Raw content of Bio::SimpleAlign
<![CDATA[# $Id: SimpleAlign.pm,v 1.65.2.1 2003/07/02 16:00:19 jason Exp $
# BioPerl module for SimpleAlign
#
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
#
# History:
# 11/3/00 Added threshold feature to consensus and consensus_aa - PS
# May 2001 major rewrite - Heikki Lehvaslaiho
=head1 NAME
Bio::SimpleAlign - Multiple alignments held as a set of sequences
=head1 SYNOPSIS
# use Bio::AlignIO to read in the alignment
$str = Bio::AlignIO->new('-file' => 't/data/testaln.pfam');
$aln = $str->next_aln();
# some descriptors
print $aln->length, "\n";
print $aln->no_residues, "\n";
print $aln->is_flush, "\n";
print $aln->no_sequences, "\n";
print $aln->percentage_identity, "\n";
print $aln->consensus_string(50), "\n";
# find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;
# extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
$res = $seq->subseq($pos, $pos);
$count{$res}++;
}
foreach $res (keys %count) {
printf "Res: %s Count: %2d\n", $res, $count{$res};
}
=head1 DESCRIPTION
SimpleAlign handles multiple alignments of sequences. It is very
permissive of types (it won't insist on things being all same length
etc): really it is a SequenceSet explicitly held in memory with a
whole series of built in manipulations and especially file format
systems for read/writing alignments.
SimpleAlign basically views an alignment as an immutable block of
text. SimpleAlign *is not* the object to be using if you want to
perform complex alignment manipulations.
However for lightweight display/formatting and minimal manipulation
(e.g. removing all-gaps columns) - this is the one to use.
SimpleAlign uses a subclass of L<Bio::PrimarySeq> class
L<Bio::LocatableSeq> to store its sequences. These are subsequences
with a start and end positions in the parent reference sequence.
Tricky concepts. SimpleAlign expects name,start,end to be 'unique' in
the alignment, and this is the key for the internal hashes.
(name,start,end is abbreviated nse in the code). However, in many
cases people don't want the name/start-end to be displayed: either
multiple names in an alignment or names specific to the alignment
(ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called
'displayname', and generally is what is used to print out the
alignment. They default to name/start-end.
The SimpleAlign Module came from Ewan Birney's Align module.
=head1 PROGRESS
SimpleAlign is being slowly converted to bioperl coding standards,
mainly by Ewan.
=over 3
=item Use Bio::Root::Object - done
=item Use proper exceptions - done
=item Use hashed constructor - not done!
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Ewan Birney, birney@sanger.ac.uk
=head1 CONTRIBUTORS
Richard Adams, Richard.Adams@ed.ac.uk,
David J. Evans, David.Evans@vir.gla.ac.uk,
Heikki Lehvaslaiho, heikki@ebi.ac.uk,
Allen Smith, allens@cpan.org,
Jason Stajich, jason@bioperl.org,
Anthony Underwood, aunderwood@phls.org.uk,
Xintao Wei & Giri Narasimhan, giri@cs.fiu.edu
=head1 SEE ALSO
L<Bio::LocatableSeq.pm>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# 'Let the code begin...
package Bio::SimpleAlign;
use vars qw(@ISA %CONSERVATION_GROUPS);
use strict;
use Bio::Root::Root;
use Bio::LocatableSeq; # uses Seq's as list
use Bio::Align::AlignI;
BEGIN {
# This data should probably be in a more centralized module...
# it is taken from Clustalw documentation
# These are all the positively scoring groups that occur in the
# Gonnet Pam250 matrix. The strong and weak groups are
# defined as strong score >0.5 and weak score =<0.5 respectively.
%CONSERVATION_GROUPS = ( 'strong' => [ qw(STA
NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW)
],
'weak' => [ qw(CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY) ],
);
}
@ISA = qw(Bio::Root::Root Bio::Align::AlignI);
=head2 new
Title : new
Usage : my $aln = new Bio::SimpleAlign();
Function : Creates a new simple align object
Returns : Bio::SimpleAlign
Args : -source => string representing the source program
where this alignment came from
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($src) = $self->_rearrange([qw(SOURCE)], @args);
$src && $self->source($src);
# we need to set up internal hashs first!
$self->{'_seq'} = {};
$self->{'_order'} = {};
$self->{'_start_end_lists'} = {};
$self->{'_dis_name'} = {};
$self->{'_id'} = 'NoName';
$self->{'_symbols'} = {};
# maybe we should automatically read in from args. Hmmm...
return $self; # success - we hope!
}
=head1 Modifier methods
These methods modify the MSE by adding, removing or shuffling complete
sequences.
=head2 add_seq
Title : add_seq
Usage : $myalign->add_seq($newseq);
Function : Adds another sequence to the alignment. *Does not* align
it - just adds it to the hashes.
Returns : nothing
Args : a Bio::LocatableSeq object
order (optional)
See L<Bio::LocatableSeq> for more information
=cut
sub addSeq {
my $self = shift;
$self->warn(ref($self). "::addSeq - deprecated method. Use add_seq() instead.");
$self->add_seq(@_);
}
sub add_seq {
my $self = shift;
my $seq = shift;
my $order = shift;
my ($name,$id,$start,$end);
if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [", ref($seq), "]");
}
$id = $seq->id() ||$seq->display_id || $seq->primary_id;
$start = $seq->start();
$end = $seq->end();
# build the symbol list for this sequence,
# will prune out the gap and missing/match chars
# when actually asked for the symbol list in the
# symbol_chars
map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq);
if( !defined $order ) {
$order = keys %{$self->{'_seq'}};
}
$name = sprintf("%s/%d-%d",$id,$start,$end);
if( $self->{'_seq'}->{$name} ) {
$self->warn("Replacing one sequence [$name]\n");
}
else {
#print STDERR "Assigning $name to $order\n";
$self->{'_order'}->{$order} = $name;
unless( exists( $self->{'_start_end_lists'}->{$id})) {
$self->{'_start_end_lists'}->{$id} = [];
}
push @{$self->{'_start_end_lists'}->{$id}}, $seq;
}
$self->{'_seq'}->{$name} = $seq;
}
=head2 remove_seq
Title : remove_seq
Usage : $aln->remove_seq($seq);
Function : Removes a single sequence from an alignment
Returns :
Argument : a Bio::LocatableSeq object
=cut
sub removeSeq {
my $self = shift;
$self->warn(ref($self). "::removeSeq - deprecated method. Use remove_seq() instead.");
$self->remove_seq(@_);
}
sub remove_seq {
my $self = shift;
my $seq = shift;
my ($name,$id,$start,$end);
$self->throw("Need Bio::Locatable seq argument ")
unless ref $seq && $seq->isa('Bio::LocatableSeq');
$id = $seq->id();
$start = $seq->start();
$end = $seq->end();
$name = sprintf("%s/%d-%d",$id,$start,$end);
if( !exists $self->{'_seq'}->{$name} ) {
$self->throw("Sequence $name does not exist in the alignment to remove!");
}
delete $self->{'_seq'}->{$name};
# we need to remove this seq from the start_end_lists hash
if (exists $self->{'_start_end_lists'}->{$id}) {
# we need to find the sequence in the array.
my ($i, $found);;
for ($i=0; $i < @{$self->{'_start_end_lists'}->{$id}}; $i++) {
if (${$self->{'_start_end_lists'}->{$id}}[$i] eq $seq) {
$found = 1;
last;
}
}
if ($found) {
splice @{$self->{'_start_end_lists'}->{$id}}, $i, 1;
}
else {
$self->throw("Could not find the sequence to remoce from the start-end list");
}
}
else {
$self->throw("There is no seq list for the name $id");
}
return 1;
# we can't do anything about the order hash but that is ok
# because each_seq will handle it
}
=head2 purge
Title : purge
Usage : $aln->purge(0.7);
Function:
Removes sequences above given sequence similarity
This function will grind on large alignments. Beware!
Example :
Returns : An array of the removed sequences
Args : float, threshold for similarity
=cut
sub purge {
my ($self,$perc) = @_;
my (%duplicate, @dups);
my @seqs = $self->each_seq();
for (my $i=0;$i< @seqs - 1;$i++ ) { #for each seq in alignment
my $seq = $seqs[$i];
#skip if already in duplicate hash
next if exists $duplicate{$seq->display_id} ;
my $one = $seq->seq();
my @one = split '', $one; #split to get 1aa per array element
for (my $j=$i+1;$j < @seqs;$j++) {
my $seq2 = $seqs[$j];
#skip if already in duplicate hash
next if exists $duplicate{$seq2->display_id} ;
my $two = $seq2->seq();
my @two = split '', $two;
my $count = 0;
my $res = 0;
for (my $k=0;$k<@one;$k++) {
if ( $one[$k] ne '.' && $one[$k] ne '-' && defined($two[$k]) &&
$one[$k] eq $two[$k]) {
$count++;
}
if ( $one[$k] ne '.' && $one[$k] ne '-' && defined($two[$k]) &&
$two[$k] ne '.' && $two[$k] ne '-' ) {
$res++;
}
}
my $ratio = 0;
$ratio = $count/$res unless $res == 0;
# if above threshold put in duplicate hash and push onto
# duplicate array for returning to get_unique
if ( $ratio > $perc ) {
print STDERR "duplicate!", $seq2->display_id, "\n" if $self->verbose > 0;
$duplicate{$seq2->display_id} = 1;
push @dups, $seq2;
}
}
}
foreach my $seq (@dups) {
$self->remove_seq($seq);
}
return @dups;
}
=head2 sort_alphabetically
Title : sort_alphabetically
Usage : $ali->sort_alphabetically
Function :
Changes the order of the alignemnt to alphabetical on name
followed by numerical by number.
Returns :
Argument :
=cut
sub sort_alphabetically {
my $self = shift;
my ($seq,$nse,@arr,%hash,$count);
foreach $seq ( $self->each_seq() ) {
$nse = $seq->get_nse;
$hash{$nse} = $seq;
}
$count = 0;
%{$self->{'_order'}} = (); # reset the hash;
foreach $nse ( sort _alpha_startend keys %hash) {
$self->{'_order'}->{$count} = $nse;
$count++;
}
1;
}
=head1 Sequence selection methods
Methods returning one or more sequences objects.
=head2 each_seq
Title : each_seq
Usage : foreach $seq ( $align->each_seq() )
Function : Gets an array of Seq objects from the alignment
Returns : an array
Argument :
=cut
sub eachSeq {
my $self = shift;
$self->warn(ref($self). "::eachSeq - deprecated method. Use each_seq() instead.");
$self->each_seq();
}
sub each_seq {
my $self = shift;
my (@arr,$order);
foreach $order ( sort { $a <=> $b } keys %{$self->{'_order'}} ) {
if( exists $self->{'_seq'}->{$self->{'_order'}->{$order}} ) {
push(@arr,$self->{'_seq'}->{$self->{'_order'}->{$order}});
}
}
return @arr;
}
=head2 each_alphabetically
Title : each_alphabetically
Usage : foreach $seq ( $ali->each_alphabetically() )
Function :
Returns an array of sequence object sorted alphabetically
by name and then by start point.
Does not change the order of the alignment
Returns :
Argument :
=cut
sub each_alphabetically {
my $self = shift;
my ($seq,$nse,@arr,%hash,$count);
foreach $seq ( $self->each_seq() ) {
$nse = $seq->get_nse;
$hash{$nse} = $seq;
}
foreach $nse ( sort _alpha_startend keys %hash) {
push(@arr,$hash{$nse});
}
return @arr;
}
sub _alpha_startend {
my ($aname,$astart,$bname,$bstart);
($aname,$astart) = split (/-/,$a);
($bname,$bstart) = split (/-/,$b);
if( $aname eq $bname ) {
return $astart <=> $bstart;
}
else {
return $aname cmp $bname;
}
}
=head2 each_seq_with_id
Title : each_seq_with_id
Usage : foreach $seq ( $align->each_seq_with_id() )
Function :
Gets an array of Seq objects from the
alignment, the contents being those sequences
with the given name (there may be more than one)
Returns : an array
Argument : a seq name
=cut
sub eachSeqWithId {
my $self = shift;
$self->warn(ref($self). "::eachSeqWithId - deprecated method. Use each_seq_with_id() instead.");
$self->each_seq_with_id(@_);
}
sub each_seq_with_id {
my $self = shift;
my $id = shift;
$self->throw("Method each_seq_with_id needs a sequence name argument")
unless defined $id;
my (@arr, $seq);
if (exists($self->{'_start_end_lists'}->{$id})) {
@arr = @{$self->{'_start_end_lists'}->{$id}};
}
return @arr;
}
=head2 get_seq_by_pos
Title : get_seq_by_pos
Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment
Function :
Gets a sequence based on its position in the alignment.
Numbering starts from 1. Sequence positions larger than
no_sequences() will thow an error.
Returns : a Bio::LocatableSeq object
Args : positive integer for the sequence osition
=cut
sub get_seq_by_pos {
my $self = shift;
my ($pos) = @_;
$self->throw("Sequence position has to be a positive integer, not [$pos]")
unless $pos =~ /^\d+$/ and $pos > 0;
$self->throw("No sequence at position [$pos]")
unless $pos <= $self->no_sequences ;
my $nse = $self->{'_order'}->{--$pos};
return $self->{'_seq'}->{$nse};
}
=head1 Create new alignments
The result of these methods are horizontal or vertical subsets of the
current MSE.
=head2 select
Title : select
Usage : $aln2 = $aln->select(1, 3) # three first sequences
Function :
Creates a new alignment from a continuous subset of
sequences. Numbering starts from 1. Sequence positions
larger than no_sequences() will thow an error.
Returns : a Bio::SimpleAlign object
Args : positive integer for the first sequence
positive integer for the last sequence to include (optional)
=cut
sub select {
my $self = shift;
my ($start, $end) = @_;
$self->throw("Select start has to be a positive integer, not [$start]")
unless $start =~ /^\d+$/ and $start > 0;
$self->throw("Select end has to be a positive integer, not [$end]")
unless $end =~ /^\d+$/ and $end > 0;
$self->throw("Select $start [$start] has to be smaller than or equal to end [$end]")
unless $start <= $end;
my $aln = new $self;
foreach my $pos ($start .. $end) {
$aln->add_seq($self->get_seq_by_pos($pos));
}
$aln->id($self->id);
return $aln;
}
=head2 select_noncont
Title : select_noncont
Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences
Function :
Creates a new alignment from a subset of
sequences. Numbering starts from 1. Sequence positions
larger than no_sequences() will thow an error.
Returns : a Bio::SimpleAlign object
Args : array of integers for the sequences
=cut
sub select_noncont {
my $self = shift;
my (@pos) = @_;
my $end = $self->no_sequences;
foreach ( @pos ) {
$self->throw("position must be a positive integer, > 0 and <= $end not [$_]")
unless( /^\d+$/ && $_ > 0 && $_ <= $end );
}
my $aln = new $self;
foreach my $p (@pos) {
$aln->add_seq($self->get_seq_by_pos($p));
}
$aln->id($self->id);
return $aln;
}
=head2 slice
Title : slice
Usage : $aln2 = $aln->slice(20, 30)
Function :
Creates a slice from the alignment inclusive of start and
end columns. Sequences with no residues in the slice are
excluded from the new alignment and a warning is printed.
Slice beyond the length of the sequence does not do
padding.
Returns : a Bio::SimpleAlign object
Args : positive integer for start column
positive integer for end column
=cut
sub slice {
my $self = shift;
my ($start, $end) = @_;
$self->throw("Slice start has to be a positive integer, not [$start]")
unless $start =~ /^\d+$/ and $start > 0;
$self->throw("Slice end has to be a positive integer, not [$end]")
unless $end =~ /^\d+$/ and $end > 0;
$self->throw("Slice $start [$start] has to be smaller than or equal to end [$end]")
unless $start <= $end;
my $aln_length = $self->length;
$self->throw("This alignment has only ". $self->length.
" residues. Slice start [$start] is too bigger.")
if $start > $self->length;
my $aln = new $self;
$aln->id($self->id);
foreach my $seq ( $self->each_seq() ) {
my $new_seq = new Bio::LocatableSeq (-id => $seq->id);
# seq
my $seq_end = $end;
$seq_end = $seq->length if $end > $seq->length;
my $slice_seq = $seq->subseq($start, $seq_end);
$new_seq->seq( $slice_seq );
# start
if ($start > 1) {
my $pre_start_seq = $seq->subseq(1, $start - 1);
$pre_start_seq =~ s/\W//g; #print "$pre_start_seq\n";
$new_seq->start( $seq->start + CORE::length($pre_start_seq) );
} else {
$new_seq->start( $seq->start);
}
# end
$slice_seq =~ s/\W//g;
$new_seq->end( $new_seq->start + CORE::length($slice_seq) - 1 );
if ($new_seq->start and $new_seq->end >= $new_seq->start) {
$aln->add_seq($new_seq);
} else {
my $nse = $seq->get_nse();
$self->warn("Slice [$start-$end] of sequence [$nse] contains no residues.".
" Sequence excluded from the new alignment.");
}
}
return $aln;
}
=head2 remove_columns
Title : remove_column
Usage : $aln2 = $aln->remove_columns(['mismatch','weak'])
Function :
Creates an aligment with columns removed corresponding to
the specified criteria.
Returns : a L<Bio::SimpleAlign> object
Args : array ref of types, 'match'|'weak'|'strong'|'mismatch'
=cut
sub remove_columns{
my ($self,$type) = @_;
my %matchchars = ( 'match' => '\*',
'weak' => '\.',
'strong' => ':',
'mismatch'=> ' ',
);
#get the characters to delete against
my $del_char;
foreach my $type(@{$type}){
$del_char.= $matchchars{$type};
}
my $match_line = $self->match_line;
my $aln = new $self;
my @remove;
my $length = 0;
#do the matching to get the segments to remove
while($match_line=~m/[$del_char]/g){
my $start = pos($match_line)-1;
$match_line=~/\G[$del_char]+/gc;
my $end = pos($match_line)-1;
#have to offset the start and end for subsequent removes
$start-=$length;
$end -=$length;
$length += ($end-$start+1);
push @remove, [$start,$end];
}
#remove the segments
$aln = $self->_remove_col($aln,\@remove);
return $aln;
}
sub _remove_col {
my ($self,$aln,$remove) = @_;
my @new;
#splice out the segments and create new seq
foreach my $seq($self->each_seq){
my $new_seq = new Bio::LocatableSeq(-id=>$seq->id);
my $sequence;
foreach my $pair(@{$remove}){
my $start = $pair->[0];
my $end = $pair->[1];
$sequence = $seq->seq unless $sequence;
my $spliced;
$spliced .= $start > 0 ? substr($sequence,0,$start) : '';
$spliced .= substr($sequence,$end+1,$seq->length-$end+1);
$sequence = $spliced;
if ($start == 1) {
$new_seq->start($end);
}
else {
$new_seq->start( $seq->start);
}
# end
if($end >= $seq->end){
$new_seq->end( $start);
}
else {
$new_seq->end($seq->end);
}
}
$new_seq->seq($sequence);
push @new, $new_seq;
}
#add the new seqs to the alignment
foreach my $new(@new){
$aln->add_seq($new);
}
return $aln;
}
=head1 Change sequences within the MSE
These methods affect characters in all sequences without changeing the
alignment.
=head2 map_chars
Title : map_chars
Usage : $ali->map_chars('\.','-')
Function :
Does a s/$arg1/$arg2/ on the sequences. Useful for gap
characters
Notice that the from (arg1) is interpretted as a regex,
so be careful about quoting meta characters (eg
$ali->map_chars('.','-') wont do what you want)
Returns :
Argument : 'from' rexexp
'to' string
=cut
sub map_chars {
my $self = shift;
my $from = shift;
my $to = shift;
my ($seq,$temp);
$self->throw("Need exactly two arguments")
unless defined $from and defined $to;
foreach $seq ( $self->each_seq() ) {
$temp = $seq->seq();
$temp =~ s/$from/$to/g;
$seq->seq($temp);
}
return 1;
}
=head2 uppercase
Title : uppercase()
Usage : $ali->uppercase()
Function : Sets all the sequences to uppercase
Returns :
Argument :
=cut
sub uppercase {
my $self = shift;
my $seq;
my $temp;
foreach $seq ( $self->each_seq() ) {
$temp = $seq->seq();
$temp =~ tr/[a-z]/[A-Z]/;
$seq->seq($temp);
}
return 1;
}
=head2 cigar_line
Title : cigar_line()
Usage : $align->cigar_line()
Function : Generates a "cigar" line for each sequence in the alignment
The format is simply A-1,60;B-1,1:4,60;C-5,10:12,58
where A,B,C,etc. are the sequence identifiers, and the numbers
refer to conserved positions within the alignment
Args : none
=cut
sub cigar_line {
my ($self) = @_;
my %cigar;
my %clines;
my @seqchars;
my $seqcount = 0;
my $sc;
foreach my $seq ( $self->each_seq ) {
push @seqchars, [ split(//, uc ($seq->seq)) ];
$sc = scalar(@seqchars);
}
foreach my $pos ( 0..$self->length ) {
my $i=0;
foreach my $seq ( @seqchars ) {
$i++;
# print STDERR "Seq $i at pos $pos: ".$seq->[$pos]."\n";
if ($seq->[$pos] eq '.') {
if (defined $cigar{$i} && $clines{$i} !~ $cigar{$i}) {
$clines{$i}.=$cigar{$i};
}
}
else {
if (! defined $cigar{$i}) {
$clines{$i}.=($pos+1).",";
}
$cigar{$i}=$pos+1;
}
if ($pos+1 == $self->length && ($clines{$i} =~ /\,$/) ) {
$clines{$i}.=$cigar{$i};
}
}
}
for(my $i=1; $i<$sc+1;$i++) {
print STDERR "Seq $i cigar line ".$clines{$i}."\n";
}
return %clines;
}
=head2 match_line
Title : match_line()
Usage : $align->match_line()
Function : Generates a match line - much like consensus string
except that a line indicating the '*' for a match.
Args : (optional) Match line characters ('*' by default)
(optional) Strong match char (':' by default)
(optional) Weak match char ('.' by default)
=cut
sub match_line {
my ($self,$matchlinechar, $strong, $weak) = @_;
my %matchchars = ( 'match' => $matchlinechar || '*',
'weak' => $weak || '.',
'strong' => $strong || ':',
'mismatch'=> ' ',
);
my @seqchars;
my $seqcount = 0;
my $alphabet;
foreach my $seq ( $self->each_seq ) {
push @seqchars, [ split(//, uc ($seq->seq)) ];
$alphabet = $seq->alphabet unless defined $alphabet;
}
my $refseq = shift @seqchars;
# let's just march down the columns
my $matchline;
POS: foreach my $pos ( 0..$self->length ) {
my $refchar = $refseq->[$pos];
next unless $refchar; # skip ''
my %col = ($refchar => 1);
my $dash = ($refchar eq '-' || $refchar eq '.' || $refchar eq ' ');
foreach my $seq ( @seqchars ) {
$dash = 1 if( $seq->[$pos] eq '-' || $seq->[$pos] eq '.' ||
$seq->[$pos] eq ' ' );
$col{$seq->[$pos]}++;
}
my @colresidues = sort keys %col;
my $char = $matchchars{'mismatch'};
# if all the values are the same
if( $dash ) { $char = $matchchars{'mismatch'} }
elsif( @colresidues == 1 ) { $char = $matchchars{'match'} }
elsif( $alphabet eq 'protein' ) { # only try to do weak/strong
# matches for protein seqs
TYPE: foreach my $type ( qw(strong weak) ) {
# iterate through categories
my %groups;
# iterate through each of the aa in the col
# look to see which groups it is in
foreach my $c ( @colresidues ) {
foreach my $f ( grep /\Q$c/, @{$CONSERVATION_GROUPS{$type}} ) {
push @{$groups{$f}},$c;
}
}
GRP: foreach my $cols ( values %groups ) {
@$cols = sort @$cols;
# now we are just testing to see if two arrays
# are identical w/o changing either one
# have to be same len
next if( scalar @$cols != scalar @colresidues );
# walk down the length and check each slot
for($_=0;$_ < (scalar @$cols);$_++ ) {
next GRP if( $cols->[$_] ne $colresidues[$_] );
}
$char = $matchchars{$type};
last TYPE;
}
}
}
$matchline .= $char;
}
return $matchline;
}
=head2 match
Title : match()
Usage : $ali->match()
Function :
Goes through all columns and changes residues that are
identical to residue in first sequence to match '.'
character. Sets match_char.
USE WITH CARE: Most MSE formats do not support match
characters in sequences, so this is mostly for output
only. NEXUS format (Bio::AlignIO::nexus) can handle
it.
Returns : 1
Argument : a match character, optional, defaults to '.'
=cut
sub match {
my ($self, $match) = @_;
$match ||= '.';
my ($matching_char) = $match;
$matching_char = "\\$match" if $match =~ /[\^.$|()\[\]]/ ; #';
$self->map_chars($matching_char, '-');
my @seqs = $self->each_seq();
return 1 unless scalar @seqs > 1;
my $refseq = shift @seqs ;
my @refseq = split //, $refseq->seq;
my $gapchar = $self->gap_char;
foreach my $seq ( @seqs ) {
my @varseq = split //, $seq->seq();
for ( my $i=0; $i < scalar @varseq; $i++) {
$varseq[$i] = $match if defined $refseq[$i] &&
( $refseq[$i] =~ /[A-Za-z\*]/ ||
$refseq[$i] =~ /$gapchar/ )
&& $refseq[$i] eq $varseq[$i];
}
$seq->seq(join '', @varseq);
}
$self->match_char($match);
return 1;
}
=head2 unmatch
Title : unmatch()
Usage : $ali->unmatch()
Function : Undoes the effect of method match. Unsets match_char.
Returns : 1
Argument : a match character, optional, defaults to '.'
See L<match> and L<match_char>
=cut
sub unmatch {
my ($self, $match) = @_;
$match ||= '.';
my @seqs = $self->each_seq();
return 1 unless scalar @seqs > 1;
my $refseq = shift @seqs ;
my @refseq = split //, $refseq->seq;
my $gapchar = $self->gap_char;
foreach my $seq ( @seqs ) {
my @varseq = split //, $seq->seq();
for ( my $i=0; $i < scalar @varseq; $i++) {
$varseq[$i] = $refseq[$i] if defined $refseq[$i] &&
( $refseq[$i] =~ /[A-Za-z\*]/ ||
$refseq[$i] =~ /$gapchar/ ) &&
$varseq[$i] eq $match;
}
$seq->seq(join '', @varseq);
}
$self->match_char('');
return 1;
}
=head1 MSE attibutes
Methods for setting and reading the MSE attributes.
Note that the methods defining character semantics depend on the user
to set them sensibly. They are needed only by certain input/output
methods. Unset them by setting to an empty string ('').
=head2 id
Title : id
Usage : $myalign->id("Ig")
Function : Gets/sets the id field of the alignment
Returns : An id string
Argument : An id string (optional)
=cut
sub id {
my ($self, $name) = @_;
if (defined( $name )) {
$self->{'_id'} = $name;
}
return $self->{'_id'};
}
=head2 missing_char
Title : missing_char
Usage : $myalign->missing_char("?")
Function : Gets/sets the missing_char attribute of the alignment
It is generally recommended to set it to 'n' or 'N'
for nucleotides and to 'X' for protein.
Returns : An missing_char string,
Argument : An missing_char string (optional)
=cut
sub missing_char {
my ($self, $char) = @_;
if (defined $char ) {
$self->throw("Single missing character, not [$char]!") if CORE::length($char) > 1;
$self->{'_missing_char'} = $char;
}
return $self->{'_missing_char'};
}
=head2 match_char
Title : match_char
Usage : $myalign->match_char('.')
Function : Gets/sets the match_char attribute of the alignment
Returns : An match_char string,
Argument : An match_char string (optional)
=cut
sub match_char {
my ($self, $char) = @_;
if (defined $char ) {
$self->throw("Single match character, not [$char]!") if CORE::length($char) > 1;
$self->{'_match_char'} = $char;
}
return $self->{'_match_char'};
}
=head2 gap_char
Title : gap_char
Usage : $myalign->gap_char('-')
Function : Gets/sets the gap_char attribute of the alignment
Returns : An gap_char string, defaults to '-'
Argument : An gap_char string (optional)
=cut
sub gap_char {
my ($self, $char) = @_;
if (defined $char || ! defined $self->{'_gap_char'} ) {
$char= '-' unless defined $char;
$self->throw("Single gap character, not [$char]!") if CORE::length($char) > 1;
$self->{'_gap_char'} = $char;
}
return $self->{'_gap_char'};
}
=head2 symbol_chars
Title : symbol_chars
Usage : my @symbolchars = $aln->symbol_chars;
Function: Returns all the seen symbols (other than gaps)
Returns : array of characters that are the seen symbols
Args : boolean to include the gap/missing/match characters
=cut
sub symbol_chars{
my ($self,$includeextra) = @_;
if( ! defined $self->{'_symbols'} ) {
$self->warn("Symbol list was not initialized");
return ();
}
my %copy = %{$self->{'_symbols'}};
if( ! $includeextra ) {
foreach my $char ( $self->gap_char, $self->match_char,
$self->missing_char) {
delete $copy{$char} if( defined $char );
}
}
return keys %copy;
}
=head1 Alignment descriptors
These read only methods describe the MSE in various ways.
=head2 consensus_string
Title : consensus_string
Usage : $str = $ali->consensus_string($threshold_percent)
Function : Makes a strict consensus
Returns :
Argument : Optional treshold ranging from 0 to 100.
The consensus residue has to appear at least threshold %
of the sequences at a given location, otherwise a '?'
character will be placed at that location.
(Default value = 0%)
=cut
sub consensus_string {
my $self = shift;
my $threshold = shift;
my $len;
my ($out,$count);
$out = "";
$len = $self->length - 1;
foreach $count ( 0 .. $len ) {
$out .= $self->_consensus_aa($count,$threshold);
}
return $out;
}
sub _consensus_aa {
my $self = shift;
my $point = shift;
my $threshold_percent = shift || -1 ;
my ($seq,%hash,$count,$letter,$key);
foreach $seq ( $self->each_seq() ) {
$letter = substr($seq->seq,$point,1);
$self->throw("--$point-----------") if $letter eq '';
($letter =~ /\./) && next;
# print "Looking at $letter\n";
$hash{$letter}++;
}
my $number_of_sequences = $self->no_sequences();
my $threshold = $number_of_sequences * $threshold_percent / 100. ;
$count = -1;
$letter = '?';
foreach $key ( sort keys %hash ) {
# print "Now at $key $hash{$key}\n";
if( $hash{$key} > $count && $hash{$key} >= $threshold) {
$letter = $key;
$count = $hash{$key};
}
}
return $letter;
}
=head2 consensus_iupac
Title : consensus_iupac
Usage : $str = $ali->consensus_iupac()
Function :
Makes a consensus using IUPAC ambiguity codes from DNA
and RNA. The output is in upper case except when gaps in
a column force output to be in lower case.
Note that if your alignment sequences contain a lot of
IUPAC ambiquity codes you often have to manually set
alphabet. Bio::PrimarySeq::_guess_type thinks they
indicate a protein sequence.
Returns : consensus string
Argument : none
Throws : on protein sequences
=cut
sub consensus_iupac {
my $self = shift;
my $out = "";
my $len = $self->length-1;
# only DNA and RNA sequences are valid
foreach my $seq ( $self->each_seq() ) {
$self->throw("Seq [". $seq->get_nse. "] is a protein")
if $seq->alphabet eq 'protein';
}
# loop over the alignment columns
foreach my $count ( 0 .. $len ) {
$out .= $self->_consensus_iupac($count);
}
return $out;
}
sub _consensus_iupac {
my ($self, $column) = @_;
my ($string, $char, $rna);
#determine all residues in a column
foreach my $seq ( $self->each_seq() ) {
$string .= substr($seq->seq, $column, 1);
}
$string = uc $string;
# quick exit if there's an N in the string
if ($string =~ /N/) {
$string =~ /\W/ ? return 'n' : return 'N';
}
# ... or if there are only gap characters
return '-' if $string =~ /^\W+$/;
# treat RNA as DNA in regexps
if ($string =~ /U/) {
$string =~ s/U/T/;
$rna = 1;
}
# the following s///'s only need to be done to the _first_ ambiguity code
# as we only need to see the _range_ of characters in $string
if ($string =~ /[VDHB]/) {
$string =~ s/V/AGC/;
$string =~ s/D/AGT/;
$string =~ s/H/ACT/;
$string =~ s/B/CTG/;
}
if ($string =~ /[SKYRWM]/) {
$string =~ s/S/GC/;
$string =~ s/K/GT/;
$string =~ s/Y/CT/;
$string =~ s/R/AG/;
$string =~ s/W/AT/;
$string =~ s/M/AC/;
}
# and now the guts of the thing
if ($string =~ /A/) {
$char = 'A'; # A A
if ($string =~ /G/) {
$char = 'R'; # A and G (purines) R
if ($string =~ /C/) {
$char = 'V'; # A and G and C V
if ($string =~ /T/) {
$char = 'N'; # A and G and C and T N
}
} elsif ($string =~ /T/) {
$char = 'D'; # A and G and T D
}
} elsif ($string =~ /C/) {
$char = 'M'; # A and C M
if ($string =~ /T/) {
$char = 'H'; # A and C and T H
}
} elsif ($string =~ /T/) {
$char = 'W'; # A and T W
}
} elsif ($string =~ /C/) {
$char = 'C'; # C C
if ($string =~ /T/) {
$char = 'Y'; # C and T (pyrimidines) Y
if ($string =~ /G/) {
$char = 'B'; # C and T and G B
}
} elsif ($string =~ /G/) {
$char = 'S'; # C and G S
}
} elsif ($string =~ /G/) {
$char = 'G'; # G G
if ($string =~ /C/) {
$char = 'S'; # G and C S
} elsif ($string =~ /T/) {
$char = 'K'; # G and T K
}
} elsif ($string =~ /T/) {
$char = 'T'; # T T
}
$char = 'U' if $rna and $char eq 'T';
$char = lc $char if $string =~ /\W/;
return $char;
}
=head2 is_flush
Title : is_flush
Usage : if( $ali->is_flush() )
:
:
Function : Tells you whether the alignment
: is flush, ie all of the same length
:
:
Returns : 1 or 0
Argument :
=cut
sub is_flush {
my ($self,$report) = @_;
my $seq;
my $length = (-1);
my $temp;
foreach $seq ( $self->each_seq() ) {
if( $length == (-1) ) {
$length = CORE::length($seq->seq());
next;
}
$temp = CORE::length($seq->seq());
if( $temp != $length ) {
$self->warn("expecting $length not $temp from ".
$seq->display_id) if( $report );
$self->debug("expecting $length not $temp from ".
$seq->display_id);
$self->debug($seq->seq(). "\n");
return 0;
}
}
return 1;
}
=head2 length
Title : length()
Usage : $len = $ali->length()
Function : Returns the maximum length of the alignment.
To be sure the alignment is a block, use is_flush
Returns :
Argument :
=cut
sub length_aln {
my $self = shift;
$self->warn(ref($self). "::length_aln - deprecated method. Use length() instead.");
$self->length(@_);
}
sub length {
my $self = shift;
my $seq;
my $length = (-1);
my ($temp,$len);
foreach $seq ( $self->each_seq() ) {
$temp = CORE::length($seq->seq());
if( $temp > $length ) {
$length = $temp;
}
}
return $length;
}
=head2 maxdisplayname_length
Title : maxdisplayname_length
Usage : $ali->maxdisplayname_length()
Function :
Gets the maximum length of the displayname in the
alignment. Used in writing out various MSE formats.
Returns : integer
Argument :
=cut
sub maxname_length {
my $self = shift;
$self->warn(ref($self). "::maxname_length - deprecated method.".
" Use maxdisplayname_length() instead.");
$self->maxdisplayname_length();
}
sub maxnse_length {
my $self = shift;
$self->warn(ref($self). "::maxnse_length - deprecated method.".
" Use maxnse_length() instead.");
$self->maxdisplayname_length();
}
sub maxdisplayname_length {
my $self = shift;
my $maxname = (-1);
my ($seq,$len);
foreach $seq ( $self->each_seq() ) {
$len = CORE::length $self->displayname($seq->get_nse());
if( $len > $maxname ) {
$maxname = $len;
}
}
return $maxname;
}
=head2 no_residues
Title : no_residues
Usage : $no = $ali->no_residues
Function : number of residues in total in the alignment
Returns : integer
Argument :
=cut
sub no_residues {
my $self = shift;
my $count = 0;
foreach my $seq ($self->each_seq) {
my $str = $seq->seq();
$count += ($str =~ s/[^A-Za-z]//g);
}
return $count;
}
=head2 no_sequences
Title : no_sequences
Usage : $depth = $ali->no_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument :
=cut
sub no_sequences {
my $self = shift;
return scalar($self->each_seq);
}
=head2 average_percentage_identity
Title : average_percentage_identity
Usage : $id = $align->average_percentage_identity
Function: The function uses a fast method to calculate the average
percentage identity of the alignment
Returns : The average percentage identity of the alignment
Args : None
Notes : This method implemented by Kevin Howe calculates a figure that is
designed to be similar to the average pairwise identity of the
alignment (identical in the absence of gaps), without having to
explicitly calculate pairwise identities proposed by Richard Durbin.
Validated by Ewan Birney ad Alex Bateman.
=cut
sub average_percentage_identity{
my ($self,@args) = @_;
my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');
my ($len, $total, $subtotal, $divisor, $subdivisor, @seqs, @countHashes);
if (! $self->is_flush()) {
$self->throw("All sequences in the alignment must be the same length");
}
@seqs = $self->each_seq();
$len = $self->length();
# load the each hash with correct keys for existence checks
for( my $index=0; $index < $len; $index++) {
foreach my $letter (@alphabet) {
$countHashes[$index]->{$letter} = 0;
}
}
foreach my $seq (@seqs) {
my @seqChars = split //, $seq->seq();
for( my $column=0; $column < @seqChars; $column++ ) {
my $char = uc($seqChars[$column]);
if (exists $countHashes[$column]->{$char}) {
$countHashes[$column]->{$char}++;
}
}
}
$total = 0;
$divisor = 0;
for(my $column =0; $column < $len; $column++) {
my %hash = %{$countHashes[$column]};
$subdivisor = 0;
foreach my $res (keys %hash) {
$total += $hash{$res}*($hash{$res} - 1);
$subdivisor += $hash{$res};
}
$divisor += $subdivisor * ($subdivisor - 1);
}
return $divisor > 0 ? ($total / $divisor )*100.0 : 0;
}
=head2 percentage_identity
Title : percentage_identity
Usage : $id = $align->percentage_identity
Function: The function calculates the average percentage identity
(aliased for average_percentage_identity)
Returns : The average percentage identity
Args : None
=cut
sub percentage_identity {
my $self = shift;
return $self->average_percentage_identity();
}
=head2 overall_percentage_identity
Title : percentage_identity
Usage : $id = $align->percentage_identity
Function: The function calculates the percentage identity of
the conserved columns
Returns : The percentage identity of the conserved columns
Args : None
=cut
sub overall_percentage_identity{
my ($self,@args) = @_;
my @alphabet = ('A','B','C','D','E','F','G','H','I','J','K','L','M',
'N','O','P','Q','R','S','T','U','V','W','X','Y','Z');
my ($len, $total, @seqs, @countHashes);
if (! $self->is_flush()) {
$self->throw("All sequences in the alignment must be the same length");
}
@seqs = $self->each_seq();
$len = $self->length();
# load the each hash with correct keys for existence checks
for( my $index=0; $index < $len; $index++) {
foreach my $letter (@alphabet) {
$countHashes[$index]->{$letter} = 0;
}
}
foreach my $seq (@seqs) {
my @seqChars = split //, $seq->seq();
for( my $column=0; $column < @seqChars; $column++ ) {
my $char = uc($seqChars[$column]);
if (exists $countHashes[$column]->{$char}) {
$countHashes[$column]->{$char}++;
}
}
}
$total = 0;
for(my $column =0; $column < $len; $column++) {
my %hash = %{$countHashes[$column]};
foreach ( values %hash ) {
next if( $_ == 0 );
$total++ if( $_ == scalar @seqs );
last;
}
}
return ($total / $len ) * 100.0;
}
=head1 Alignment positions
Methods to map a sequence position into an alignment column and back.
column_from_residue_number() does the former. The latter is really a
property of the sequence object and can done using
L<Bio::LocatableSeq::location_from_column>:
# select somehow a sequence from the alignment, e.g.
my $seq = $aln->get_seq_by_pos(1);
#$loc is undef or Bio::LocationI object
my $loc = $seq->location_from_column(5);
=head2 column_from_residue_number
Title : column_from_residue_number
Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber)
Function:
This function gives the position in the alignment
(i.e. column number) of the given residue number in the
sequence with the given name. For example, for the
alignment
Seq1/91-97 AC..DEF.GH
Seq2/24-30 ACGG.RTY..
Seq3/43-51 AC.DDEFGHI
column_from_residue_number( "Seq1", 94 ) returns 5.
column_from_residue_number( "Seq2", 25 ) returns 2.
column_from_residue_number( "Seq3", 50 ) returns 9.
An exception is thrown if the residue number would lie
outside the length of the aligment
(e.g. column_from_residue_number( "Seq2", 22 )
Note: If the the parent sequence is represented by more than
one alignment sequence and the residue number is present in
them, this method finds only the first one.
Returns : A column number for the position in the alignment of the
given residue in the given sequence (1 = first column)
Args : A sequence id/name (not a name/start-end)
A residue number in the whole sequence (not just that
segment of it in the alignment)
=cut
sub column_from_residue_number {
my ($self, $name, $resnumber) = @_;
$self->throw("No sequence with name [$name]") unless $self->{'_start_end_lists'}->{$name};
$self->throw("Second argument residue number missing") unless $resnumber;
foreach my $seq ($self->each_seq_with_id($name)) {
my $col;
eval {
$col = $seq->column_from_residue_number($resnumber);
};
next if $@;
return $col;
}
$self->throw("Could not find a sequence segment in $name ".
"containing residue number $resnumber");
}
=head1 Sequence names
Methods to manipulate the display name. The default name based on the
sequence id and subsequence positions can be overridden in various
ways.
=head2 displayname
Title : displayname
Usage : $myalign->displayname("Ig", "IgA")
Function : Gets/sets the display name of a sequence in the alignment
:
Returns : A display name string
Argument : name of the sequence
displayname of the sequence (optional)
=cut
sub get_displayname {
my $self = shift;
$self->warn(ref($self). "::get_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);
}
sub set_displayname {
my $self = shift;
$self->warn(ref($self). "::set_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);
}
sub displayname {
my ($self, $name, $disname) = @_;
$self->throw("No sequence with name [$name]") unless $self->{'_seq'}->{$name};
if( $disname and $name) {
$self->{'_dis_name'}->{$name} = $disname;
return $disname;
}
elsif( defined $self->{'_dis_name'}->{$name} ) {
return $self->{'_dis_name'}->{$name};
} else {
return $name;
}
}
=head2 set_displayname_count
Title : set_displayname_count
Usage : $ali->set_displayname_count
Function :
Sets the names to be name_# where # is the number of
times this name has been used.
Returns :
Argument :
=cut
sub set_displayname_count {
my $self= shift;
my (@arr,$name,$seq,$count,$temp,$nse);
foreach $seq ( $self->each_alphabetically() ) {
$nse = $seq->get_nse();
#name will be set when this is the second
#time (or greater) is has been seen
if( defined $name and $name eq ($seq->id()) ) {
$temp = sprintf("%s_%s",$name,$count);
$self->displayname($nse,$temp);
$count++;
} else {
$count = 1;
$name = $seq->id();
$temp = sprintf("%s_%s",$name,$count);
$self->displayname($nse,$temp);
$count++;
}
}
return 1;
}
=head2 set_displayname_flat
Title : set_displayname_flat
Usage : $ali->set_displayname_flat()
Function : Makes all the sequences be displayed as just their name,
not name/start-end
Returns : 1
Argument :
=cut
sub set_displayname_flat {
my $self = shift;
my ($nse,$seq);
foreach $seq ( $self->each_seq() ) {
$nse = $seq->get_nse();
$self->displayname($nse,$seq->id());
}
return 1;
}
=head2 set_displayname_normal
Title : set_displayname_normal
Usage : $ali->set_displayname_normal()
Function : Makes all the sequences be displayed as name/start-end
Returns :
Argument :
=cut
sub set_displayname_normal {
my $self = shift;
my ($nse,$seq);
foreach $seq ( $self->each_seq() ) {
$nse = $seq->get_nse();
$self->displayname($nse,$nse);
}
return 1;
}
=head2 source
Title : source
Usage : $obj->source($newval)
Function: sets the Alignment source program
Example :
Returns : value of source
Args : newvalue (optional)
=cut
sub source{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_source'} = $value;
}
return $self->{'_source'};
}
1;
]]>