Bio::Tools SeqPattern
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Summary
Bio::Tools::SeqPattern - represent a sequence pattern or motif
Package variables
Privates (from "my" definitions)
$BEE = 'DN'
$Regexp_chars = '\w,.\*()\[\]<>\{\}^\$'
(%Processed_braces, %Processed_asterics);
$PURINES = 'AG'
$PYRIMIDINES = 'CT'
$ZED = 'EQ'
Inherit
Bio::Root::Root
Synopsis
 use Bio::Tools::SeqPattern;
my $pat1 = 'T[GA]AA...TAAT'; my $pattern1 = Bio::Tools::SeqPattern->new(-SEQ =>$pat1, -TYPE =>'Dna'); my $pat2 = '[VILM]R(GXX){3,2}...[^PG]'; my $pattern2 = Bio::Tools::SeqPattern->new(-SEQ =>$pat2, -TYPE =>'Amino');
Description
Bio::Tools::SeqPattern module encapsulates generic data and
methods for manipulating regular expressions describing nucleic or
amino acid sequence patterns (a.k.a, "motifs"), such as the ones produced by
Bio::Tools::IUPAC.
Bio::Tools::SeqPattern is a concrete class that inherits from Bio::Seq.
This class grew out of a need to have a standard module for doing routine
tasks with sequence patterns such as:
  -- Forming a reverse-complement version of a nucleotide sequence pattern
-- Expanding patterns containing ambiguity codes
-- Checking for invalid regexp characters
-- Untainting yet preserving special characters in the pattern
Other features to look for in the future:
  -- Full pattern syntax checking
-- Conversion between expanded and condensed forms of the pattern
Methods
newDescriptionCode
alphabet_okDescriptionCode
expandDescriptionCode
_expand_pepDescriptionCode
_expand_nucDescriptionCode
revcomDescriptionCode
backtranslateDescriptionCode
_fixpat_1DescriptionCode
_fixpat_2DescriptionCode
_fixpat_3DescriptionCode
_fixpat_4DescriptionCode
_fixpat_5DescriptionCode
_fixpat_6DescriptionCode
strDescriptionCode
typeDescriptionCode
Methods description
newcode    nextTop
 Title     : new
Usage : my $seqpat = Bio::Tools::SeqPattern->new();
Purpose : Verifies that the type is correct for superclass (Bio::Seq.pm)
: and calls superclass constructor last.
Returns : n/a
Argument : Parameters passed to new()
Throws : Exception if the pattern string (seq) is empty.
Comments : The process of creating a new SeqPattern.pm object
: ensures that the pattern string is untained.
See Also : Bio::Root::Root::new,
Bio::Seq::_initialize
alphabet_okcodeprevnextTop
 Title     : alphabet_ok
Usage : $mypat->alphabet_ok;
Purpose : Checks for invalid regexp characters.
: Overrides Bio::Seq::alphabet_ok() to allow
: additional regexp characters ,.*()[]<>{}^$
: in addition to the standard genetic alphabet.
: Also untaints the pattern and sets the sequence
: object's sequence to the untained string.
Returns : Boolean (1 | 0)
Argument : n/a
Throws : Exception if the pattern contains invalid characters.
Comments : Does not call the superclass method.
: Actually permits any alphanumeric, not just the
: standard genetic alphabet.
expandcodeprevnextTop
 Title     : expand
Usage : $seqpat_object->expand();
Purpose : Expands the sequence pattern using special ambiguity codes.
Example : $pat = $seq_pat->expand();
Returns : String containing fully expanded sequence pattern
Argument : n/a
Throws : Exception if sequence type is not recognized
: (i.e., is not one of [DR]NA, Amino)
See Also : Extended Alphabet Support, _expand_pep(), _expand_nuc()
_expand_pepcodeprevnextTop
 Title     : _expand_pep
Usage : n/a; automatically called by expand()
Purpose : Expands peptide patterns
Returns : String (the expanded pattern)
Argument : String (the unexpanded pattern)
Throws : n/a
See Also : expand(), _expand_nuc()
_expand_nuccodeprevnextTop
 Title     : _expand_nuc
Purpose : Expands nucleotide patterns
Returns : String (the expanded pattern)
Argument : String (the unexpanded pattern)
Throws : n/a
See Also : expand(), _expand_pep()
revcomcodeprevnextTop
 Title     : revcom
Usage : revcom([1]);
Purpose : Forms a pattern capable of recognizing the reverse complement
: version of a nucleotide sequence pattern.
Example : $pattern_object->revcom();
: $pattern_object->revcom(1); ## returns expanded rev complement pattern.
Returns : Object reference for a new Bio::Tools::SeqPattern containing
: the revcom of the current pattern as its sequence.
Argument : (1) boolean (optional) (default= false)
: true : expand the pattern before rev-complementing.
: false: don't expand pattern before or after rev-complementing.
Throws : Exception if called for amino acid sequence pattern.
Comments : This method permits the simultaneous searching of both
: sense and anti-sense versions of a nucleotide pattern
: by means of a grep-type of functionality in which any
: number of patterns may be or-ed into the recognition
: pattern.
: Overrides Bio::Seq::revcom() and calls it first thing.
: The order of _fixpat() calls is critical.
See Also : Bio::Seq::revcom, /_fixpat_1, /_fixpat_2, /_fixpat_3, /_fixpat_4, /_fixpat_5
backtranslatecodeprevnextTop
 Title     : backtranslate
Usage : backtranslate();
Purpose : Produce a degenerate oligonucleotide whose translation would produce
: the original protein motif.
Example : $pattern_object->backtranslate();
Returns : Object reference for a new Bio::Tools::SeqPattern containing
: the reverse translation of the current pattern as its sequence.
Throws : Exception if called for nucleotide sequence pattern.
_fixpat_1codeprevnextTop
 Title     : _fixpat_1
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all {7,5} --> {5,7} (Part I)
: and [T^] --> [^T] (Part II)
: and *N --> N* (Part III)
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded pattern)
Throws : n/a
See Also : revcom()
_fixpat_2codeprevnextTop
 Title     : _fixpat_2
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all {5,7}Y ---> Y{5,7}
: and {10,}. ---> .{10,}
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded, partially reversed pattern)
Throws : n/a
See Also : revcom()
_fixpat_3codeprevnextTop
 Title     : _fixpat_3
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all {5,7}(XXX) ---> (XXX){5,7}
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded, partially reversed pattern)
Throws : n/a
See Also : revcom()
_fixpat_4codeprevnextTop
 Title     : _fixpat_4
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all {5,7}[XXX] ---> [XXX]{5,7}
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded, partially reversed pattern)
Throws : n/a
See Also : revcom()
_fixpat_5codeprevnextTop
 Title     : _fixpat_5
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all *[XXX] ---> [XXX]*
: and *(XXX) ---> (XXX)*
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded, partially reversed pattern)
Throws : n/a
See Also : revcom()
_fixpat_6codeprevnextTop
 Title     : _fixpat_6
Usage : n/a; called automatically by revcom()
Purpose : Utility method for revcom()
: Converts all ?Y{5,7} ---> Y{5,7}?
: and ?(XXX){5,7} ---> (XXX){5,7}?
: and ?[XYZ]{5,7} ---> [XYZ]{5,7}?
Returns : String (the new, partially reversed pattern)
Argument : String (the expanded, partially reversed pattern)
Throws : n/a
See Also : revcom()
strcodeprevnextTop
 Title   : str
Usage : $obj->str($newval)
Function:
Returns : value of str
Args : newvalue (optional)
typecodeprevnextTop
 Title   : type
Usage : $obj->type($newval)
Function:
Returns : value of type
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
sub new {
#----------------
my($class, %param) = @_; my $self = $class->SUPER::new(%param); my ($seq,$type) = $self->_rearrange([qw(SEQ TYPE)], %param); $seq || $self->throw("Empty pattern."); my $t; # Get the type ready for Bio::Seq.pm
if ($type =~ /nuc|[dr]na/i) { $t = 'Dna'; } elsif ($type =~ /amino|pep|prot/i) { $t = 'Amino'; } $seq =~ tr/a-z/A-Z/; #ps 8/8/00 Canonicalize to upper case
$self->str($seq); $self->type($t); return $self;
}
alphabet_okdescriptionprevnextTop
sub alphabet_ok {
#----------------
my( $self) = @_; return 1 if $self->{'_alphabet_checked'}; $self->{'_alphabet_checked'} = 1; my $pat = $self->seq(); if($pat =~ /[^$Regexp_chars]/io) { $self->throw("Pattern contains invalid characters: $pat", 'Legal characters: a-z,A-Z,0-9,,.*()[]<>{}^$ '); } # Untaint pattern (makes code taint-safe).
$pat =~ /([$Regexp_chars]+)/io; $self->setseq(uc($1)); # print STDERR "\npattern ok: $pat\n";
1;
}
expanddescriptionprevnextTop
sub expand {
#----------
my $self = shift; if($self->type =~ /[DR]na/i) { $self->_expand_nuc(); } elsif($self->type =~ /Amino/i) { $self->_expand_pep(); } else{ $self->throw("Don't know how to expand ${\$self->type} patterns.\n"); }
}
_expand_pepdescriptionprevnextTop
sub _expand_pep {
#----------------
my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/X/./g; $pat =~ s/^</\^/; $pat =~ s/>$/\$/; ## Avoid nested situations: [bmnq] --/--> [[$ZED]mnq]
## Yet correctly deal with: fze[bmnq] ---> f[$BEE]e[$ZEDmnq]
if($pat =~ /\[\w*[BZ]\w*\]/) { $pat =~ s/\[(\w*)B(\w*)\]/\[$1$ZED$2\]/g; $pat =~ s/\[(\w*)Z(\w*)\]/\[$1$BEE$2\]/g; $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } else { $pat =~ s/B/\[$ZED\]/g; $pat =~ s/Z/\[$BEE\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing these last since:
$pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [B] (for example)
return $pat;
}
_expand_nucdescriptionprevnextTop
sub _expand_nuc {
#---------------
my ($self,$pat) = @_; $pat ||= $self->str; $pat =~ s/N|X/./g; $pat =~ s/pu/R/ig; $pat =~ s/py/Y/ig; $pat =~ s/U/T/g; $pat =~ s/^</\^/; $pat =~ s/>$/\$/; ## Avoid nested situations: [ya] --/--> [[ct]a]
## Yet correctly deal with: sg[ya] ---> [gc]g[cta]
if($pat =~ /\[\w*[RYSWMK]\w*\]/) { $pat =~ s/\[(\w*)R(\w*)\]/\[$1$PURINES$2\]/g; $pat =~ s/\[(\w*)Y(\w*)\]/\[$1$PYRIMIDINES$2\]/g; $pat =~ s/\[(\w*)S(\w*)\]/\[$1GC$2\]/g; $pat =~ s/\[(\w*)W(\w*)\]/\[$1AT$2\]/g; $pat =~ s/\[(\w*)M(\w*)\]/\[$1AC$2\]/g; $pat =~ s/\[(\w*)K(\w*)\]/\[$1GT$2\]/g; $pat =~ s/\[(\w*)V(\w*)\]/\[$1ACG$2\]/g; $pat =~ s/\[(\w*)H(\w*)\]/\[$1ACT$2\]/g; $pat =~ s/\[(\w*)D(\w*)\]/\[$1AGT$2\]/g; $pat =~ s/\[(\w*)B(\w*)\]/\[$1CGT$2\]/g; $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } else { $pat =~ s/R/\[$PURINES\]/g; $pat =~ s/Y/\[$PYRIMIDINES\]/g; $pat =~ s/S/\[GC\]/g; $pat =~ s/W/\[AT\]/g; $pat =~ s/M/\[AC\]/g; $pat =~ s/K/\[GT\]/g; $pat =~ s/V/\[ACG\]/g; $pat =~ s/H/\[ACT\]/g; $pat =~ s/D/\[AGT\]/g; $pat =~ s/B/\[CGT\]/g; } $pat =~ s/\((.)\)/$1/g; ## Doing thses last since:
$pat =~ s/\[(.)\]/$1/g; ## Pattern could contain [y] (for example)
return $pat;
}
revcomdescriptionprevnextTop
sub revcom {
#-----------
my($self,$expand) = @_; if ($self->type !~ /Dna|Rna/i) { $self->throw("Can't get revcom for ${\$self->type} sequence types.\n"); } # return $self->{'_rev'} if defined $self->{'_rev'};
$expand ||= 0; my $str = $self->str; $str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/; my $rev = CORE::reverse $str; $rev =~ tr/[](){}<>/][)(}{></; if($expand) { $rev = $self->_expand_nuc($rev); # print "\nExpanded: $rev\n";
} %Processed_braces = (); %Processed_asterics = (); my $fixrev = _fixpat_1($rev); # print "FIX 1: $fixrev";<STDIN>;
$fixrev = _fixpat_2($fixrev); # print "FIX 2: $fixrev";<STDIN>;
$fixrev = _fixpat_3($fixrev); # print "FIX 3: $fixrev";<STDIN>;
$fixrev = _fixpat_4($fixrev); # print "FIX 4: $fixrev";<STDIN>;
$fixrev = _fixpat_5($fixrev); # print "FIX 5: $fixrev";<STDIN>;
##### Added by ps 8/7/00 to allow non-greedy matching
$fixrev = _fixpat_6($fixrev); # print "FIX 6: $fixrev";<STDIN>;
# $self->{'_rev'} = $fixrev;
return new Bio::Tools::SeqPattern(-seq =>$fixrev, -type =>$self->type);
}
backtranslatedescriptionprevnextTop
sub backtranslate {
    my $self = shift;
    
    # _load_module loads dynamically, caches call if successful
$self->_load_module('Bio::Tools::SeqPattern::Backtranslate'); Bio::Tools::SeqPattern::Backtranslate->import("_reverse_translate_motif"); if ($self->type ne 'Amino') { $self->throw( "Can't get backtranslate for ${\$self->type} sequence types.\n" ); } return __PACKAGE__->new( -SEQ => _reverse_translate_motif($self->str), -TYPE => 'Dna', );
}
_fixpat_1descriptionprevnextTop
sub _fixpat_1 {
#--------------
my $pat = shift; ## Part I:
my (@done,@parts); while(1) { $pat =~ /(.*)\{(\S+?)\}(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#{'.reverse($2).'}'.$3; # print "1: $1\n2: $2\n3: $3\n";
# print "modified pat: $pat";<STDIN>;
@parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } $pat = join('', reverse @done); ## Part II:
@done = (); while(1) { $pat =~ /(.*)\[(\S+?)\](.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#['.reverse($2).']'.$3; # print "1: $1\n2: $2\n3: $3\n";
# print "modified pat: $pat";<STDIN>;
@parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } $pat = join('', reverse @done); ## Part III:
@done = (); while(1) { $pat =~ /(.*)\*([\w.])(.*)/ or do{ push @done, $pat; last; }; $pat = $1.'#'.$2.'*'.$3; $Processed_asterics{$2}++; # print "1: $1\n2: $2\n3: $3\n";
# print "modified pat: $pat";<STDIN>;
@parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done);
}
_fixpat_2descriptionprevnextTop
sub _fixpat_2 {
#--------------
my $pat = shift; local($^W) = 0; my (@done,@parts,$braces); while(1) { # $pat =~ s/(.*)([^])])(\{\S+?\})([\w.])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; };
$pat =~ s/(.*)(\{\S+?\})([\w.])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; }; $braces = $2; $braces =~ s/[{}]//g; $Processed_braces{"$3$braces"}++; # print "modified pat: $pat";<STDIN>;
@parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done);
}
_fixpat_3descriptionprevnextTop
sub _fixpat_3 {
#-------------
my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.+)(\{\S+\})(\(\w+\))(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; };
if( $pat =~ /(.*)(.)(\{\S+\})(\(\w+\))(.*)/) { $newpat = "$1#$2$4$3$5"; ##ps $oldpat = "$1#$2$3$4$5";
# print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n";
##ps $braces = $3;
##ps $braces =~ s/[{}]//g;
##ps if( exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) {
##ps $pat = $oldpat; # Don't change it. Already processed.
# print "saved pat: $pat";<STDIN>;
##ps } else {
# print "new pat: $newpat";<STDIN>;
$pat = $newpat; # Change it.
##ps }
} elsif( $pat =~ /^(\{\S+\})(\(\w+\))(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done);
}
_fixpat_4descriptionprevnextTop
sub _fixpat_4 {
#---------------
my $pat = shift; my (@done,@parts,$braces,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; };
# $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; };
if( $pat =~ /(.*)(.)(\{\S+\})(\[\w+\])(.*)/) { $newpat = "$1#$2$4$3$5"; $oldpat = "$1#$2$3$4$5"; # print "1: $1\n2: $2\n3: $3\n4: $4\n5: $5\n";
$braces = $3; $braces =~ s/[{}]//g; if( (defined $braces and defined $2) and exists $Processed_braces{"$2$braces"} || exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed.
# print "saved pat: $pat";<STDIN>;
} else { $pat = $newpat; # Change it.
# print "new pat: $pat";<STDIN>;
} } elsif( $pat =~ /^(\{\S+\})(\[\w+\])(.*)/) { $pat = "#$2$1$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done);
}
_fixpat_5descriptionprevnextTop
sub _fixpat_5 {
#--------------
my $pat = shift; my (@done,@parts,$newpat,$oldpat); while(1) { # $pat =~ s/(.*)(\{\S+\})(\[\w+\])(.*)/$1#$3$2$4/ or do{ push @done, $pat; last; };
# $pat =~ s/(.*)([^\w.])(\{\S+\})(\[\w+\])(.*)/$1$2#$4$3$5/ or do{ push @done, $pat; last; };
if( $pat =~ /(.*)(.)\*(\[\w+\]|\(\w+\))(.*)/) { $newpat = "$1#$2$3*$4"; $oldpat = "$1#$2*$3$4"; # print "1: $1\n2: $2\n3: $3\n4: $4\n";
if( exists $Processed_asterics{$2}) { $pat = $oldpat; # Don't change it. Already processed.
# print "saved pat: $pat";<STDIN>;
} else { $pat = $newpat; # Change it.
# print "new pat: $pat";<STDIN>;
} } elsif( $pat =~ /^\*(\[\w+\]|\(\w+\))(.*)/) { $pat = "#$1*$3"; } else { push @done, $pat; last; } @parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done); } ############################
#
# PS: Added 8/7/00 to allow non-greedy matching patterns
#
######################################
}
_fixpat_6descriptionprevnextTop
sub _fixpat_6 {
#--------------
my $pat = shift; my (@done,@parts); @done = (); while(1) { $pat =~ /(.*)\?(\[\w+\]|\(\w+\)|\w)(\{\S+?\})?(.*)/ or do{ push @done, $pat; last; }; my $quantifier = $3 ? $3 : ""; # Shut up warning if no explicit quantifier
$pat = $1.'#'.$2.$quantifier.'?'.$4; # $pat = $1.'#'.$2.$3.'?'.$4;
# print "1: $1\n2: $2\n3: $3\n";
# print "modified pat: $pat";<STDIN>;
@parts = split '#', $pat; push @done, $parts[1]; $pat = $parts[0]; # print "done: $parts[1]<---\nnew pat: $pat<---";<STDIN>;
last if not $pat; } return join('', reverse @done);
}
strdescriptionprevnextTop
sub str {
   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'str'} = $value;
    }
    return $obj->{'str'};
}
typedescriptionprevnextTop
sub type {
   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'type'} = $value;
    }
    return $obj->{'type'};

}

1;

__END__

#########################################################################
# End of class
#########################################################################
}
General documentation
MOTIVATIONSTop
A key motivation for Bio::Tools::SeqPattern is to have a way to
generate a reverse complement of a nucleotide sequence pattern.
This makes possible simultaneous pattern matching on both sense and
anti-sense strands of a query sequence.
In principle, one could do such a search more inefficiently by testing
against both sense and anti-sense versions of a sequence.
It is entirely equivalent to test a regexp containing both sense and
anti-sense versions of the *pattern* against one copy of the sequence.
The latter approach is much more efficient since:
   1) You need only one copy of the sequence.
2) Only one regexp is executed.
3) Regexp patterns are typically much smaller than sequences.
Patterns can be quite complex and it is often difficult to
generate the reverse complement pattern. The Bioperl SeqPattern.pm
addresses this problem, providing a convenient set of tools
for working with biological sequence regular expressions.
Not all patterns have been tested. If you discover a pattern that
is not handled properly by Bio::Tools::SeqPattern.pm, please
send me some email (sac@bioperl.org). Thanks.
OTHER FEATURESTop
Extended Alphabet SupportTop
This module supports the same set of ambiguity codes for nucleotide
sequences as supported by Bio::Seq. These ambiguity codes
define the behavior or the expand method.
 ------------------------------------------
Symbol Meaning Nucleic Acid
------------------------------------------
A A (A)denine
C C (C)ytosine
G G (G)uanine
T T (T)hymine
U U (U)racil
M A or C a(M)ino group
R A or G pu(R)ine
W A or T (W)eak bond
S C or G (S)trong bond
Y C or T p(Y)rimidine
K G or T (K)eto group
V A or C or G
H A or C or T
D A or G or T
B C or G or T
X G or A or T or C
N G or A or T or C
. G or A or T or C
------------------------------------------ Symbol Meaning ------------------------------------------ A Alanine C Cysteine D Aspartic Acid E Glutamic Acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine P Proline Q Glutamine R Arginine S Serine T Threonine V Valine W Tryptophan Y Tyrosine B Aspartic Acid, Asparagine Z Glutamic Acid, Glutamine X Any amino acid . Any amino acid
Multiple Format SupportTop
Ultimately, this module should be able to build SeqPattern.pm objects
using a variety of pattern formats such as ProSite, Blocks, Prints, GCG, etc.
Currently, this module only supports patterns using a grep-like syntax.
USAGETop
A simple demo script called seq_pattern.pl is included in the examples/
directory of the central Bioperl distribution.
SEE ALSOTop
Bio::Seq - Lightweight sequence object.
Bio::Tools::IUPAC - The IUPAC code for degenerate residues and their
conversion to a regular expression.
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.
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Support Top
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/
AUTHORTop
Steve Chervitz, sac-at-bioperl.org
COPYRIGHTTop
Copyright (c) 1997-8 Steve Chervitz. All Rights Reserved.
This module is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
FOR DEVELOPERS ONLYTop
Data MembersTop
Information about the various data members of this module is provided
for those wishing to modify or understand the code. Two things to bear
in mind:
  1 Do NOT rely on these in any code outside of this module.
  All data members are prefixed with an underscore to signify that they
are private. Always use accessor methods. If the accessor doesn't
exist or is inadequate, create or modify an accessor (and let me know,
too!).
  2 This documentation may be incomplete and out of date.
  It is easy for this documentation to become obsolete as this module is
still evolving. Always double check this info and search for members
not described here.
An instance of Bio::Tools::RestrictionEnzyme.pm is a blessed reference
to a hash containing all or some of the following fields:
 FIELD          VALUE
------------------------------------------------------------------------
_rev : The corrected reverse complement of the fully expanded pattern.
INHERITED DATA MEMBERS: _seq : (From Bio::Seq.pm) The original, unexpanded input sequence after untainting. _type : (From Bio::Seq.pm) 'Dna' or 'Amino'