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.\" ========================================================================
.\"
.IX Title "Bio::SeqUtils 3pm"
.TH Bio::SeqUtils 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::SeqUtils \- Additional methods for PrimarySeq objects
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 6
\&    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 => \*(Aqc\*(Aq,
\&                                                      \-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 positions 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 sequence (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
\&    );
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.PP
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.
.PP
The first two methods, \fBseq3()\fR and \fBseq3in()\fR, give out or read in protein
sequences coded in three letter \s-1IUPAC\s0 amino acid codes.
.PP
The next two methods, \fBtranslate_3frames()\fR and \fBtranslate_6frames()\fR, wrap
around the standard translate method to give back an array of three
forward or all six frame translations.
.PP
The \fBmutate()\fR method mutates the sequence string with a mutation
description object.
.PP
The \fBcat()\fR 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.
.PP
The \fBrevcom_with_features()\fR and \fBtrunc_with_features()\fR methods are similar
to the \fBrevcom()\fR and \fBtrunc()\fR methods from Bio::Seq, but also adjust any
features associated with the sequence as appropriate.
.PP
There are also methods that simulate molecular cloning with rich
sequence objects. 
The \fBdelete()\fR 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.
.PP
The \fBinsert()\fR 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.
.PP
The \fBligate()\fR 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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Heikki Lehvaslaiho"
.IX Header "AUTHOR - Heikki Lehvaslaiho"
Email:  heikki-at-bioperl-dot-org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Roy R. Chaudhuri \- roy.chaudhuri at gmail.com
Frank Schwach \- frank.schwach@sanger.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "seq3"
.IX Subsection "seq3"
.Vb 8
\& 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
\&           \*(Aqprotein\*(Aq. Output follows the IUPAC standard plus \*(AqTer\*(Aq for
\&           terminator. Any unknown character, including the default
\&           unknown character \*(AqX\*(Aq, is changed into \*(AqXaa\*(Aq. A noncoded
\&           aminoacid selenocystein is recognized (Sec, U).
\&
\& Returns : A scalar
\& Args    : character used for stop in the protein sequence optional,
\&           defaults to \*(Aq*\*(Aq string used to separate the output amino
\&           acid codes, optional, defaults to \*(Aq\*(Aq
.Ve
.SS "seq3in"
.IX Subsection "seq3in"
.Vb 7
\& Title   : seq3in
\& Usage   : $seq = Bio::SeqUtils\->seq3in($seq, \*(AqMetGlyTer\*(Aq)
\& 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 \*(AqXaa\*(Aq, is
\&           converted into \*(AqX\*(Aq.
\&
\& Returns : Bio::PrimarySeq object
\& Args    : sequence string
\&           optional character to be used for stop in the protein sequence,
\&              defaults to \*(Aq*\*(Aq
\&           optional character to be used for unknown in the protein sequence,
\&              defaults to \*(AqX\*(Aq
.Ve
.SS "translate_3frames"
.IX Subsection "translate_3frames"
.Vb 7
\& Title   : translate_3frames
\& Usage   : @prots = Bio::SeqUtils\->translate_3frames($seq)
\& Function: Translate a nucleotide sequence in three forward frames.
\&           The IDs of the sequences are appended with \*(Aq\-0F\*(Aq, \*(Aq\-1F\*(Aq, \*(Aq\-2F\*(Aq.
\& Returns : An array of seq objects
\& Args    : sequence object
\&           same arguments as to Bio::PrimarySeqI::translate
.Ve
.SS "translate_6frames"
.IX Subsection "translate_6frames"
.Vb 8
\& Title   : translate_6frames
\& Usage   : @prots = Bio::SeqUtils\->translate_6frames($seq)
\& Function: translate a nucleotide sequence in all six frames
\&           The IDs of the sequences are appended with \*(Aq\-0F\*(Aq, \*(Aq\-1F\*(Aq, \*(Aq\-2F\*(Aq,
\&           \*(Aq\-0R\*(Aq, \*(Aq\-1R\*(Aq, \*(Aq\-2R\*(Aq.
\& Returns : An array of seq objects
\& Args    : sequence object
\&           same arguments as to Bio::PrimarySeqI::translate
.Ve
.SS "valid_aa"
.IX Subsection "valid_aa"
.Vb 9
\& 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 [\*(AqB\*(Aq, \*(AqZ\*(Aq, \*(AqX\*(Aq, \*(Aq*\*(Aq].
\& Returns : array of all the valid amino acid codes
\& Args    : [optional] $code => [0 \-> return list of 1 letter aa codes,
\&                                1 \-> return list of 3 letter aa codes,
\&                                2 \-> return associative array of both ]
.Ve
.SS "mutate"
.IX Subsection "mutate"
.Vb 3
\& Title   : mutate
\& Usage   : Bio::SeqUtils\->mutate($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
.Ve
.PP
See Bio::LiveSeq::Mutation.
.SS "cat"
.IX Subsection "cat"
.Vb 9
\&  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
.Ve
.PP
Note that annotations have no sequence locations. If you concatenate
sequences with the same annotations they will all be added.
.SS "trunc_with_features"
.IX Subsection "trunc_with_features"
.Vb 7
\& 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)
.Ve
.SS "delete"
.IX Subsection "delete"
.Vb 10
\& 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\*(Aqs class 
\&
\& Returns : a new Bio::Seq object
.Ve
.SS "insert"
.IX Subsection "insert"
.Vb 10
\& 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\*(Aqs class 
\& Returns : a new Bio::Seq object
.Ve
.SS "ligate"
.IX Subsection "ligate"
.Vb 10
\& 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 
\&           L</"delete"> amd L</"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
.Ve
.SS "_coord_adjust_deletion"
.IX Subsection "_coord_adjust_deletion"
.Vb 10
\& 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
.Ve
.SS "_coord_adjust_insertion"
.IX Subsection "_coord_adjust_insertion"
.Vb 10
\& 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
.Ve
.SS "_single_loc_object_from_collection"
.IX Subsection "_single_loc_object_from_collection"
.Vb 7
\& 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
.Ve
.SS "_location_objects_from_coordinate_list"
.IX Subsection "_location_objects_from_coordinate_list"
.Vb 10
\& 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( 
\&             \e@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 (\*(AqBEFORE\*(Aq, \*(AqAFTER\*(Aq, \*(AqEXACT\*(Aq,\*(AqWITHIN\*(Aq, \*(AqBETWEEN\*(Aq)
\&           strand (all locations must be on same strand)
\&           location\-type (EXACT, IN\-BETWEEN etc)
\& Returns : list of Bio::Location objects
.Ve
.SS "_new_seq_via_clone"
.IX Subsection "_new_seq_via_clone"
.Vb 6
\& 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
.Ve
.SS "_new_seq_from_old"
.IX Subsection "_new_seq_from_old"
.Vb 7
\& 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 => \*(Aqsome_ID\*(Aq});
\& Args    : old sequence object
\&           hashref of attributes for the new sequence (sequence string etc.)
\& Returns : a new Bio::Seq object
.Ve
.SS "_coord_adjust"
.IX Subsection "_coord_adjust"
.Vb 6
\&  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
.Ve
.SS "revcom_with_features"
.IX Subsection "revcom_with_features"
.Vb 6
\& 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
.Ve
.SS "_feature_revcom"
.IX Subsection "_feature_revcom"
.Vb 5
\&  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
.Ve
.SS "evolve"
.IX Subsection "evolve"
.Vb 10
\&  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)
.Ve
.PP
Set the verbosity of the Bio::SeqUtils object to positive integer to
see the mutations as they happen.
.PP
This method works only on nucleotide sequences. It prints a warning if
you set the target similarity to be less than 25%.
.PP
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.