Bio::Variation::VariantI - Sequence Change SeqFeature abstract class

  #get Bio::Variant::VariantI somehow
  print $var->restriction_changes, "\n";
  foreach $allele ($var->each_Allele) {
      #work on Bio::Variation::Allele objects
  }

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://redmine.open-bio.org/projects/bioperl/

 Title   : id
 Usage   : $obj->id
 Function:

           Read only method. Returns the id of the variation object.
           The id is the id of the first DBLink object attached to this object.

 Example :
 Returns : scalar
 Args    : none

 Title   : add_Allele
 Usage   : $self->add_Allele($allele)
 Function: 

	    Adds one Bio::Variation::Allele into the list of alleles.
            Note that the method forces the convention that nucleotide
            sequence is in lower case and amino acds are in upper
            case.

 Example : 
 Returns : 1 when succeeds, 0 for failure.
 Args    : Allele object

 Title   : alleles
 Usage   : $obj->each_Allele();
 Function: 

	     Returns a list of Bio::Variation::Allele objects

 Example : 
 Returns : list of Alleles
 Args    : none

 Title   : isMutation
 Usage   : print join('/', $obj->each_Allele) if not $obj->isMutation;
 Function:

           Returns or sets the boolean value indicating that the
           variant descibed is a canonical mutation with two alleles
           assinged to be the original (wild type) allele and mutated
           allele, respectively. If this value is not set, it is
           assumed that the Variant descibes polymorphisms.

 Returns : a boolean

 Title   : allele_ori
 Usage   : $obj->allele_ori();
 Function: 

            Links to and returns the Bio::Variation::Allele object.
            If value is not set, returns false. All other Alleles are
            compared to this.

            Amino acid sequences are stored in upper case characters,
            others in lower case.

 Example : 
 Returns : string
 Args    : string

 Title   : allele_mut
 Usage   : $obj->allele_mut();
 Function: 

             Links to and returns the Bio::Variation::Allele
             object.  Sets and returns the mutated allele sequence.
             If value is not set, returns false.

             Amino acid sequences are stored in upper case characters,
             others in lower case.

 Example : 
 Returns : string
 Args    : string

 Title   : length
 Usage   : $obj->length();
 Function: 

            Sets and returns the length of the affected original
            allele sequence.  If value is not set, returns false == 0.

            Value 0 means that the variant position is before the
            start=end sequence position. (Value 1 would denote a point
            mutation). This follows the convension to report an
            insertion (2insT) in equivalent way to a corresponding
            deletion (2delT) (Think about indel polymorpism ATC <=> AC
            where the origianal state is not known ).

 Example : 
 Returns : string
 Args    : string

 Title   : upStreamSeq
 Usage   : $obj->upStreamSeq();
 Function: 

            Sets and returns upstream flanking sequence string.  If
            value is not set, returns false. The sequence should be
            >=25 characters long, if possible.

 Example : 
 Returns : string or false
 Args    : string

 Title   : dnStreamSeq
 Usage   : $obj->dnStreamSeq();
 Function: 

            Sets and returns dnstream flanking sequence string.  If
            value is not set, returns false. The sequence should be
            >=25 characters long, if possible.

 Example : 
 Returns : string or false
 Args    : string

 Title   : label
 Usage   : $obj->label();
 Function: 

            Sets and returns mutation event label(s).  If value is not
            set, or no argument is given returns false.  Each
            instantiable class needs to implement this method. Valid
            values are listed in 'Mutation event controlled vocabulary' in
            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

 Example : 
 Returns : string
 Args    : string

 Title   : status
 Usage   : $obj->status()
 Function: 

           Returns the status of the sequence change object.
           Valid values are: 'suspected' and 'proven'

 Example : $obj->status('proven');
 Returns : scalar
 Args    : valid string (optional, for setting)

 Title   : proof
 Usage   : $obj->proof()
 Function: 

           Returns the proof of the sequence change object.
           Valid values are: 'computed' and 'experimental'.

 Example : $obj->proof('computed');
 Returns : scalar
 Args    : valid string (optional, for setting)

 Title   : region
 Usage   : $obj->region();
 Function: 

            Sets and returns the name of the sequence region type or
            protein domain at this location.  If value is not set,
            returns false.

 Example : 
 Returns : string
 Args    : string

 Title   : region_value
 Usage   : $obj->region_value();
 Function: 

            Sets and returns the name of the sequence region_value or
            protein domain at this location.  If value is not set,
            returns false.

 Example : 
 Returns : string
 Args    : string

 Title   : region_dist
 Usage   : $obj->region_dist();
 Function: 

            Sets and returns the distance tot the closest region
            (i.e. intro/exon or domain) boundary. If distance is not
            set, returns false.

 Example : 
 Returns : integer
 Args    : integer

 Title   : numbering
 Usage   : $obj->numbering()
 Function: 

           Returns the numbering chema used locating sequnce features.
           Valid values are: 'entry' and 'coding'

 Example : $obj->numbering('coding');
 Returns : scalar
 Args    : valid string (optional, for setting)

 Title   : mut_number
 Usage   : $num = $obj->mut_number;
         : $num = $obj->mut_number($number);
 Function: 

           Returns or sets the number identifying the order in which the
           mutation has been issued. Numbers shouldstart from 1.
           If the number has never been set, the method will return ''

           If you want the output from IO modules look nice and, for
           multivariant/allele variations, make sense you better set
           this attribute.

 Returns : an integer

 Title   : SeqDiff
 Usage   : $mutobj = $obj->SeqDiff;
         : $mutobj = $obj->SeqDiff($objref);
 Function: 

           Returns or sets the link-reference to the umbrella
           Bio::Variation::SeqDiff object.  If there is no link,
           it will return undef

           Note: Adding a variant into a SeqDiff object will
           automatically set this value.

 Returns : an obj_ref or undef

 Title   : add_DBLink
 Usage   : $self->add_DBLink($ref)
 Function: adds a link object
 Example :
 Returns : 
 Args    :

 Title   : each_DBLink
 Usage   : foreach $ref ( $self->each_DBlink() )
 Function: gets an array of DBlink of objects
 Example :
 Returns : 
 Args    :

 Title   : restriction_changes
 Usage   : $obj->restriction_changes();
 Function: 

            Returns a string containing a list of restriction
            enzyme changes of form +EcoRI, separated by
            commas. Strings need to be valid restriction enzyme names
            as stored in REBASE. allele_ori and allele_mut need to be assigned.

 Example : 
 Returns : string
 Args    : string

#
# BioPerl module for Bio::Variation::VariantI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

# Let the code begin...


package Bio::Variation::VariantI;
use strict;
# Object preamble - inheritance

use base qw(Bio::Root::Root Bio::SeqFeature::Generic Bio::DBLinkContainerI);

sub id {
   my ($self) = @_;
   my @ids = $self->each_DBLink;
   my $id = $ids[0] if scalar @ids > 0;
   return $id->database. "::". $id->primary_id if $id;
}

sub add_Allele {
  my ($self,$value) = @_;
  if (defined $value) {
      if( ! $value->isa('Bio::Variation::Allele') ) {
	  my $com = ref $value;
	  $self->throw("Is not a Allele object but a  [$com]");
	  return 0;
      } else {
	  if ( $self->isa('Bio::Variation::AAChange') ) {
	      $value->seq( uc $value->seq) if $value->seq;
	  } else {
	      $value->seq( lc $value->seq) if $value->seq;
	  } 
	  push(@{$self->{'alleles'}},$value); 
	  $self->allele_mut($value); #????
	  return 1;
      }
  } else {
      return 0;
  }
}

sub each_Allele{
   my ($self,@args) = @_;
   return @{$self->{'alleles'}};
}

sub isMutation {
    my ($self,$value) = @_;
    if (defined $value) {
        if ($value ) {
            $self->{'isMutation'} = 1;
        } else {
            $self->{'isMutation'} = 0;
        }
    }
    return $self->{'isMutation'};
} 

sub allele_ori {
   my ($self,$value) = @_;
   if( defined $value) {
       if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) {
	   $self->throw("Value is not Bio::Variation::Allele but [$value]");
       } else {
	   if ( $self->isa('Bio::Variation::AAChange') ) {
	       $value->seq( uc $value->seq) if $value->seq;
	   } else {
	       $value->seq( lc $value->seq) if $value->seq;
	   } 
	   $self->{'allele_ori'} = $value;
       }
   }
   return $self->{'allele_ori'};
}

sub allele_mut {
   my ($self,$value) = @_;
   if( defined $value) {
       if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) {
	   $self->throw("Value is not Bio::Variation::Allele but [$value]");
       } else {
	   if ( $self->isa('Bio::Variation::AAChange') ) {
	       $value->seq( uc $value->seq) if $value->seq;
	   } else {
	       $value->seq( lc $value->seq) if $value->seq;
	   } 
	   $self->{'allele_mut'} = $value;
       }
   }
   return $self->{'allele_mut'};
}

sub length {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'length'} = $value;
  }
   if ( ! exists $self->{'length'} ) {
       return 0;
   } 
   return $self->{'length'};
}

sub upStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'upstreamseq'} = $value;
    }
   return $self->{'upstreamseq'};
}

sub dnStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'dnstreamseq'} = $value;
    }
    return $self->{'dnstreamseq'};
    
}

sub label {
    my ($self,$value) = @_;
    $self->throw_not_implemented();
}

sub status {
   my ($self,$value) = @_;
   my %status = (suspected => 1,
		 proven => 1
		 );

   if( defined $value) {
       $value = lc $value;
       if ($status{$value}) {
	   $self->{'status'} = $value;
       } 
       else {
	   $self->throw("$value is not valid status value!");
       }
    }
   if( ! exists $self->{'status'} ) {
       return "$self";
   }
   return $self->{'status'};
}

sub proof {
    my ($self,$value) = @_;
    my %proof = (computed => 1,
		 experimental => 1
		 );

    if( defined $value) {
	$value = lc $value;
	if ($proof{$value}) {
	    $self->{'proof'} = $value;
	} else {
	    $self->throw("$value is not valid proof value!");
	}
    }
    return $self->{'proof'};
}

sub region {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'region'} = $value;
    }
    return $self->{'region'};
}

sub region_value {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'region_value'} = $value;
    }
    return $self->{'region_value'};
}

sub region_dist {
    my ($self,$value) = @_;
    if( defined $value) {
       if (  not $value =~ /^[+-]?\d+$/ ) {
	   $self->throw("[$value] for region_dist has to be an integer\n");
        } else {
	    $self->{'region_dist'} = $value;
        }
    }
    return $self->{'region_dist'};
}

sub numbering {
   my ($self,$value) = @_;
   my %numbering = (entry => 1,
		    coding => 1
		    );

   if( defined $value) {
       $value = lc $value;
       if ($numbering{$value}) {
	   $self->{'numbering'} = $value;
       } 
       else {
	   $self->throw("'$value' is not a valid for numbering!");
       }
    }
   if( ! exists $self->{'numbering'} ) {
       return "$self";
   }
   return $self->{'numbering'};
}

sub mut_number {
    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'mut_number'} = $value;
    }
    unless (exists $self->{'mut_number'}) {
	return ('');
    } else {
	return $self->{'mut_number'};
    }
}       

sub SeqDiff {
    my ($self,$value) = @_;
    if (defined $value) {
	if( ! $value->isa('Bio::Variation::SeqDiff') ) {
	    $self->throw("Is not a Bio::Variation::SeqDiff object but a [$value]");
	    return;
	}
	else {
	    $self->{'seqDiff'} = $value;
	}
    }
    unless (exists $self->{'seqDiff'}) {
	return;
    } else {
	return $self->{'seqDiff'};
    }
}

sub add_DBLink{
   my ($self,$com) = @_;
   if( $com && ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   $com && push(@{$self->{'link'}},$com);
}

sub each_DBLink{
   my ($self) = @_;
   
   return @{$self->{'link'}}; 
}

sub restriction_changes { 
    my ($self) = @_;

    if (not $self->{'re_changes'}) { 
	my %re = &_enzymes;
	
	# complain if used on AA data
	if ($self->isa('Bio::Variation::AAChange')) {
	    $self->throw('Restriction enzymes do not bite polypeptides!');
	}
	
	#sanity checks
	$self->warn('Upstream sequence is empty!')
	    if $self->upStreamSeq eq '';
	$self->warn('Downstream sequence is empty!')
	    if $self->dnStreamSeq eq '';
#	 $self->warn('Original allele sequence is empty!')
#	     if $self->allele_ori eq '';
#	 $self->warn('Mutated allele sequence is empty!')
#	     if $self->allele_mut eq '';
	
	#reuse the non empty DNA level list at RNA level if the flanks are identical
	#Hint: Check DNAMutation object first
	if ($self->isa('Bio::Variation::RNAChange') and  $self->DNAMutation and
	    $self->upStreamSeq eq $self->DNAMutation->upStreamSeq  and 
	    $self->dnStreamSeq eq $self->DNAMutation->dnStreamSeq and
	    $self->DNAMutation->restriction_changes ne '' ) {
	    $self->{'re_changes'} = $self->DNAMutation->restriction_changes;
	} else {
	    
	    #maximum length of a type II restriction site in the current REBASE
	    my ($le_dn) = 15; 
	    my ($le_up) = $le_dn;

	    #reduce the flank lengths if the desired length is not available
	    $le_dn = CORE::length ($self->dnStreamSeq) if $le_dn > CORE::length ($self->dnStreamSeq);
	    $le_up = CORE::length ($self->upStreamSeq) if $le_up > CORE::length ($self->upStreamSeq);

	    #Build sequence strings to compare
	    my ($oriseq, $mutseq);    
	    $oriseq  = $mutseq = substr($self->upStreamSeq, -$le_up, $le_up);
	    $oriseq .= $self->allele_ori->seq if $self->allele_ori->seq;
	    $mutseq .= $self->allele_mut->seq if $self->allele_mut->seq;
	    $oriseq .= substr($self->dnStreamSeq, 0, $le_dn);
	    $mutseq .= substr($self->dnStreamSeq, 0, $le_dn);
	    
	    # ... and their reverse complements
	    my $oriseq_rev = _revcompl ($oriseq);
	    my $mutseq_rev = _revcompl ($mutseq);

	    # collect results into a string
	    my $rec = '';
	    foreach my $enz (sort keys (%re)) {
		my $site = $re{$enz};
		my @ori = ($oriseq=~ /$site/g);
		my @mut = ($mutseq=~ /$site/g);
		my @ori_r = ($oriseq_rev =~ /$site/g);
		my @mut_r = ($mutseq_rev =~ /$site/g);
		
		$rec .= '+'. $enz. ", " 
		    if (scalar @ori < scalar @mut) or (scalar @ori_r < scalar @mut_r);
		$rec .= '-'. $enz. ", " 		    
		    if (scalar @ori > scalar @mut) or (scalar @ori_r > scalar @mut_r);
		
	    }
	    $rec = substr($rec, 0, CORE::length($rec) - 2) if $rec ne '';
	    $self->{'re_changes'} =  $rec;
	}
    }
    return $self->{'re_changes'}
}


sub _revcompl { 
    # side effect: lower case letters
    my ($seq) = shift;

    $seq = lc $seq;
    $seq =~ tr/acgtrymkswhbvdnx/tgcayrkmswdvbhnx/;
    return CORE::reverse $seq;
}


sub _enzymes {
 #REBASE version 005   type2.005
 my %enzymes =  (
         'AarI' => 'cacctgc',
         'AatII' => 'gacgtc',
         'AccI' => 'gt[ac][gt]ac',
         'AceIII' => 'cagctc',
         'AciI' => 'ccgc',
         'AclI' => 'aacgtt',
         'AcyI' => 'g[ag]cg[ct]c',
         'AflII' => 'cttaag',
         'AflIII' => 'ac[ag][ct]gt',
         'AgeI' => 'accggt',
         'AhaIII' => 'tttaaa',
         'AloI' => 'gaac[acgt][acgt][acgt][acgt][acgt][acgt]tcc',
         'AluI' => 'agct',
         'AlwNI' => 'cag[acgt][acgt][acgt]ctg',
         'ApaBI' => 'gca[acgt][acgt][acgt][acgt][acgt]tgc',
         'ApaI' => 'gggccc',
         'ApaLI' => 'gtgcac',
         'ApoI' => '[ag]aatt[ct]',
         'AscI' => 'ggcgcgcc',
         'AsuI' => 'gg[acgt]cc',
         'AsuII' => 'ttcgaa',
         'AvaI' => 'c[ct]cg[ag]g',
         'AvaII' => 'gg[at]cc',
         'AvaIII' => 'atgcat',
         'AvrII' => 'cctagg',
         'BaeI' => 'ac[acgt][acgt][acgt][acgt]gta[ct]c',
         'BalI' => 'tggcca',
         'BamHI' => 'ggatcc',
         'BbvCI' => 'cctcagc',
         'BbvI' => 'gcagc',
         'BbvII' => 'gaagac',
         'BccI' => 'ccatc',
         'Bce83I' => 'cttgag',
         'BcefI' => 'acggc',
         'BcgI' => 'cga[acgt][acgt][acgt][acgt][acgt][acgt]tgc',
         'BciVI' => 'gtatcc',
         'BclI' => 'tgatca',
         'BetI' => '[at]ccgg[at]',
         'BfiI' => 'actggg',
         'BglI' => 'gcc[acgt][acgt][acgt][acgt][acgt]ggc',
         'BglII' => 'agatct',
         'BinI' => 'ggatc',
         'BmgI' => 'g[gt]gccc',
         'BplI' => 'gag[acgt][acgt][acgt][acgt][acgt]ctc',
         'Bpu10I' => 'cct[acgt]agc',
         'BsaAI' => '[ct]acgt[ag]',
         'BsaBI' => 'gat[acgt][acgt][acgt][acgt]atc',
         'BsaXI' => 'ac[acgt][acgt][acgt][acgt][acgt]ctcc',
         'BsbI' => 'caacac',
         'BscGI' => 'cccgt',
         'BseMII' => 'ctcag',
         'BsePI' => 'gcgcgc',
         'BseRI' => 'gaggag',
         'BseSI' => 'g[gt]gc[ac]c',
         'BsgI' => 'gtgcag',
         'BsiI' => 'cacgag',
         'BsiYI' => 'cc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gg',
         'BsmAI' => 'gtctc',
         'BsmI' => 'gaatgc',
         'Bsp1407I' => 'tgtaca',
         'Bsp24I' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]tgg',
         'BspGI' => 'ctggac',
         'BspHI' => 'tcatga',
         'BspLU11I' => 'acatgt',
         'BspMI' => 'acctgc',
         'BspMII' => 'tccgga',
         'BsrBI' => 'ccgctc',
         'BsrDI' => 'gcaatg',
         'BsrI' => 'actgg',
         'BstEII' => 'ggt[acgt]acc',
         'BstXI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]tgg',
         'BtrI' => 'cacgtc',
         'BtsI' => 'gcagtg',
         'Cac8I' => 'gc[acgt][acgt]gc',
         'CauII' => 'cc[cg]gg',
         'Cfr10I' => '[ag]ccgg[ct]',
         'CfrI' => '[ct]ggcc[ag]',
         'CjeI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]gt',
         'CjePI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt]tc',
         'ClaI' => 'atcgat',
         'CviJI' => '[ag]gc[ct]',
         'CviRI' => 'tgca',
         'DdeI' => 'ct[acgt]ag',
         'DpnI' => 'gatc',
         'DraII' => '[ag]gg[acgt]cc[ct]',
         'DraIII' => 'cac[acgt][acgt][acgt]gtg',
         'DrdI' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]gtc',
         'DrdII' => 'gaacca',
         'DsaI' => 'cc[ag][ct]gg',
         'Eam1105I' => 'gac[acgt][acgt][acgt][acgt][acgt]gtc',
         'EciI' => 'ggcgga',
         'Eco31I' => 'ggtctc',
         'Eco47III' => 'agcgct',
         'Eco57I' => 'ctgaag',
         'EcoNI' => 'cct[acgt][acgt][acgt][acgt][acgt]agg',
         'EcoRI' => 'gaattc',
         'EcoRII' => 'cc[at]gg',
         'EcoRV' => 'gatatc',
         'Esp3I' => 'cgtctc',
         'EspI' => 'gct[acgt]agc',
         'FauI' => 'cccgc',
         'FinI' => 'gggac',
         'Fnu4HI' => 'gc[acgt]gc',
         'FnuDII' => 'cgcg',
         'FokI' => 'ggatg',
         'FseI' => 'ggccggcc',
         'GdiII' => 'cggcc[ag]',
         'GsuI' => 'ctggag',
         'HaeI' => '[at]ggcc[at]',
         'HaeII' => '[ag]gcgc[ct]',
         'HaeIII' => 'ggcc',
         'HaeIV' => 'ga[ct][acgt][acgt][acgt][acgt][acgt][ag]tc',
         'HgaI' => 'gacgc',
         'HgiAI' => 'g[at]gc[at]c',
         'HgiCI' => 'gg[ct][ag]cc',
         'HgiEII' => 'acc[acgt][acgt][acgt][acgt][acgt][acgt]ggt',
         'HgiJII' => 'g[ag]gc[ct]c',
         'HhaI' => 'gcgc',
         'Hin4I' => 'ga[cgt][acgt][acgt][acgt][acgt][acgt][acg]tc',
         'HindII' => 'gt[ct][ag]ac',
         'HindIII' => 'aagctt',
         'HinfI' => 'ga[acgt]tc',
         'HpaI' => 'gttaac',
         'HpaII' => 'ccgg',
         'HphI' => 'ggtga',
         'Hpy178III' => 'tc[acgt][acgt]ga',
         'Hpy188I' => 'tc[acgt]ga',
         'Hpy99I' => 'cg[at]cg',
         'KpnI' => 'ggtacc',
         'Ksp632I' => 'ctcttc',
         'MaeI' => 'ctag',
         'MaeII' => 'acgt',
         'MaeIII' => 'gt[acgt]ac',
         'MboI' => 'gatc',
         'MboII' => 'gaaga',
         'McrI' => 'cg[ag][ct]cg',
         'MfeI' => 'caattg',
         'MjaIV' => 'gt[acgt][acgt]ac',
         'MluI' => 'acgcgt',
         'MmeI' => 'tcc[ag]ac',
         'MnlI' => 'cctc',
         'MseI' => 'ttaa',
         'MslI' => 'ca[ct][acgt][acgt][acgt][acgt][ag]tg',
         'MstI' => 'tgcgca',
         'MwoI' => 'gc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gc',
         'NaeI' => 'gccggc',
         'NarI' => 'ggcgcc',
         'NcoI' => 'ccatgg',
         'NdeI' => 'catatg',
         'NheI' => 'gctagc',
         'NlaIII' => 'catg',
         'NlaIV' => 'gg[acgt][acgt]cc',
         'NotI' => 'gcggccgc',
         'NruI' => 'tcgcga',
         'NspBII' => 'c[ac]gc[gt]g',
         'NspI' => '[ag]catg[ct]',
         'PacI' => 'ttaattaa',
         'Pfl1108I' => 'tcgtag',
         'PflMI' => 'cca[acgt][acgt][acgt][acgt][acgt]tgg',
         'PleI' => 'gagtc',
         'PmaCI' => 'cacgtg',
         'PmeI' => 'gtttaaac',
         'PpiI' => 'gaac[acgt][acgt][acgt][acgt][acgt]ctc',
         'PpuMI' => '[ag]gg[at]cc[ct]',
         'PshAI' => 'gac[acgt][acgt][acgt][acgt]gtc',
         'PsiI' => 'ttataa',
         'PstI' => 'ctgcag',
         'PvuI' => 'cgatcg',
         'PvuII' => 'cagctg',
         'RleAI' => 'cccaca',
         'RsaI' => 'gtac',
         'RsrII' => 'cgg[at]ccg',
         'SacI' => 'gagctc',
         'SacII' => 'ccgcgg',
         'SalI' => 'gtcgac',
         'SanDI' => 'ggg[at]ccc',
         'SapI' => 'gctcttc',
         'SauI' => 'cct[acgt]agg',
         'ScaI' => 'agtact',
         'ScrFI' => 'cc[acgt]gg',
         'SduI' => 'g[agt]gc[act]c',
         'SecI' => 'cc[acgt][acgt]gg',
         'SexAI' => 'acc[at]ggt',
         'SfaNI' => 'gcatc',
         'SfeI' => 'ct[ag][ct]ag',
         'SfiI' => 'ggcc[acgt][acgt][acgt][acgt][acgt]ggcc',
         'SgfI' => 'gcgatcgc',
         'SgrAI' => 'c[ag]ccgg[ct]g',
         'SimI' => 'gggtc',
         'SmaI' => 'cccggg',
         'SmlI' => 'ct[ct][ag]ag',
         'SnaBI' => 'tacgta',
         'SnaI' => 'gtatac',
         'SpeI' => 'actagt',
         'SphI' => 'gcatgc',
         'SplI' => 'cgtacg',
         'SrfI' => 'gcccgggc',
         'Sse232I' => 'cgccggcg',
         'Sse8387I' => 'cctgcagg',
         'Sse8647I' => 'agg[at]cct',
         'SspI' => 'aatatt',
         'Sth132I' => 'cccg',
         'StuI' => 'aggcct',
         'StyI' => 'cc[at][at]gg',
         'SwaI' => 'atttaaat',
         'TaqI' => 'tcga',
         'TaqII' => 'gaccga',
         'TatI' => '[at]gtac[at]',
         'TauI' => 'gc[cg]gc',
         'TfiI' => 'ga[at]tc',
         'TseI' => 'gc[at]gc',
         'Tsp45I' => 'gt[cg]ac',
         'Tsp4CI' => 'ac[acgt]gt',
         'TspEI' => 'aatt',
         'TspRI' => 'ca[cg]tg[acgt][acgt]',
         'Tth111I' => 'gac[acgt][acgt][acgt]gtc',
         'Tth111II' => 'caa[ag]ca',
         'UbaGI' => 'cac[acgt][acgt][acgt][acgt]gtg',
         'UbaPI' => 'cgaacg',
         'VspI' => 'attaat',
         'XbaI' => 'tctaga',
         'XcmI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt]tgg',
         'XhoI' => 'ctcgag',
         'XhoII' => '[ag]gatc[ct]',
         'XmaIII' => 'cggccg',
         'XmnI' => 'gaa[acgt][acgt][acgt][acgt]ttc'
        );

    return %enzymes;
}

1;