PrimarySeqI sequence object. The three letter amino
acid input string is converted into one letter code. Any
unknown character triplet, including the default 'Xaa', is
converted into 'X'.
Returns : Bio::PrimarySeq object Args : sequence string optional character to be used for stop in the protein sequence, defaults to '*' optional character to be used for unknown in the protein sequence, defaults to 'X'
translate_3framescodeprevnextTop
 Title   : translate_3frames
Usage : @prots = Bio::SeqUtils->translate_3frames($seq)
Function: Translate a nucleotide sequence in three forward frames.
The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translate
translate_6framescodeprevnextTop
 Title   : translate_6frames
Usage : @prots = Bio::SeqUtils->translate_6frames($seq)
Function: translate a nucleotide sequence in all six frames
The IDs of the sequences are appended with '-0F', '-1F', '-2F',
'-0R', '-1R', '-2R'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translate
valid_aacodeprevnextTop
 Title   : valid_aa
Usage : my @aa = $table->valid_aa
Function: Retrieves a list of the valid amino acid codes.
The list is ordered so that first 21 codes are for unique
amino acids. The rest are ['B', 'Z', 'X', '*'].
Returns : array of all the valid amino acid codes
Args : [optional] $code => [0 -> return list of 1 letter aa codes,
1 -> return list of 3 letter aa codes,
2 -> return associative array of both ]
mutatecodeprevnextTop
 Title   : mutate
Usage : Bio::SeqUtils->mutate($seq,$mutation1, $mutation2);
Function: Inplace editing of the sequence.
The second argument can be a Bio::LiveSeq::Mutation object or an array of them. The mutations are applied sequentially checking only that their position is within the current sequence. Insertions are inserted before the given position. Returns : boolean Args : sequence object mutation, a Bio::LiveSeq::Mutation object, or an array of them
See Bio::LiveSeq::Mutation.
catcodeprevnextTop
  Title   : cat
Usage : Bio::SeqUtils->cat(@seqs);
my $catseq=$seqs[0];
Function: Concatenates a list of Bio::Seq objects, adding them all on to the
end of the first sequence. Annotations and sequence features are
copied over from any additional objects, and the coordinates of any
copied features are adjusted appropriately.
Returns : a boolean
Args : array of sequence objects
Note that annotations have no sequence locations. If you concatenate
sequences with the same annotations they will all be added.
trunc_with_featurescodeprevnextTop
 Title   : trunc_with_features
Usage : $trunc=Bio::SeqUtils->trunc_with_features($seq, $start, $end);
Function: Like Bio::Seq::trunc, but keeps features (adjusting coordinates
where necessary. Features that partially overlap the region have
their location changed to a Bio::Location::Fuzzy.
Returns : A new sequence object
Args : A sequence object, start coordinate, end coordinate (inclusive)
deletecodeprevnextTop
 
Title : delete
Function: cuts a segment out of a sequence and re-joins the left and right fragments
(like splicing or digesting and re-ligating a molecule).
Positions (and types) of sequence features are adjusted accordingly:
Features that span the cut site are converted to split featuress to
indicate the disruption.
Features that extend into the cut-out fragment are truncated.
A new molecule is created and returned.
Usage : my $cutseq = Bio::SeqUtils::PbrTools->cut( $seq, 1000, 1100 );
Args : a Bio::PrimarySeqI compliant object to cut,
first nt of the segment to be deleted
last nt of the segment to be deleted
optional:
hash-ref of options:
clone_obj: if true, clone the input sequence object rather
than calling "new" on the object's class
Returns : a new Bio::Seq object
insertcodeprevnextTop
 
Title : insert
Function: inserts a fragment (a Bio::Seq object) into a nother sequence object
adding all annotations and features to the final product.
Features that span the insertion site are converted to split
features to indicate the disruption.
A new feature is added to indicate the inserted fragment itself.
A new molecule is created and returned.
Usage : # insert a fragment after pos 1000
my $insert_seq = Bio::SeqUtils::PbrTools->insert(
$recipient_seq,
$fragment_seq,
1000
);
Args : recipient sequence (a Bio::PrimarySeqI compliant object),
a fragmetn to insert (Bio::PrimarySeqI compliant object),
insertion position (fragment is inserted to the right of this pos)
pos=0 will prepend the fragment to the recipient
optional:
hash-ref of options:
clone_obj: if true, clone the input sequence object rather
than calling "new" on the object's class
Returns : a new Bio::Seq object
ligatecodeprevnextTop
 
title : ligate
function: pastes a fragment (which can also have features) into a recipient
sequence between two "cut" sites, preserving features and adjusting
their locations.
This is a shortcut for deleting a segment from a sequence object followed
by an insertion of a fragmnet and is supposed to be used to simulate
in-vitro cloning where a recipient (a vector) is digested and a fragment
is then ligated into the recipient molecule. The fragment can be flipped
(reverse-complemented with all its features).
A new sequence object is returned to represent the product of the reaction.
Features and annotations are transferred from the insert to the product
and features on the recipient are adjusted according to the methods
/"delete" amd /"insert":
Features spanning the insertion site will be split up into two sub-locations.
(Sub-)features in the deleted region are themselves deleted.
(Sub-)features that extend into the deleted region are truncated.
The class of the product object depends on the class of the recipient (vector)
sequence object. if it is not possible to instantiate a new
object of that class, a Bio::Primaryseq object is created instead.
usage : # insert the flipped fragment between positions 1000 and 1100 of the
# vector, i.e. everything between these two positions is deleted and
# replaced by the fragment
my $new_molecule = Bio::Sequtils::Pbrtools->ligate(
-recipient => $vector,
-fragment => $fragment,
-left => 1000,
-right => 1100,
-flip => 1,
-clone_obj => 1
);
args : recipient: the recipient/vector molecule
fragment: molecule that is to be ligated into the vector
left: left cut site (fragment will be inserted to the right of
this position)
optional:
right: right cut site (fragment will be inseterted to the
left of this position). defaults to left+1
flip: boolean, if true, the fragment is reverse-complemented
(including features) before inserting
clone_obj: if true, clone the recipient object to create the product
instead of calling "new" on its class
returns : a new Bio::Seq object of the ligated fragments
_coord_adjust_deletioncodeprevnextTop
 
title : _coord_adjust_deletion
function: recursively adjusts coordinates of seqfeatures on a molecule
where a segment has been deleted.
(sub)features that span the deletion site become split features.
(sub)features that extend into the deletion site are truncated.
A note is added to the feature to inform about the size and
position of the deletion.
usage : my $adjusted_feature = Bio::Sequtils::_coord_adjust_deletion(
$feature,
$start,
$end
);
args : a Bio::SeqFeatureI compliant object,
start (inclusive) position of the deletion site,
end (inclusive) position of the deletion site
returns : a Bio::SeqFeatureI compliant object
_coord_adjust_insertioncodeprevnextTop
 
title : _coord_adjust_insertion
function: recursively adjusts coordinates of seqfeatures on a molecule
where another sequence has been inserted.
(sub)features that span the insertion site become split features
and a note is added about the size and positin of the insertion.
Features with an IN-BETWEEN location at the insertion site
are lost (such features can only exist between adjacent bases)
usage : my $adjusted_feature = Bio::Sequtils::_coord_adjust_insertion(
$feature,
$insert_pos,
$insert_length
);
args : a Bio::SeqFeatureI compliant object,
insertion position (insert to the right of this position)
length of inserted fragment
returns : a Bio::SeqFeatureI compliant object
_single_loc_object_from_collectioncodeprevnextTop
 
Title : _single_loc_object_from_collection
Function: takes an array of location objects. Returns either a split
location object if there are more than one locations in the
array or returns the single location if there is only one
Usage : my $loc = _single_loc_object_from_collection( @sublocs );
Args : array of Bio::Location objects
Returns : a single Bio:;Location object containing all locations
_location_objects_from_coordinate_listcodeprevnextTop
 
Title : _location_objects_from_coordinate_list
Function: takes an array-ref of start/end coordinates, a strand and a
type and returns a list of Bio::Location objects (Fuzzy by
default, Simple in case of in-between coordinates).
If location type is not "IN-BETWEEN", individual types may be
passed in for start and end location as per Bio::Location::Fuzzy
documentation.
Usage : my @loc_objs = $self->_location_objects_from_coordinate_list(
\@coords,
$strand,
$type
);
Args : array-ref of array-refs each containing:
start, end [, start-type, end-type]
where types are optional. If given, must be
a one of ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
strand (all locations must be on same strand)
location-type (EXACT, IN-BETWEEN etc)
Returns : list of Bio::Location objects
_new_seq_via_clonecodeprevnextTop
 
Title : _new_seq_via_clone
Function: clone a sequence object using Bio::Root::Root::clone and set the new sequence string
sequence features are removed.
Usage : my $new_seq = $self->_new_seq_via_clone( $seq_obj, $seq_str );
Args : original seq object [, new sequence string]
Returns : a clone of the original sequence object, optionally with new sequence string
_new_seq_from_oldcodeprevnextTop
 
Title : _new_seq_from_old
Function: creates a new sequence obejct, if possible of the same class as the old and adds
attributes to it. Also copies annotation across to the new object.
Usage : my $new_seq = $self->_new_seq_from_old( $seq_obj, { seq => $seq_str, display_id => 'some_ID'});
Args : old sequence object
hashref of attributes for the new sequence (sequence string etc.)
Returns : a new Bio::Seq object
_coord_adjustcodeprevnextTop
  Title   : _coord_adjust
Usage : my $newfeat=Bio::SeqUtils->_coord_adjust($feature, 100, $seq->length);
Function: Recursive subroutine to adjust the coordinates of a feature
and all its subfeatures. If a sequence length is specified, then
any adjusted features that have locations beyond the boundaries
of the sequence are converted to Bio::Location::Fuzzy objects.
Returns : A Bio::SeqFeatureI compliant object. Args : A Bio::SeqFeatureI compliant object, the number of bases to add to the coordinates (optional) the length of the parent sequence
revcom_with_featurescodeprevnextTop
 Title   : revcom_with_features
Usage : $revcom=Bio::SeqUtils->revcom_with_features($seq);
Function: Like Bio::Seq::revcom, but keeps features (adjusting coordinates
as appropriate.
Returns : A new sequence object
Args : A sequence object
_feature_revcomcodeprevnextTop
  Title   : _feature_revcom
Usage : my $newfeat=Bio::SeqUtils->_feature_revcom($feature, $seq->length);
Function: Recursive subroutine to reverse complement a feature and
all its subfeatures. The length of the parent sequence must be
specified.
Returns : A Bio::SeqFeatureI compliant object. Args : A Bio::SeqFeatureI compliant object, the length of the parent sequence
evolvecodeprevnextTop
  Title   : evolve
Usage : my $newseq = Bio::SeqUtils->
evolve($seq, $similarity, $transition_transversion_rate);
Function: Mutates the sequence by point mutations until the similarity of
the new sequence has decreased to the required level.
Transition/transversion rate is adjustable.
Returns : A new Bio::PrimarySeq object
Args : sequence object
percentage similarity (e.g. 80)
tr/tv rate, optional, defaults to 1 (= 1:1)
Set the verbosity of the Bio::SeqUtils object to positive integer to
see the mutations as they happen.
This method works only on nucleotide sequences. It prints a warning if
you set the target similarity to be less than 25%.
Transition/transversion ratio is an observed attribute of an sequence
comparison. We are dealing here with the transition/transversion rate
that we set for our model of sequence evolution.
Methods code
BEGINTop
BEGIN {
    # Note : Ambiguity code 'J' = I/L (used for ambiguities in mass-spec data)
%ONECODE = ('Ala' => 'A', 'Asx' => 'B', 'Cys' => 'C', 'Asp' => 'D', 'Glu' => 'E', 'Phe' => 'F', 'Gly' => 'G', 'His' => 'H', 'Ile' => 'I', 'Lys' => 'K', 'Leu' => 'L', 'Met' => 'M', 'Asn' => 'N', 'Pro' => 'P', 'Gln' => 'Q', 'Arg' => 'R', 'Ser' => 'S', 'Thr' => 'T', 'Val' => 'V', 'Trp' => 'W', 'Xaa' => 'X', 'Tyr' => 'Y', 'Glx' => 'Z', 'Ter' => '*', 'Sec' => 'U', 'Pyl' => 'O', 'Xle' => 'J' ); %THREECODE = ('A' => 'Ala', 'B' => 'Asx', 'C' => 'Cys', 'D' => 'Asp', 'E' => 'Glu', 'F' => 'Phe', 'G' => 'Gly', 'H' => 'His', 'I' => 'Ile', 'K' => 'Lys', 'L' => 'Leu', 'M' => 'Met', 'N' => 'Asn', 'P' => 'Pro', 'Q' => 'Gln', 'R' => 'Arg', 'S' => 'Ser', 'T' => 'Thr', 'V' => 'Val', 'W' => 'Trp', 'Y' => 'Tyr', 'Z' => 'Glx', 'X' => 'Xaa', '*' => 'Ter', 'U' => 'Sec', 'O' => 'Pyl', 'J' => 'Xle' );
}
seq3descriptionprevnextTop
sub seq3 {
   my ($self, $seq, $stop, $sep ) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
       $self->throw('Not a Bio::PrimarySeqI object but [$self]');
   $seq->alphabet eq 'protein' ||
       $self->throw('Not a protein sequence');

   if (defined $stop) {
       length $stop != 1 and $self->throw('One character stop needed, not [$stop]');
       $THREECODE{$stop} = "Ter";
   }
   $sep ||= '';

   my $aa3s;
   foreach my $aa  (split //, uc $seq->seq) {
       $THREECODE{$aa} and $aa3s .= $THREECODE{$aa}. $sep, next;
       $aa3s .= 'Xaa'. $sep;
   }
   $sep and substr($aa3s, -(length $sep), length $sep) = '' ;
   return $aa3s;
}
seq3indescriptionprevnextTop
sub seq3in {
   my ($self, $seq, $string, $stop, $unknown) = @_;

   $seq->isa('Bio::PrimarySeqI') ||
	  $self->throw("Not a Bio::PrimarySeqI object but [$self]");
   $seq->alphabet eq 'protein' ||
	  $self->throw('Not a protein sequence');

   if (defined $stop) {
		length $stop != 1 and $self->throw("One character stop needed, not [$stop]");
		$ONECODE{'Ter'} = $stop;
   }
   if (defined $unknown) {
		length $unknown != 1 and $self->throw("One character stop needed, not [$unknown]");
		$ONECODE{'Xaa'} = $unknown;
   }

   my ($aas, $aa3);
   my $length = (length $string) - 2;
   for (my $i = 0 ; $i < $length ; $i += 3)  {
		$aa3 = substr($string, $i, 3);
		$aa3 = ucfirst(lc($aa3));
		$ONECODE{$aa3} and $aas .= $ONECODE{$aa3}, next;
		$aas .= $ONECODE{'Xaa'};
   }
   $seq->seq($aas);
   return $seq;
}
translate_3framesdescriptionprevnextTop
sub translate_3frames {
    my ($self, $seq, @args ) = @_;

    $self->throw('Object [$seq] '. 'of class ['. ref($seq).  ']  can not be translated.')
	unless $seq->can('translate');

    my ($stop, $unknown, $frame, $tableid, $fullCDS, $throw) = @args;
    my @seqs;
    my $f = 0;
    while ($f != 3) {
        my $translation = $seq->translate($stop, $unknown,$f,$tableid, $fullCDS, $throw );
	$translation->id($seq->id. "-". $f. "F");
	push @seqs, $translation;
	$f++;
    }

    return @seqs;
}
translate_6framesdescriptionprevnextTop
sub translate_6frames {
    my ($self, $seq, @args ) = @_;

    my @seqs = $self->translate_3frames($seq, @args);
    my @seqs2 = $self->translate_3frames($seq->revcom, @args);
    foreach my $seq2 (@seqs2) {
	my ($tmp) = $seq2->id;
	$tmp =~ s/F$/R/g;
	$seq2->id($tmp);
    }
    return @seqs, @seqs2;
}
valid_aadescriptionprevnextTop
sub valid_aa {
   my ($self,$code) = @_;

   if( ! $code ) {
       my @codes;
       foreach my $c ( sort values %ONECODE ) {
	   push @codes, $c unless ( $c =~ /[BZX\*]/ );
       }
       push @codes, qw(B Z X *); # so they are in correct order ?
return @codes; } elsif( $code == 1 ) { my @codes; foreach my $c ( sort keys %ONECODE ) { push @codes, $c unless ( $c =~ /(Asx|Glx|Xaa|Ter)/ ); } push @codes, ('Asx', 'Glx', 'Xaa', 'Ter' ); return @codes; } elsif( $code == 2 ) { my %codes = %ONECODE; foreach my $c ( keys %ONECODE ) { my $aa = $ONECODE{$c}; $codes{$aa} = $c; } return %codes; } else { $self->warn("unrecognized code in ".ref($self)." method valid_aa()"); return (); }
}
mutatedescriptionprevnextTop
sub mutate {
    my ($self, $seq, @mutations ) = @_;

    $self->throw('Object [$seq] '. 'of class ['. ref($seq).
                 '] should be a Bio::PrimarySeqI ')
	unless $seq->isa('Bio::PrimarySeqI');
    $self->throw('Object [$mutations[0]] '. 'of class ['. ref($mutations[0]).
                 '] should be a Bio::LiveSeq::Mutation')
	unless $mutations[0]->isa('Bio::LiveSeq::Mutation');

    foreach my $mutation (@mutations) {
        $self->throw('Attempting to mutate sequence beyond its length')
            unless $mutation->pos - 1 <= $seq->length;

        my $string = $seq->seq;
        substr $string, $mutation->pos - 1, $mutation->len, $mutation->seq;
        $seq->seq($string);
    }
    1;
}
catdescriptionprevnextTop
sub cat {
    my ($self, $seq, @seqs) = @_;
    $self->throw('Object [$seq] '. 'of class ['. ref($seq).
                 '] should be a Bio::PrimarySeqI ')
        unless $seq->isa('Bio::PrimarySeqI');


    for my $catseq (@seqs) {
        $self->throw('Object [$catseq] '. 'of class ['. ref($catseq).
                     '] should be a Bio::PrimarySeqI ')
            unless $catseq->isa('Bio::PrimarySeqI');

        $self->throw('Trying to concatenate sequences with different alphabets: '.
                     $seq->display_id. '('. $seq->alphabet. ') and '. $catseq->display_id.
                     '('. $catseq->alphabet. ')')
            unless $catseq->alphabet eq $seq->alphabet;


        my $length=$seq->length;
        $seq->seq($seq->seq.$catseq->seq);

        # move annotations
if ($seq->isa("Bio::AnnotatableI") and $catseq->isa("Bio::AnnotatableI")) { foreach my $key ( $catseq->annotation->get_all_annotation_keys() ) { foreach my $value ( $catseq->annotation->get_Annotations($key) ) { $seq->annotation->add_Annotation($key, $value); } } } # move SeqFeatures
if ( $seq->isa('Bio::SeqI') and $catseq->isa('Bio::SeqI')) { for my $feat ($catseq->get_SeqFeatures) { $seq->add_SeqFeature($self->_coord_adjust($feat, $length)); } } } 1;
}
trunc_with_featuresdescriptionprevnextTop
sub trunc_with_features {
    use Bio::Range;
    my ($self,$seq,$start,$end) = @_;
    $self->throw('Object [$seq] '. 'of class ['. ref($seq).
                 '] should be a Bio::SeqI ')
    unless $seq->isa('Bio::SeqI');
    my $trunc=$seq->trunc($start, $end);
    my $truncrange=Bio::Range->new(-start=>$start, -end=>$end, -strand=>0);
    # move annotations
foreach my $key ( $seq->annotation->get_all_annotation_keys() ) { foreach my $value ( $seq->annotation->get_Annotations($key) ) { $trunc->annotation->add_Annotation($key, $value); } } # move features
foreach ( grep { $_=$self->_coord_adjust($_, 1-$start, $end+1-$start) if $_->overlaps($truncrange) } $seq->get_SeqFeatures ) { $trunc->add_SeqFeature($_); } return $trunc;
}
deletedescriptionprevnextTop
sub delete {
  my $self = shift;
  my ( $seq, $left, $right, $opts_ref) = @_ ;
  $self->throw( 'was expecting 3-4 paramters but got '.@_) unless @_ == 3 || @_ == 4;

  $self->throw( 'Object of class ['
    . ref($seq)
    . '] should be a Bio::PrimarySeqI ' )
    unless blessed ($seq) && $seq->isa('Bio::PrimarySeqI');

  $self->throw("Left coordinate ($left) must be >= 1") if $left < 1;
  if ($right > $seq->length ){
    $self->throw("Right coordinate ($right) must be less than "
      . 'sequence length ('. $seq->length .')');
  }

  # piece together the sequence string of the remaining fragments
my $left_seq = $seq->subseq( 1, $left - 1) ; my $right_seq = $seq->subseq( $right + 1, $seq->length); if (!$left_seq || !$right_seq ){ $self->throw('could not assemble sequences. At least one of the fragments is empty'); } my $seq_str = $left_seq . $right_seq; # create the new seq object with the same class as the recipient
# or (if requested), make a clone of the existing object. In the
# latter case we need to remove sequence features from the cloned
# object instead of copying them
my $product; if ($opts_ref->{clone_obj}){ $product = $self->_new_seq_via_clone( $seq, $seq_str ); } else { $product = $self->_new_seq_from_old( $seq, { seq => $seq_str } ); } # move sequence features
if ( $product->isa('Bio::SeqI') && $seq->isa('Bio::SeqI') ) { for my $feat ( $seq->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust_deletion( $feat, $left, $right ); $product->add_SeqFeature( $adjfeat ) if $adjfeat; } } # add a feature to annotatde the deletion
my $deletion_feature = Bio::SeqFeature::Generic->new( -primary_tag => 'misc_feature', -tag => { note => 'deletion of ' . ( $right - $left + 1 ) .'bp' }, -location => Bio::Location::Simple->new( -start => $left - 1, -end => $left, -location_type => 'IN-BETWEEN' ) ); $product->add_SeqFeature( $deletion_feature ); return $product;
}
insertdescriptionprevnextTop
sub insert {
  my $self = shift;
  my ( $recipient, $fragment, $insert_pos, $opts_ref) = @_ ;
  $self->throw( 'was expecting 3-4 paramters but got '.@_) unless @_ == 3 || @_ == 4;

  $self->throw( 'Recipient object of class ['
    . ref($recipient)
    . '] should be a Bio::PrimarySeqI ' )
    unless blessed ($recipient) && $recipient->isa('Bio::PrimarySeqI');

  $self->throw( 'Fragment object of class ['
    . ref($fragment)
    . '] should be a Bio::PrimarySeqI ' )
    unless blessed ($fragment) && $fragment->isa('Bio::PrimarySeqI');

  $self->throw( 'Can\'t concatenate sequences with different alphabets: '
    . 'recipient is '.$recipient->alphabet
    . ' and fragment is '. $fragment->alphabet )
    unless  $recipient->alphabet eq $fragment->alphabet;

  if ($insert_pos < 0 or $insert_pos > $recipient->length ){
    $self->throw("insertion position ($insert_pos) must be between 0 and "
      . 'recipient sequence length ('. $recipient->length .')');
  }

  if ($fragment->can('is_circular') && $fragment->is_circular){
    $self->throw('Can\'t insert circular fragments');
  }

  if ( !$recipient->seq ){
    $self->throw('Recipient has no sequence, can not insert into this object');
  }

  # construct raw sequence of the new molecule 
my $left_seq = $insert_pos > 0 ? $recipient->subseq( 1, $insert_pos ) : ''; my $mid_seq = $fragment->seq; my $right_seq = $insert_pos < $recipient->length ? $recipient->subseq( $insert_pos + 1, $recipient->length) : ''; my $seq_str = $left_seq . $mid_seq . $right_seq; # create the new seq object with the same class as the recipient
# or (if requested), make a clone of the existing object. In the
# latter case we need to remove sequence features from the cloned
# object instead of copying them
my $product; if ($opts_ref->{clone_obj}){ $product = $self->_new_seq_via_clone( $recipient, $seq_str ); } else { my @desc; push @desc, 'Inserted fragment: '.$fragment->desc if defined $fragment->desc; push @desc, 'Recipient: '.$recipient->desc if defined $recipient->desc; $product = $self->_new_seq_from_old( $recipient, { seq => $seq_str, display_id => $recipient->display_id, accession_number => $recipient->accession_number || '', alphabet => $recipient->alphabet, desc => join('; ', @desc), verbose => $recipient->verbose || $fragment->verbose, is_circular => $recipient->is_circular || 0, } ); } # if clone_obj
# move annotations from fragment to product
if ( $product->isa("Bio::AnnotatableI") && $fragment->isa("Bio::AnnotatableI") ) { foreach my $key ( $fragment->annotation->get_all_annotation_keys ) { foreach my $value ( $fragment->annotation->get_Annotations($key) ) { $product->annotation->add_Annotation( $key, $value ); } } } # move sequence features to product with adjusted coordinates
if ( $product->isa('Bio::SeqI') ) { # for the fragment, just shift the features to new position
if ( $fragment->isa('Bio::SeqI') ) { for my $feat ( $fragment->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust( $feat, $insert_pos ) ; $product->add_SeqFeature( $adjfeat ) if $adjfeat ; } } # for recipient, shift and modify features according to insertion.
if ( $recipient->isa('Bio::SeqI') ) { for my $feat ( $recipient->get_SeqFeatures ) { my $adjfeat = $self->_coord_adjust_insertion( $feat, $insert_pos, $fragment->length ); $product->add_SeqFeature($adjfeat) if $adjfeat; } } } # add a feature to annotate the insertion
my $insertion_feature = Bio::SeqFeature::Generic->new( -start => $insert_pos + 1, -end => $insert_pos + $fragment->length, -primary_tag => 'misc_feature', -tag => {note => 'inserted fragment'}, ); $product->add_SeqFeature( $insertion_feature ); return $product;
}
ligatedescriptionprevnextTop
sub ligate {
  my $self = shift;
  my ($recipient, $fragment, $left, $right, $flip, $clone_obj ) =  $self->_rearrange(
    [qw(RECIPIENT FRAGMENT LEFT RIGHT FLIP CLONE_OBJ )],@_);
  $self->throw("missing required parameter 'recipient'") unless $recipient;
  $self->throw("missing required parameter 'fragment'") unless $fragment;
  $self->throw("missing required parameter 'left'") unless defined $left;

  $right ||= $left + 1;

  $self->throw("Fragment must be a Bio::PrimarySeqI compliant object but it is a ".
    ref($fragment)) unless blessed($fragment) && $fragment->isa('Bio::PrimarySeqI');

  $fragment = $self->revcom_with_features($fragment) if $flip;

  my $opts_ref = {};
  $opts_ref->{clone_obj} = 1 if $clone_obj;

  # clone in two steps: first delete between the insertion sites,
# then insert the fragment. Step 1 is skipped if insert positions
# are adjacent (no deletion)
my ($product1, $product2) ; eval { if ($right == $left + 1){ $product1 = $recipient ; } else { $product1 = $self->delete($recipient, $left + 1, $right - 1, $opts_ref ) ; } }; $self->throw("Failed in step 1 (cut recipient): ".$@) if $@; eval { $product2 = $self->insert( $product1, $fragment, $left, $opts_ref ) }; $self->throw("Failed in step 2 (insert fragment): ".$@) if $@; return $product2;
}
_coord_adjust_deletiondescriptionprevnextTop
sub _coord_adjust_deletion {
  my ($self, $feat, $left, $right)=@_;

  $self->throw('object [$feat] '. 'of class ['. ref($feat)
    . '] should be a Bio::SeqFeatureI ')
    unless $feat->isa('Bio::SeqFeatureI');
  $self->throw('missing coordinates: need a left and a right position')
    unless defined $left && defined $right;

  if ($left > $right){
    if ($feat->can('is_circular') && $feat->is_circular){
      # todo handle circular molecules
$self->throw('can not yet handle deletions in circular molecules if deletion spans origin'); } else { $self->throw("left coordinate ($left) must be less than right ($right)" . " but it was greater"); } } my $deletion = Bio::Location::Simple->new( -start => $left, -end => $right, ); my $del_length = $right - $left + 1; my @adjsubfeat; for my $subfeat ($feat->get_SeqFeatures) { my $adjsubfeat = $self->_coord_adjust_deletion($subfeat, $left, $right); push @adjsubfeat, $adjsubfeat if $adjsubfeat; } my @loc; my $note; for ($feat->location->each_Location) { next if $deletion->contains( $_ ); # this location will be deleted;
my $strand = $_->strand; my $type = $_->location_type; my $start = $_->start; my $start_type = $_->can('start_pos_type') ? $_->start_pos_type : undef; my $end = $_->end; my $end_type = $_->can('end_pos_type') ? $_->end_pos_type : undef; my @newcoords=(); if ($_->start < $deletion->start && $_->end > $deletion->end){ # split the feature
@newcoords = ( [ $start, ($deletion->start - 1), $start_type, $end_type ], [ ($deletion->start ), $end - $del_length, $start_type, $end_type ] ); $note = $del_length . 'bp internal deletion between pos ' . ($deletion->start - 1) . ' and ' . $deletion->start; } elsif ($_->contains( $deletion->start )){ # truncate feature end
@newcoords = ([$start, ($deletion->start - 1), $start_type, $end_type ]); $note = ($end - $deletion->start + 1). 'bp deleted from feature '; if ($feat->strand){ $note .= $feat->strand == 1 ? "3' " : "5' "; } $note .= 'end' } elsif ($_->contains( $deletion->end )){ # truncate feature start and shift end
@newcoords = ([($deletion->start), $end - $del_length, $start_type, $end_type]); $note = ( $deletion->end - $start + 1) . 'bp deleted from feature '; if ($feat->strand){ $note .= $feat->strand == 1 ? "5' end" : "3' end"; } else { $note .= 'start'; } } elsif ($start >= $deletion->end){ # just shift entire location
@newcoords = ([$start - $del_length, $end - $del_length, $start_type, $end_type ]); } else { # not affected by deletion
@newcoords = ( [$start, $end, $start_type, $end_type ]); } # if we have no coordinates, we return nothing
# the feature is deleted
return unless @newcoords; my @subloc = $self->_location_objects_from_coordinate_list(\@ newcoords, $strand, $type ); # put together final location which could be a split now
push @loc, $self->_single_loc_object_from_collection( @subloc ); } # each location
# create new feature based on original one and move annotation across
my $newfeat=Bio::SeqFeature::Generic->new(-primary=>$feat->primary_tag); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation($key, $value); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value($key, $feat->get_tag_values($key)); } # If we have a note about the deleted bases, add it
if ($note){ $newfeat->add_tag_value('note',$note); } # set modified location(s) for the new feature and
# add its subfeatures if any
my $loc = $self->_single_loc_object_from_collection( @loc ); $loc ? $newfeat->location( $loc ) : return ; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat;
}
_coord_adjust_insertiondescriptionprevnextTop
sub _coord_adjust_insertion {
  my ($self, $feat, $insert_pos, $insert_len)=@_;

  $self->throw('object [$feat] '. 'of class ['. ref($feat)
    . '] should be a Bio::SeqFeatureI ')
    unless $feat->isa('Bio::SeqFeatureI');
  $self->throw('missing insert position') unless defined $insert_pos;
  $self->throw('missing insert length') unless defined $insert_len;

  my @adjsubfeat;
  for my $subfeat ($feat->get_SeqFeatures) {
    push @adjsubfeat, $self->_coord_adjust_insertion($subfeat, $insert_pos, $insert_len);
  }

  my @loc;
  my $note;
  for ($feat->location->each_Location) {
    # loose IN-BETWEEN features at the insertion site
if ($_->location_type eq 'IN-BETWEEN' && $_->start == $insert_pos ){ next; } my $strand = $_->strand; my $type = $_->location_type; my $start = $_->start; my $start_type = $_->can('start_pos_type') ? $_->start_pos_type : undef; my $end = $_->end; my $end_type = $_->can('end_pos_type') ? $_->end_pos_type : undef; my @newcoords=(); if ($start <= $insert_pos && $end > $insert_pos){ # split the feature
@newcoords = ( [ $start, $insert_pos, $start_type, $end_type ], [ ($insert_pos + 1 + $insert_len ), $end + $insert_len, $start_type, $end_type ] ); $note = $insert_len . 'bp internal insertion between pos ' . $insert_pos . ' and ' . ( $insert_pos + $insert_len + 1); } elsif ($start > $insert_pos){ # just shift entire location
@newcoords = ([$start + $insert_len, $end + $insert_len, $start_type, $end_type ]); } else { # not affected
@newcoords = ( [$start, $end, $start_type, $end_type ]); } # if we have deleted all coordinates, return nothing
# (possible if all locations are IN-BETWEEN)
return unless @newcoords; my @subloc = $self->_location_objects_from_coordinate_list(\@ newcoords, $strand, $type ); # put together final location which could be a split now
push @loc, $self->_single_loc_object_from_collection( @subloc ); } # each location
# create new feature based on original one and move annotation across
my $newfeat=Bio::SeqFeature::Generic->new(-primary=>$feat->primary_tag); foreach my $key ( $feat->annotation->get_all_annotation_keys() ) { foreach my $value ( $feat->annotation->get_Annotations($key) ) { $newfeat->annotation->add_Annotation($key, $value); } } foreach my $key ( $feat->get_all_tags() ) { $newfeat->add_tag_value($key, $feat->get_tag_values($key)); } # If we have a note about the inserted bases, add it
if ($note){ $newfeat->add_tag_value('note',$note); } # set modified location(s) for the new feature and
# add its subfeatures if any
my $loc = $self->_single_loc_object_from_collection( @loc ); $loc ? $newfeat->location( $loc ) : return ; $newfeat->add_SeqFeature($_) for @adjsubfeat; return $newfeat;
}
_single_loc_object_from_collectiondescriptionprevnextTop
sub _single_loc_object_from_collection {
  my ($self, @locs) = @_;
  my $loc;
  if (@locs > 1){
    $loc = Bio::Location::Split->new;
    $loc->add_sub_Location( @locs);
  } elsif (@locs == 1) {
    $loc = shift @locs;
  } 
  return $loc;
} # _single_loc_object_from_collection
}
_location_objects_from_coordinate_listdescriptionprevnextTop
sub _location_objects_from_coordinate_list {
  my $self = shift;
  my ($coords_ref, $strand, $type) = @_;
  $self->throw('expected 3 parameters but got '.@_) unless @_ == 3;
  $self->throw('first argument must be an ARRAY reference#') 
    unless ref($coords_ref) eq 'ARRAY';

  my @loc;
  foreach my $coords_set (@$coords_ref){
    my ($start, $end, $start_type, $end_type ) = @$coords_set;
    # taken from Bio::SeqUtils::_coord_adjust
unless ( $type eq 'IN-BETWEEN' ) { my $loc = Bio::Location::Fuzzy->new( -start => $start, -end => $end, -strand => $strand, -location_type => $type ); $loc->start_pos_type( $start_type ) if $start_type; $loc->end_pos_type( $end_type ) if $end_type; push @loc, $loc; } else { push @loc, Bio::Location::Simple->new( -start => $start, -end => $end, -strand => $strand, -location_type => $type ); } } # each coords_set
return @loc; } # _location_objects_from_coordinate_list
}
_new_seq_via_clonedescriptionprevnextTop
sub _new_seq_via_clone {
  my ($self, $in_seq_obj, $seq_str) = @_;
  my $out_seq_obj = $in_seq_obj->clone;
  $out_seq_obj->remove_SeqFeatures if $out_seq_obj->can('remove_SeqFeatures');
  if ( blessed $out_seq_obj->seq && $out_seq_obj->seq->isa('Bio::PrimarySeq')){
    $out_seq_obj->seq->seq( $seq_str );
  } else {
    $out_seq_obj->seq( $seq_str );
  }
  return $out_seq_obj;

} # _new_seq_via_clone
}
_new_seq_from_olddescriptionprevnextTop
sub _new_seq_from_old {
  my ($self, $in_seq_obj, $attr) = @_ ;
  $self->throw('attributes must be a hashref') if $attr && ref($attr) ne 'HASH';

  my $seqclass;
  if ( $in_seq_obj->can_call_new ) {
    $seqclass = ref($in_seq_obj);
  } else {
    $seqclass = 'Bio::Primaryseq';
    $self->_attempt_to_load_seq;
  }

  my $out_seq_obj = $seqclass->new(
    -seq              => $attr->{seq} || $in_seq_obj->seq,
    -display_id       => $attr->{display_id} || $in_seq_obj->display_id,
    -accession_number => $attr->{accession_number} || $in_seq_obj->accession_number || '',
    -alphabet         => $in_seq_obj->alphabet,
    -desc             => $attr->{desc} || $in_seq_obj->desc, 
    -verbose          => $attr->{verbose} || $in_seq_obj->verbose,
    -is_circular      => $attr->{is_circular} || $in_seq_obj->is_circular || 0,
  );
  # move the annotation across to the product
if ( $out_seq_obj->isa("Bio::AnnotatableI") && $in_seq_obj->isa("Bio::AnnotatableI") ) { foreach my $key ( $in_seq_obj->annotation->get_all_annotation_keys ) { foreach my $value ( $in_seq_obj->annotation->get_Annotations($key) ) { $out_seq_obj->annotation->add_Annotation( $key, $value ); } } } return $out_seq_obj; } # _new_seq_from_old
}
_coord_adjustdescriptionprevnextTop
sub _coord_adjust {
    my ($self, $feat, $add, $length)=@_;
    $self->throw('Object [$feat] '. 'of class ['. ref($feat).
                 '] should be a Bio::SeqFeatureI ')
        unless $feat->isa('Bio::SeqFeatureI');
    my @adjsubfeat;
    for my $subfeat ($feat->get_SeqFeatures) {
        push @adjsubfeat, $self->_coord_adjust($subfeat, $add, $length);
    }
    my @loc;
    for ($feat->location->each_Location) {
        my @coords=($_->start, $_->end);
        my $strand=$_->strand;
	my $type=$_->location_type;
        map s/[<>]?(-?\d+)/if ($add+$1<1) {'<1'} elsif (defined $length and $add+$1>$length) {">$length"} else {$add+$1}/ge, @coords;
        push @coords, $_->start_pos_type, $_->end_pos_type;
        $coords[2]='BEFORE' if substr($coords[0],0,1) eq '<';
        $coords[3]='AFTER' if substr($coords[1],0,1) eq '>';
        push @loc, $self->_location_objects_from_coordinate_list(
          [\@coords], $strand, $type
        );
    }
    my $newfeat=Bio::SeqFeature::Generic->new(-primary=>$feat->primary_tag);
    foreach my $key ( $feat->annotation->get_all_annotation_keys() ) {
	foreach my $value ( $feat->annotation->get_Annotations($key) ) {
	    $newfeat->annotation->add_Annotation($key, $value);
	}
    }
    foreach my $key ( $feat->get_all_tags() ) {
	    $newfeat->add_tag_value($key, $feat->get_tag_values($key));
    }
    my $loc = $self->_single_loc_object_from_collection( @loc );
    $loc ? $newfeat->location( $loc ) : return ;
    $newfeat->add_SeqFeature($_) for @adjsubfeat;
    return $newfeat;
}
revcom_with_featuresdescriptionprevnextTop
sub revcom_with_features {
    my ($self,$seq) = @_;
    $self->throw('Object [$seq] '. 'of class ['. ref($seq).
                 '] should be a Bio::SeqI ')
    unless $seq->isa('Bio::SeqI');
    my $revcom=$seq->revcom;

    #move annotations
foreach my $key ( $seq->annotation->get_all_annotation_keys() ) { foreach my $value ( $seq->annotation->get_Annotations($key) ) { $revcom->annotation->add_Annotation($key, $value); } } #move features
for (map {$self->_feature_revcom($_, $seq->length)} reverse $seq->get_SeqFeatures) { $revcom->add_SeqFeature($_); } return $revcom;
}
_feature_revcomdescriptionprevnextTop
sub _feature_revcom {
    my ($self, $feat, $length)=@_;
    $self->throw('Object [$feat] '. 'of class ['. ref($feat).
                 '] should be a Bio::SeqFeatureI ')
        unless $feat->isa('Bio::SeqFeatureI');
    my @adjsubfeat;
    for my $subfeat ($feat->get_SeqFeatures) {
        push @adjsubfeat, $self->_feature_revcom($subfeat, $length);
    }
    my @loc;
    for ($feat->location->each_Location) {
	my $type=$_->location_type;
        my $strand;
	if ($_->strand==-1) {$strand=1}
	elsif ($_->strand==1) {$strand=-1}
	else {$strand=$_->strand}
	my $newend=$self->_coord_revcom($_->start,
					$_->start_pos_type,
					$length);
	my $newstart=$self->_coord_revcom($_->end,
					  $_->end_pos_type,
					  $length);
        my $newstart_type=$_->end_pos_type;
        $newstart_type='BEFORE' if $_->end_pos_type eq 'AFTER';
        $newstart_type='AFTER' if $_->end_pos_type eq 'BEFORE';
        my $newend_type=$_->start_pos_type;
        $newend_type='BEFORE' if $_->start_pos_type eq 'AFTER';
        $newend_type='AFTER' if $_->start_pos_type eq 'BEFORE';
        push @loc, $self->_location_objects_from_coordinate_list(
          [[$newstart, $newend, $newstart_type, $newend_type]], $strand, $type
        );
    }
    my $newfeat=Bio::SeqFeature::Generic->new(-primary=>$feat->primary_tag);
    foreach my $key ( $feat->annotation->get_all_annotation_keys() ) {
	foreach my $value ( $feat->annotation->get_Annotations($key) ) {
	    $newfeat->annotation->add_Annotation($key, $value);
	}
    }
    foreach my $key ( $feat->get_all_tags() ) {
	    $newfeat->add_tag_value($key, $feat->get_tag_values($key));
    }
  
    my $loc = $self->_single_loc_object_from_collection( @loc );
    $loc ? $newfeat->location( $loc ) : return ;

    $newfeat->add_SeqFeature($_) for @adjsubfeat;
    return $newfeat;
}
_coord_revcomdescriptionprevnextTop
sub _coord_revcom {
    my ($self, $coord, $type, $length)=@_;
    if ($type eq 'BETWEEN' or $type eq 'WITHIN') {
	$coord=~s/(\d+)(\D*)(\d+)/$length+1-$3.$2.$length+1-$1/ge;
} else { $coord=~s/(\d+)/$length+1-$1/ge;
$coord=~tr/<>/></;
$coord='>'.$coord if $type eq 'BEFORE' and substr($coord,0,1) ne '>'; $coord='<'.$coord if $type eq 'AFTER' and substr($coord,0,1) ne '<'; } return $coord;
}
evolvedescriptionprevnextTop
sub evolve {
    my ($self, $seq, $sim, $rate) = @_;
    $rate ||= 1;

    $self->throw('Object [$seq] '. 'of class ['. ref($seq).
                     '] should be a Bio::PrimarySeqI ')
            unless $seq->isa('Bio::PrimarySeqI');

    $self->throw("[$sim] ". ' should be a positive integer or float under 100')
            unless $sim =~ /^[+\d.]+$/ and $sim <= 100;

    $self->warn("Nucleotide sequences are 25% similar by chance.
        Do you really want to set similarity to [$sim]%?\n")
            unless $sim >25 ;

    $self->throw('Only nucleotide sequences are supported')
            if $seq->alphabet eq 'protein';


    # arrays of possible changes have transitions as first items
my %changes; $changes{'a'} = ['t', 'c', 'g']; $changes{'t'} = ['a', 'c', 'g']; $changes{'c'} = ['g', 'a', 't']; $changes{'g'} = ['c', 'a', 't']; # given the desired rate, find out where cut off points need to be
# when random numbers are generated from 0 to 100
# we are ignoring identical mutations (e.g. A->A) to speed things up
my $bin_size = 100/($rate + 2);
my $transition = 100 - (2*$bin_size); my $first_transversion = $transition + $bin_size; # unify the look of sequence strings
my $string = lc $seq->seq; # lower case
$string =~ s/u/t/; # simplyfy our life; modules should deal with the change anyway
# store the original sequence string
my $oristring = $string; my $length = $seq->length; while (1) { # find the location in the string to change
my $loc = int (rand $length) + 1; # nucleotide to change
my $oldnuc = substr $string, $loc-1, 1; my $newnuc; # nucleotide it is changed to
my $choose = rand(100); if ($choose < $transition ) { $newnuc = $changes{$oldnuc}[0]; } elsif ($choose < $first_transversion ) { $newnuc = $changes{$oldnuc}[1]; } else { $newnuc = $changes{$oldnuc}[2]; } # do the change
substr $string, $loc-1, 1 , $newnuc; $self->debug("$loc$oldnuc>$newnuc\n"); # stop evolving if the limit has been reached
last if $self->_get_similarity($oristring, $string) <= $sim; } return new Bio::PrimarySeq(-id => $seq->id. "-$sim", -description => $seq->description, -seq => $string )
}
_get_similaritydescriptionprevnextTop
sub _get_similarity {
    my ($self, $oriseq, $seq) = @_;

    my $len = length($oriseq);
    my $c;

    for (my $i = 0; $i< $len; $i++ ) {
        $c++ if substr($oriseq, $i, 1) eq substr($seq, $i, 1);
    }
    return 100 * $c/$len;
} 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Roy R. Chaudhuri - roy.chaudhuri at gmail.com
Frank Schwach - frank.schwach@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _