# BioPerl module for SimpleAlign
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# 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();
# Describe
print $aln->length;
print $aln->num_residues;
print $aln->is_flush;
print $aln->num_sequences;
print $aln->score;
print $aln->percentage_identity;
print $aln->consensus_string(50);
# 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};
}
# Manipulate
$aln->remove_seq($seq);
$mini_aln = $aln->slice(20,30); # get a block of columns
$mini_aln = $aln->select_noncont(1,3,5,7,11); # select certain sequences
$new_aln = $aln->remove_columns([20,30]); # remove by position
$new_aln = $aln->remove_columns(['mismatch']); # remove by property
# Analyze
$str = $aln->consensus_string($threshold_percent);
$str = $aln->match_line();
$str = $aln->cigar_line();
$id = $aln->percentage_identity;
# See the module documentation for details and more methods.
=head1 DESCRIPTION
SimpleAlign is an object that handles a multiple sequence alignment
(MSA). It is very permissive of types (it does not insist on sequences
being all same length, for example). Think of it as a set of sequences
with a whole series of built-in manipulations and methods for reading and
writing alignments.
SimpleAlign uses L<Bio::LocatableSeq>, a subclass of L<Bio::PrimarySeq>,
to store its sequences. These are subsequences with a start and end
positions in the parent reference sequence. Each sequence in the
SimpleAlign object is a Bio::LocatableSeq.
SimpleAlign expects the combination of name, start, and end for a
given sequence to be unique in the alignment, and this is the key for the
internal hashes (name, start, end are abbreviated C<nse> in the code).
However, in some cases people do not 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
C<displayname>, and generally is what is used to print out the
alignment. They default to name/start-end.
The SimpleAlign Module is derived from the Align module by Ewan Birney.
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=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 the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Ewan Birney, birney@ebi.ac.uk
=head1 CONTRIBUTORS
Allen Day, allenday-at-ucla.edu,
Richard Adams, Richard.Adams-at-ed.ac.uk,
David J. Evans, David.Evans-at-vir.gla.ac.uk,
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org,
Allen Smith, allens-at-cpan.org,
Jason Stajich, jason-at-bioperl.org,
Anthony Underwood, aunderwood-at-phls.org.uk,
Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu
Brian Osborne, bosborne at alum.mit.edu
Weigang Qiu, Weigang at GENECTR-HUNTER-CUNY-EDU
Hongyu Zhang, forward at hongyu.org
Jay Hannah, jay at jays.net
Alexandr Bezginov, albezg at gmail.com
=head1 SEE ALSO
L<Bio::LocatableSeq>
=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(%CONSERVATION_GROUPS);
use strict;
use Bio::LocatableSeq; # uses Seq's as list
use Bio::Seq;
use Bio::SeqFeature::Generic;
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 )],);
}
use base qw(Bio::Root::Root Bio::Align::AlignI Bio::AnnotatableI
Bio::FeatureHolderI);
=head2 new
Title : new
Usage : my $aln = Bio::SimpleAlign->new();
Function : Creates a new simple align object
Returns : Bio::SimpleAlign
Args : -source => string representing the source program
where this alignment came from
-annotation => Bio::AnnotationCollectionI
-seq_annotation => Bio::AnnotationCollectionI for sequences (requires -annotation also be set)
-seqs => array ref containing Bio::LocatableSeq or Bio::Seq::Meta
-consensus => consensus string
-consensus_meta => Bio::Seq::Meta object containing consensus met information (kludge)
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($src, $score, $id, $acc, $desc, $seqs, $feats, $coll, $sa, $con, $cmeta) = $self->_rearrange([qw(
SOURCE
SCORE
ID
ACCESSION
DESCRIPTION
SEQS
FEATURES
ANNOTATION
SEQ_ANNOTATION
CONSENSUS
CONSENSUS_META
)], @args);
$src && $self->source($src);
defined $score && $self->score($score);
# we need to set up internal hashs first!
$self->{'_seq'} = {};
$self->{'_order'} = {};
$self->{'_start_end_lists'} = {};
$self->{'_dis_name'} = {};
$self->{'_id'} = 'NoName';
# maybe we should automatically read in from args. Hmmm...
$id && $self->id($id);
$acc && $self->accession($acc);
$desc && $self->description($desc);
$coll && $self->annotation($coll);
# sequence annotation is layered into a provided annotation collection (or dies)
if ($sa) {
$self->throw("Must supply an alignment-based annotation collection (-annotation) ".
"with a sequence annotation collection")
if !$coll;
$coll->add_Annotation('seq_annotation', $sa);
}
if ($feats && ref $feats eq 'ARRAY') {
for my $feat (@$feats) {
$self->add_SeqFeature($feat);
}
}
$con && $self->consensus($con);
$cmeta && $self->consensus_meta($cmeta);
# assumes these are in correct alignment order
if ($seqs && ref($seqs) eq 'ARRAY') {
for my $seq (@$seqs) {
$self->add_seq($seq);
}
}
return $self; # success - we hope!
}
=head1 Modifier methods
These methods modify the MSA by adding, removing or shuffling complete
sequences.
=head2 add_seq
Title : add_seq
Usage : $myalign->add_seq($newseq);
$myalign->add_seq(-SEQ=>$newseq, -ORDER=>5);
Function : Adds another sequence to the alignment. *Does not* align
it - just adds it to the hashes.
If -ORDER is specified, the sequence is inserted at the
the position spec'd by -ORDER, and existing sequences
are pushed down the storage array.
Returns : nothing
Args : A Bio::LocatableSeq object
Positive integer for the sequence position (optional)
See L<Bio::LocatableSeq> for more information
=cut
sub addSeq {
my $self = shift;
$self->deprecated("addSeq - deprecated method. Use add_seq() instead.");
$self->add_seq(@_);
}
sub add_seq {
my $self = shift;
my @args = @_;
my ($seq, $order) = $self->_rearrange([qw(SEQ ORDER)], @args);
my ($name,$id,$start,$end);
unless ($seq) {
$self->throw("LocatableSeq argument required");
}
if( ! ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
$self->throw("Unable to process non locatable sequences [". ref($seq). "]");
}
!defined($order) and $order = 1 + keys %{$self->{'_seq'}}; # default
$order--; # jay's patch (user-specified order is 1-origin)
if ($order < 0) {
$self->throw("User-specified value for ORDER must be >= 1");
}
$id = $seq->id() ||$seq->display_id || $seq->primary_id;
# 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 $seq->seq;
$name = $seq->get_nse;
if( $self->{'_seq'}->{$name} ) {
$self->warn("Replacing one sequence [$name]\n") unless $self->verbose < 0;
}
else {
$self->debug( "Assigning $name to $order\n");
my $ordh = $self->{'_order'};
if ($ordh->{$order}) {
# make space to insert
# $c->() returns (in reverse order) the first subsequence
# of consecutive integers; i.e., $c->(1,2,3,5,6,7) returns
# (3,2,1), and $c->(2,4,5) returns (2).
my $c;
$c = sub { return (($_[1]-$_[0] == 1) ? ($c->(@_[1..$#_]),$_[0]) : $_[0]); };
map {
$ordh->{$_+1} = $ordh->{$_}
} $c->(sort {$a <=> $b} grep {$_ >= $order} keys %{$ordh});
}
$ordh->{$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->deprecated("removeSeq - deprecated method. Use remove_seq() instead.");
$self->remove_seq(@_);
}
sub remove_seq {
my $self = shift;
my $seq = shift;
my ($name,$id);
$self->throw("Need Bio::Locatable seq argument ")
unless ref $seq && $seq->isa( 'Bio::LocatableSeq');
$id = $seq->id();
$name = $seq->get_nse;
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 $id");
}
# we need to shift order hash
my %rev_order = reverse %{$self->{'_order'}};
my $no = $rev_order{$name};
my $num_sequences = $self->num_sequences;
for (; $no < $num_sequences; $no++) {
$self->{'_order'}->{$no} = $self->{'_order'}->{$no+1};
}
delete $self->{'_order'}->{$no};
return 1;
}
=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 ) {
$self->warn("duplicate: ", $seq2->display_id) 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 alignment 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;
}
=head2 sort_by_list
Title : sort_by_list
Usage : $aln_ordered=$aln->sort_by_list($list_file)
Function : Arbitrarily order sequences in an alignment
Returns : A new Bio::SimpleAlign object
Argument : a file listing sequence names in intended order (one name per line)
=cut
sub sort_by_list {
my ($self, $list) = @_;
my (@seq, @ids, %order);
foreach my $seq ( $self->each_seq() ) {
push @seq, $seq;
push @ids, $seq->display_id;
}
my $ct=1;
open(my $listfh, '<', $list) || $self->throw("can't open file for reading: $list");
while (<$listfh>) {
chomp;
my $name=$_;
$self->throw("Not found in alignment: $name") unless &_in_aln($name, \@ids);
$order{$name}=$ct++;
}
close($listfh);
# use the map-sort-map idiom:
my @sorted= map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$order{$_->id()}, $_] } @seq;
my $aln = $self->new;
foreach (@sorted) { $aln->add_seq($_) }
return $aln;
}
=head2 set_new_reference
Title : set_new_reference
Usage : $aln->set_new_reference(3 or 'B31'): Select the 3rd sequence, or
the sequence whoes name is "B31" (full, exact, and case-sensitive),
as the reference (1st) sequence
Function : Change/Set a new reference (i.e., the first) sequence
Returns : a new Bio::SimpleAlign object.
Throws an exception if designated sequence not found
Argument : a positive integer of sequence order, or a sequence name
in the original alignment
=cut
sub set_new_reference {
my ($self, $seqid) = @_;
my $aln = $self->new;
my (@seq, @ids, @new_seq);
my $is_num=0;
foreach my $seq ( $self->each_seq() ) {
push @seq, $seq;
push @ids, $seq->display_id;
}
if ($seqid =~ /^\d+$/) { # argument is seq position
$is_num=1;
$self->throw("The new reference sequence number has to be a positive integer >1 and <= num_sequences ") if ($seqid <= 1 || $seqid > $self->num_sequences);
} else { # argument is a seq name
$self->throw("The new reference sequence not in alignment ") unless &_in_aln($seqid, \@ids);
}
for (my $i=0; $i<=$#seq; $i++) {
my $pos=$i+1;
if ( ($is_num && $pos == $seqid) || ($seqid eq $seq[$i]->display_id) ) {
unshift @new_seq, $seq[$i];
} else {
push @new_seq, $seq[$i];
}
}
foreach (@new_seq) { $aln->add_seq($_); }
return $aln;
}
sub _in_aln { # check if input name exists in the alignment
my ($str, $ref) = @_;
foreach (@$ref) {
return 1 if $str eq $_;
}
return 0;
}
=head2 uniq_seq
Title : uniq_seq
Usage : $aln->uniq_seq(): Remove identical sequences in
in the alignment. Ambiguous base ("N", "n") and
leading and ending gaps ("-") are NOT counted as
differences.
Function : Make a new alignment of unique sequence types (STs)
Returns : 1a. if called in a scalar context,
a new Bio::SimpleAlign object (all sequences renamed as "ST")
1b. if called in an array context,
a new Bio::SimpleAlign object, and a hashref whose keys
are sequence types, and whose values are arrayrefs to
lists of sequence ids within the corresponding sequence type
2. if $aln->verbose > 0, ST of each sequence is sent to
STDERR (in a tabular format)
Argument : None
=cut
sub uniq_seq {
my ($self, $seqid) = @_;
my $aln = $self->new;
my (%member, %order, @seq, @uniq_str, $st);
my $order=0;
my $len = $self->length();
$st = {};
foreach my $seq ( $self->each_seq() ) {
my $str = $seq->seq();
# it's necessary to ignore "n", "N", leading gaps and ending gaps in
# comparing two sequence strings
# 1st, convert "n", "N" to "?" (for DNA sequence only):
$str =~ s/n/\?/gi if $str =~ /^[atcgn-]+$/i;
# 2nd, convert leading and ending gaps to "?":
$str = &_convert_leading_ending_gaps($str, '-', '?');
# Note that '?' also can mean unknown residue.
# I don't like making global class member changes like this, too
# prone to errors... -- cjfields 08-11-18
local $Bio::LocatableSeq::GAP_SYMBOLS = '-\?';
my $new = Bio::LocatableSeq->new(
-id => $seq->id(),
-alphabet=> $seq->alphabet,
-seq => $str,
-start => $seq->start,
-end => $seq->end
);
push @seq, $new;
}
foreach my $seq (@seq) {
my $str = $seq->seq();
my ($seen, $key) = &_check_uniq($str, \@uniq_str, $len);
if ($seen) { # seen before
my @memb = @{$member{$key}};
push @memb, $seq;
$member{$key} = \@memb;
} else { # not seen
push @uniq_str, $key;
$order++;
$member{$key} = [ ($seq) ];
$order{$key} = $order;
}
}
foreach my $str (sort {$order{$a} <=> $order{$b}} keys %order) { # sort by input order
# convert leading/ending "?" back into "-" ("?" throws errors by SimpleAlign):
my $str2 = &_convert_leading_ending_gaps($str, '?', '-');
# convert middle "?" back into "N" ("?" throws errors by SimpleAlign):
$str2 =~ s/\?/N/g if $str2 =~ /^[atcg\-\?]+$/i;
my $gap='-';
my $end= CORE::length($str2);
$end -= CORE::length($1) while $str2 =~ m/($gap+)/g;
my $new = Bio::LocatableSeq->new(-id =>"ST".$order{$str},
-seq =>$str2,
-start=>1,
-end =>$end
);
$aln->add_seq($new);
foreach (@{$member{$str}}) {
push @{$$st{$order{$str}}}, $_->id(); # per Tristan's patch/Bug #2805
$self->debug($_->id(), "\t", "ST", $order{$str}, "\n");
}
}
return wantarray ? ($aln, $st) : $aln;
}
sub _check_uniq { # check if same seq exists in the alignment
my ($str1, $ref, $length) = @_;
my @char1=split //, $str1;
my @array=@$ref;
return (0, $str1) if @array==0; # not seen (1st sequence)
foreach my $str2 (@array) {
my $diff=0;
my @char2=split //, $str2;
for (my $i=0; $i<=$length-1; $i++) {
next if $char1[$i] eq '?';
next if $char2[$i] eq '?';
$diff++ if $char1[$i] ne $char2[$i];
}
return (1, $str2) if $diff == 0; # seen before
}
return (0, $str1); # not seen
}
sub _convert_leading_ending_gaps {
my $s=shift;
my $sym1=shift;
my $sym2=shift;
my @array=split //, $s;
# convert leading char:
for (my $i=0; $i<=$#array; $i++) {
($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last);
}
# convert ending char:
for (my $i = $#array; $i>= 0; $i--) {
($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last);
}
my $s_new=join '', @array;
return $s_new;
}
=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 a Seq object from the alignment
Returns : Seq object
Argument :
=cut
sub eachSeq {
my $self = shift;
$self->deprecated("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 a sequence object, but the objects are returned
in alphabetically sorted order.
Does not change the order of the alignment.
Returns : Seq object
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 a Seq objects from the alignment, the contents
being those sequences with the given name (there may be
more than one)
Returns : Seq object
Argument : a seq name
=cut
sub eachSeqWithId {
my $self = shift;
$self->deprecated("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
num_sequences() will throw an error.
Returns : a Bio::LocatableSeq object
Args : positive integer for the sequence position
=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->num_sequences ;
my $nse = $self->{'_order'}->{--$pos};
return $self->{'_seq'}->{$nse};
}
=head2 get_seq_by_id
Title : get_seq_by_id
Usage : $seq = $aln->get_seq_by_id($name) # seq named $name
Function : Gets a sequence based on its name.
Sequences that do not exist will warn and return undef
Returns : a Bio::LocatableSeq object
Args : string for sequence name
=cut
sub get_seq_by_id {
my ($self,$name) = @_;
unless( defined $name ) {
$self->warn("Must provide a sequence name");
return;
}
for my $seq ( values %{$self->{'_seq'}} ) {
if ( $seq->id eq $name) {
return $seq;
}
}
return;
}
=head2 seq_with_features
Title : seq_with_features
Usage : $seq = $aln->seq_with_features(-pos => 1,
-consensus => 60
-mask =>
sub { my $consensus = shift;
for my $i (1..5){
my $n = 'N' x $i;
my $q = '\?' x $i;
while($consensus =~ /[^?]$q[^?]/){
$consensus =~ s/([^?])$q([^?])/$1$n$2/;
}
}
return $consensus;
}
);
Function: produces a Bio::Seq object by first splicing gaps from -pos
(by means of a splice_by_seq_pos() call), then creating
features using non-? chars (by means of a consensus_string()
call with stringency -consensus).
Returns : a Bio::Seq object
Args : -pos : required. sequence from which to build the Bio::Seq
object
-consensus : optional, defaults to consensus_string()'s
default cutoff value
-mask : optional, a coderef to apply to consensus_string()'s
output before building features. this may be useful for
closing gaps of 1 bp by masking over them with N, for
instance
=cut
sub seq_with_features{
my ($self,%arg) = @_;
#first do the preparatory splice
$self->throw("must provide a -pos argument") unless $arg{-pos};
$self->splice_by_seq_pos($arg{-pos});
my $consensus_string = $self->consensus_string($arg{-consensus});
$consensus_string = $arg{-mask}->($consensus_string)
if defined($arg{-mask});
my(@bs,@es);
push @bs, 1 if $consensus_string =~ /^[^?]/;
while($consensus_string =~ /\?[^?]/g){
push @bs, pos($consensus_string);
}
while($consensus_string =~ /[^?]\?/g){
push @es, pos($consensus_string);
}
push @es, CORE::length($consensus_string) if $consensus_string =~ /[^?]$/;
my $seq = Bio::Seq->new();
# my $rootfeature = Bio::SeqFeature::Generic->new(
# -source_tag => 'location',
# -start => $self->get_seq_by_pos($arg{-pos})->start,
# -end => $self->get_seq_by_pos($arg{-pos})->end,
# );
# $seq->add_SeqFeature($rootfeature);
while(my $b = shift @bs){
my $e = shift @es;
$seq->add_SeqFeature(
Bio::SeqFeature::Generic->new(
-start => $b - 1 + $self->get_seq_by_pos($arg{-pos})->start,
-end => $e - 1 + $self->get_seq_by_pos($arg{-pos})->start,
-source_tag => $self->source || 'MSA',
)
);
}
return $seq;
}
=head1 Create new alignments
The result of these methods are horizontal or vertical subsets of the
current MSA.
=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 num_sequences() will throw 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 = $self->new;
foreach my $pos ($start .. $end) {
$aln->add_seq($self->get_seq_by_pos($pos));
}
$aln->id($self->id);
# fix for meta, sf, ann
return $aln;
}
=head2 select_noncont
Title : select_noncont
Usage : # 1st and 3rd sequences, sorted
$aln2 = $aln->select_noncont(1, 3)
# 1st and 3rd sequences, sorted (same as first)
$aln2 = $aln->select_noncont(3, 1)
# 1st and 3rd sequences, unsorted
$aln2 = $aln->select_noncont('nosort',3, 1)
Function : Creates a new alignment from a subset of sequences. Numbering
starts from 1. Sequence positions larger than num_sequences() will
throw an error. Sorts the order added to new alignment by default,
to prevent sorting pass 'nosort' as the first argument in the list.
Returns : a Bio::SimpleAlign object
Args : array of integers for the sequences. If the string 'nosort' is
passed as the first argument, the sequences will not be sorted
in the new alignment but will appear in the order listed.
=cut
sub select_noncont {
my $self = shift;
my $nosort = 0;
my (@pos) = @_;
if ($pos[0] !~ m{^\d+$}) {
my $sortcmd = shift @pos;
if ($sortcmd eq 'nosort') {
$nosort = 1;
} else {
$self->throw("Command not recognized: $sortcmd. Only 'nosort' implemented at this time.");
}
}
my $end = $self->num_sequences;
foreach ( @pos ) {
$self->throw("position must be a positive integer, > 0 and <= $end not [$_]")
unless( /^\d+$/ && $_ > 0 && $_ <= $end );
}
@pos = sort {$a <=> $b} @pos unless $nosort;
my $aln = $self->new;
foreach my $p (@pos) {
$aln->add_seq($self->get_seq_by_pos($p));
}
$aln->id($self->id);
# fix for meta, sf, ann
return $aln;
}
=head2 select_noncont_by_name
Title : select_noncont_by_name
Usage : my $aln2 = $aln->select_noncont_by_name('A123', 'B456');
Function : Creates a new alignment from a subset of sequences which are
selected by name (sequence ID).
Returns : a Bio::SimpleAlign object
Args : array of names (i.e., identifiers) for the sequences.
=cut
sub select_noncont_by_name {
my ($self, @names) = @_;
my $aln = $self->new;
foreach my $name (@names) {
$aln->add_seq($self->get_seq_by_id($name));
}
$aln->id($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, and the first column in the alignment is denoted 1.
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,
optional boolean which if true will keep gap-only columns in the newly
created slice. Example:
$aln2 = $aln->slice(20,30,1)
=cut
sub slice {
my $self = shift;
my ($start, $end, $keep_gap_only) = @_;
$self->throw("Slice start has to be a positive integer, not [$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;
$self->throw("This alignment has only ". $self->length . " residues. Slice start " .
"[$start] is too big.") if $start > $self->length;
my $cons_meta = $self->consensus_meta;
my $aln = $self->new;
$aln->id($self->id);
foreach my $seq ( $self->each_seq() ) {
my $new_seq = $seq->isa('Bio::Seq::MetaI') ?
Bio::Seq::Meta->new
(-id => $seq->id,
-alphabet => $seq->alphabet,
-strand => $seq->strand,
-verbose => $self->verbose) :
Bio::LocatableSeq->new
(-id => $seq->id,
-alphabet => $seq->alphabet,
-strand => $seq->strand,
-verbose => $self->verbose);
# 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 );
$slice_seq =~ s/\W//g;
if ($start > 1) {
my $pre_start_seq = $seq->subseq(1, $start - 1);
$pre_start_seq =~ s/\W//g;
if (!defined($seq->strand)) {
$new_seq->start( $seq->start + CORE::length($pre_start_seq) );
} elsif ($seq->strand < 0){
$new_seq->start( $seq->end - CORE::length($pre_start_seq) - CORE::length($slice_seq) + 1);
} else {
$new_seq->start( $seq->start + CORE::length($pre_start_seq) );
}
} else {
if ((defined $seq->strand)&&($seq->strand < 0)){
$new_seq->start( $seq->end - CORE::length($slice_seq) + 1);
} else {
$new_seq->start( $seq->start);
}
}
if ($new_seq->isa('Bio::Seq::MetaI')) {
for my $meta_name ($seq->meta_names) {
$new_seq->named_meta($meta_name, $seq->named_submeta($meta_name, $start, $end));
}
}
$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 {
if( $keep_gap_only ) {
$aln->add_seq($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.");
}
}
}
if ($cons_meta) {
my $new = Bio::Seq::Meta->new();
for my $meta_name ($cons_meta->meta_names) {
$new->named_meta($meta_name, $cons_meta->named_submeta($meta_name, $start, $end));
}
$aln->consensus_meta($new);
}
$aln->annotation($self->annotation);
# fix for meta, sf, ann
return $aln;
}
=head2 remove_columns
Title : remove_columns
Usage : $aln2 = $aln->remove_columns(['mismatch','weak']) or
$aln2 = $aln->remove_columns([0,0],[6,8])
Function : Creates an aligment with columns removed corresponding to
the specified type or by specifying the columns by number.
Returns : Bio::SimpleAlign object
Args : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'|
'all_gaps_columns') or array ref where the referenced array
contains a pair of integers that specify a range.
The first column is 0
=cut
sub remove_columns {
my ($self,@args) = @_;
@args || $self->throw("Must supply column ranges or column types");
my $aln;
if ($args[0][0] =~ /^[a-z_]+$/i) {
$aln = $self->_remove_columns_by_type($args[0]);
} elsif ($args[0][0] =~ /^\d+$/) {
$aln = $self->_remove_columns_by_num(\@args);
} else {
$self->throw("You must pass array references to remove_columns(), not @args");
}
# fix for meta, sf, ann
$aln;
}
=head2 remove_gaps
Title : remove_gaps
Usage : $aln2 = $aln->remove_gaps
Function : Creates an aligment with gaps removed
Returns : a Bio::SimpleAlign object
Args : a gap character(optional) if none specified taken
from $self->gap_char,
[optional] $all_gaps_columns flag (1 or 0, default is 0)
indicates that only all-gaps columns should be deleted
Used from method L<remove_columns> in most cases. Set gap character
using L<gap_char()|gap_char>.
=cut
sub remove_gaps {
my ($self,$gapchar,$all_gaps_columns) = @_;
my $gap_line;
if ($all_gaps_columns) {
$gap_line = $self->all_gap_line($gapchar);
} else {
$gap_line = $self->gap_line($gapchar);
}
my $aln = $self->new;
my @remove;
my $length = 0;
my $del_char = $gapchar || $self->gap_char;
# Do the matching to get the segments to remove
while ($gap_line =~ m/[$del_char]/g) {
my $start = pos($gap_line)-1;
$gap_line =~ m/\G[$del_char]+/gc;
my $end = pos($gap_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 = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
# fix for meta, sf, ann
return $aln;
}
sub _remove_col {
my ($self,$aln,$remove) = @_;
my @new;
my $gap = $self->gap_char;
# splice out the segments and create new seq
foreach my $seq($self->each_seq){
my $new_seq = Bio::LocatableSeq->new(
-id => $seq->id,
-alphabet=> $seq->alphabet,
-strand => $seq->strand,
-verbose => $self->verbose);
my $sequence = $seq->seq;
foreach my $pair(@{$remove}){
my $start = $pair->[0];
my $end = $pair->[1];
$sequence = $seq->seq unless $sequence;
my $orig = $sequence;
my $head = $start > 0 ? substr($sequence, 0, $start) : '';
my $tail = ($end + 1) >= CORE::length($sequence) ? '' : substr($sequence, $end + 1);
$sequence = $head.$tail;
# start
unless (defined $new_seq->start) {
if ($start == 0) {
my $start_adjust = () = substr($orig, 0, $end + 1) =~ /$gap/g;
$new_seq->start($seq->start + $end + 1 - $start_adjust);
}
else {
my $start_adjust = $orig =~ /^$gap+/;
if ($start_adjust) {
$start_adjust = $+[0] == $start;
}
$new_seq->start($seq->start + $start_adjust);
}
}
# end
if (($end + 1) >= CORE::length($orig)) {
my $end_adjust = () = substr($orig, $start) =~ /$gap/g;
$new_seq->end($seq->end - (CORE::length($orig) - $start) + $end_adjust);
}
else {
$new_seq->end($seq->end);
}
}
if ($new_seq->end < $new_seq->start) {
# we removed all columns except for gaps: set to 0 to indicate no
# sequence
$new_seq->start(0);
$new_seq->end(0);
}
$new_seq->seq($sequence) if $sequence;
push @new, $new_seq;
}
# add the new seqs to the alignment
foreach my $new(@new){
$aln->add_seq($new);
}
# fix for meta, sf, ann
return $aln;
}
sub _remove_columns_by_type {
my ($self,$type) = @_;
my $aln = $self->new;
my @remove;
my $gap = $self->gap_char if (grep { $_ eq 'gaps'} @{$type});
my $all_gaps_columns = $self->gap_char if (grep /all_gaps_columns/,@{$type});
my %matchchars = ( 'match' => '\*',
'weak' => '\.',
'strong' => ':',
'mismatch' => ' ',
'gaps' => '',
'all_gaps_columns' => ''
);
# get the characters to delete against
my $del_char;
foreach my $type (@{$type}){
$del_char.= $matchchars{$type};
}
my $length = 0;
my $match_line = $self->match_line;
# do the matching to get the segments to remove
if($del_char){
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 = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
$aln = $aln->remove_gaps() if $gap;
$aln = $aln->remove_gaps('', 1) if $all_gaps_columns;
# fix for meta, sf, ann
$aln;
}
sub _remove_columns_by_num {
my ($self,$positions) = @_;
my $aln = $self->new;
# sort the positions
@$positions = sort { $a->[0] <=> $b->[0] } @$positions;
my @remove;
my $length = 0;
foreach my $pos (@{$positions}) {
my ($start, $end) = @{$pos};
#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 = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
# fix for meta, sf, ann
$aln;
}
=head1 Change sequences within the MSA
These methods affect characters in all sequences without changing the
alignment.
=head2 splice_by_seq_pos
Title : splice_by_seq_pos
Usage : $status = splice_by_seq_pos(1);
Function: splices all aligned sequences where the specified sequence
has gaps.
Example :
Returns : 1 on success
Args : position of sequence to splice by
=cut
sub splice_by_seq_pos{
my ($self,$pos) = @_;
my $guide = $self->get_seq_by_pos($pos);
my $guide_seq = $guide->seq;
$guide_seq =~ s/\./\-/g;
my @gaps = ();
$pos = -1;
while(($pos = index($guide_seq, '-', $pos)) > -1 ){
unshift @gaps, $pos;
$pos++;
}
foreach my $seq ($self->each_seq){
my @bases = split '', $seq->seq;
splice(@bases, $_, 1) foreach @gaps;
$seq->seq(join('', @bases));
}
1;
}
=head2 map_chars
Title : map_chars
Usage : $ali->map_chars('\.','-')
Function : Does a s/$arg1/$arg2/ on the sequences. Useful for gap
characters.
Note that the first argument is interpreted as a regexp
so be careful and escape any wild card characters (e.g.
do $ali->map_chars('\.','-') to replace periods with dashes.
Returns : 1 on success
Argument : A regexp and a string
=cut
sub map_chars {
my $self = shift;
my $from = shift;
my $to = shift;
my ( $seq, $temp );
$self->throw("Need two arguments: a regexp and a string")
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 : 1 on success
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 : %cigars = $align->cigar_line()
Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment
Report) line for each sequence in the alignment. Examples are
"1,60" or "5,10:12,58", where the numbers refer to conserved
positions within the alignment. The keys of the hash are the
NSEs (name/start/end) assigned to each sequence.
Args : threshold (optional, defaults to 100)
Returns : Hash of strings (cigar lines)
=cut
sub cigar_line {
my $self = shift;
my $thr=shift||100;
my %cigars;
my @consensus = split "",($self->consensus_string($thr));
my $len = $self->length;
my $gapchar = $self->gap_char;
# create a precursor, something like (1,4,5,6,7,33,45),
# where each number corresponds to a conserved position
foreach my $seq ( $self->each_seq ) {
my @seq = split "", uc ($seq->seq);
my $pos = 1;
for (my $x = 0 ; $x < $len ; $x++ ) {
if ($seq[$x] eq $consensus[$x]) {
push @{$cigars{$seq->get_nse}},$pos;
$pos++;
} elsif ($seq[$x] ne $gapchar) {
$pos++;
}
}
}
# duplicate numbers - (1,4,5,6,7,33,45) becomes (1,1,4,5,6,7,33,33,45,45)
for my $name (keys %cigars) {
splice @{$cigars{$name}}, 1, 0, ${$cigars{$name}}[0] if
( ${$cigars{$name}}[0] + 1 < ${$cigars{$name}}[1] );
push @{$cigars{$name}}, ${$cigars{$name}}[$#{$cigars{$name}}] if
( ${$cigars{$name}}[($#{$cigars{$name}} - 1)] + 1 <
${$cigars{$name}}[$#{$cigars{$name}}] );
for ( my $x = 1 ; $x < $#{$cigars{$name}} - 1 ; $x++) {
if (${$cigars{$name}}[$x - 1] + 1 < ${$cigars{$name}}[$x] &&
${$cigars{$name}}[$x + 1] > ${$cigars{$name}}[$x] + 1) {
splice @{$cigars{$name}}, $x, 0, ${$cigars{$name}}[$x];
}
}
}
# collapse series - (1,1,4,5,6,7,33,33,45,45) becomes (1,1,4,7,33,33,45,45)
for my $name (keys %cigars) {
my @remove;
for ( my $x = 0 ; $x < $#{$cigars{$name}} ; $x++) {
if ( ${$cigars{$name}}[$x] == ${$cigars{$name}}[($x - 1)] + 1 &&
${$cigars{$name}}[$x] == ${$cigars{$name}}[($x + 1)] - 1 ) {
unshift @remove,$x;
}
}
for my $pos (@remove) {
splice @{$cigars{$name}}, $pos, 1;
}
}
# join and punctuate
for my $name (keys %cigars) {
my ($start,$end,$str) = "";
while ( ($start,$end) = splice @{$cigars{$name}}, 0, 2 ) {
$str .= ($start . "," . $end . ":");
}
$str =~ s/:$//;
$cigars{$name} = $str;
}
%cigars;
}
=head2 match_line
Title : match_line()
Usage : $line = $align->match_line()
Function : Generates a match line - much like consensus string
except that a line indicating the '*' for a match.
Args : (optional) Match line characters ('*' by default)
(optional) Strong match char (':' by default)
(optional) Weak match char ('.' by default)
Returns : String
=cut
sub match_line {
my ($self,$matchlinechar, $strong, $weak) = @_;
my %matchchars = ('match' => $matchlinechar || '*',
'weak' => $weak || '.',
'strong' => $strong || ':',
'mismatch' => ' ',
);
my @seqchars;
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];
my $char = $matchchars{'mismatch'};
unless( defined $refchar ) {
last if $pos == $self->length; # short circuit on last residue
# this in place to handle jason's soon-to-be-committed
# intron mapping code
goto bottom;
}
my %col = ($refchar => 1);
my $dash = ($refchar eq '-' || $refchar eq '.' || $refchar eq ' ');
foreach my $seq ( @seqchars ) {
next if $pos >= scalar @$seq;
$dash = 1 if( $seq->[$pos] eq '-' || $seq->[$pos] eq '.' ||
$seq->[$pos] eq ' ' );
$col{$seq->[$pos]}++ if defined $seq->[$pos];
}
my @colresidues = sort keys %col;
# 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 $f ( grep { index($_,$c) >= 0 } @{$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;
}
}
}
bottom:
$matchline .= $char;
}
return $matchline;
}
=head2 gap_line
Title : gap_line()
Usage : $line = $align->gap_line()
Function : Generates a gap line - much like consensus string
except that a line where '-' represents gap
Args : (optional) gap line characters ('-' by default)
Returns : string
=cut
sub gap_line {
my ($self,$gapchar) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh; # column gaps vector
foreach my $seq ( $self->each_seq ) {
my $i = 0;
map {$gap_hsh{$_->[0]} = undef} grep {$_->[1] =~ m/[$gapchar]/}
map {[$i++, $_]} split(//, uc ($seq->seq));
}
my $gap_line;
foreach my $pos ( 0..$self->length-1 ) {
$gap_line .= (exists $gap_hsh{$pos}) ? $self->gap_char:'.';
}
return $gap_line;
}
=head2 all_gap_line
Title : all_gap_line()
Usage : $line = $align->all_gap_line()
Function : Generates a gap line - much like consensus string
except that a line where '-' represents all-gap column
Args : (optional) gap line characters ('-' by default)
Returns : string
=cut
sub all_gap_line {
my ($self,$gapchar) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh; # column gaps counter hash
my @seqs = $self->each_seq;
foreach my $seq ( @seqs ) {
my $i = 0;
map {$gap_hsh{$_->[0]}++} grep {$_->[1] =~ m/[$gapchar]/}
map {[$i++, $_]} split(//, uc ($seq->seq));
}
my $gap_line;
foreach my $pos ( 0..$self->length-1 ) {
if (exists $gap_hsh{$pos} && $gap_hsh{$pos} == scalar @seqs) {
# gaps column
$gap_line .= $self->gap_char;
} else {
$gap_line .= '.';
}
}
return $gap_line;
}
=head2 gap_col_matrix
Title : gap_col_matrix()
Usage : my $cols = $align->gap_col_matrix()
Function : Generates an array where each element in the array is a
hash reference with a key of the sequence name and a
value of 1 if the sequence has a gap at that column
Returns : Reference to an array
Args : Optional: gap line character ($aln->gap_char or '-' by default)
=cut
sub gap_col_matrix {
my ( $self, $gapchar ) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh; # column gaps vector
my @cols;
foreach my $seq ( $self->each_seq ) {
my $i = 0;
my $str = $seq->seq;
my $len = $seq->length;
my $ch;
my $id = $seq->display_id;
while ( $i < $len ) {
$ch = substr( $str, $i, 1 );
$cols[ $i++ ]->{$id} = ( $ch =~ m/[$gapchar]/ );
}
}
return \@cols;
}
=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 MSA 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 on success
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 on success
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 MSA attributes
Methods for setting and reading the MSA 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 accession
Title : accession
Usage : $myalign->accession("PF00244")
Function : Gets/sets the accession field of the alignment
Returns : An acc string
Argument : An acc string (optional)
=cut
sub accession {
my ( $self, $acc ) = @_;
if ( defined($acc) ) {
$self->{'_accession'} = $acc;
}
return $self->{'_accession'};
}
=head2 description
Title : description
Usage : $myalign->description("14-3-3 proteins")
Function : Gets/sets the description field of the alignment
Returns : An description string
Argument : An description string (optional)
=cut
sub description {
my ( $self, $name ) = @_;
if ( defined($name) ) {
$self->{'_description'} = $name;
}
return $self->{'_description'};
}
=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,$includeextra) = @_;
unless ($self->{'_symbols'}) {
foreach my $seq ($self->each_seq) {
map { $self->{'_symbols'}->{$_} = 1; } split(//,$seq->seq);
}
}
my %copy = %{$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 MSA in various ways.
=head2 score
Title : score
Usage : $str = $ali->score()
Function : get/set a score of the alignment
Returns : a score for the alignment
Argument : an optional score to set
=cut
sub score {
my $self = shift;
$self->{score} = shift if @_;
return $self->{score};
}
=head2 consensus_string
Title : consensus_string
Usage : $str = $ali->consensus_string($threshold_percent)
Function : Makes a strict consensus
Returns : Consensus string
Argument : Optional threshold 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 $out = "";
my $len = $self->length - 1;
foreach ( 0 .. $len ) {
$out .= $self->_consensus_aa( $_, $threshold );
}
return $out;
}
=head2 consensus_conservation
Title : consensus_conservation
Usage : @conservation = $ali->consensus_conservation();
Function : Conservation (as a percent) of each position of alignment
Returns : Array of percentages [0-100]. Gap columns are 0% conserved.
Argument :
=cut
sub consensus_conservation {
my $self = shift;
my @cons;
my $num_sequences = $self->num_sequences;
foreach my $point (0..$self->length-1) {
my %hash = $self->_consensus_counts($point);
# max frequency of a non-gap letter
my $max = (sort {$b<=>$a} values %hash )[0];
push @cons, 100 * $max / $num_sequences;
}
return @cons;
}
sub _consensus_aa {
my $self = shift;
my $point = shift;
my $threshold_percent = shift || -1 ;
my ($seq,%hash,$count,$letter,$key);
my $gapchar = $self->gap_char;
%hash = $self->_consensus_counts($point);
my $number_of_sequences = $self->num_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;
}
# Frequency of each letter in one column
sub _consensus_counts {
my $self = shift;
my $point = shift;
my %hash;
my $gapchar = $self->gap_char;
foreach my $seq ( $self->each_seq() ) {
my $letter = substr($seq->seq,$point,1);
$self->throw("--$point-----------") if $letter eq '';
($letter eq $gapchar || $letter =~ /\./) && next;
$hash{$letter}++;
}
return %hash;
}
=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 consensus_meta
Title : consensus_meta
Usage : $seqmeta = $ali->consensus_meta()
Function : Returns a Bio::Seq::Meta object containing the consensus
strings derived from meta data analysis.
Returns : Bio::Seq::Meta
Argument : Bio::Seq::Meta
Throws : non-MetaI object
=cut
sub consensus_meta {
my ($self, $meta) = @_;
if ($meta && (!ref $meta || !$meta->isa('Bio::Seq::MetaI'))) {
$self->throw('Not a Bio::Seq::MetaI object');
}
return $self->{'_aln_meta'} = $meta if $meta;
return $self->{'_aln_meta'}
}
=head2 is_flush
Title : is_flush
Usage : if ( $ali->is_flush() )
Function : Tells you whether the alignment
: is flush, i.e. 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 : Integer
Argument :
=cut
sub length_aln {
my $self = shift;
$self->deprecated("length_aln - deprecated method. Use length() instead.");
$self->length(@_);
}
sub length {
my $self = shift;
my $seq;
my $length = -1;
my $temp;
foreach $seq ( $self->each_seq() ) {
$temp = $seq->length();
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 MSA formats.
Returns : integer
Argument :
=cut
sub maxname_length {
my $self = shift;
$self->deprecated("maxname_length - deprecated method.".
" Use maxdisplayname_length() instead.");
$self->maxdisplayname_length();
}
sub maxnse_length {
my $self = shift;
$self->deprecated("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 max_metaname_length
Title : max_metaname_length
Usage : $ali->max_metaname_length()
Function : Gets the maximum length of the meta name tags in the
alignment for the sequences and for the alignment.
Used in writing out various MSA formats.
Returns : integer
Argument : None
=cut
sub max_metaname_length {
my $self = shift;
my $maxname = (-1);
my ($seq,$len);
# check seq meta first
for $seq ( $self->each_seq() ) {
next if !$seq->isa('Bio::Seq::MetaI' || !$seq->meta_names);
for my $mtag ($seq->meta_names) {
$len = CORE::length $mtag;
if( $len > $maxname ) {
$maxname = $len;
}
}
}
# alignment meta
for my $meta ($self->consensus_meta) {
next unless $meta;
for my $name ($meta->meta_names) {
$len = CORE::length $name;
if( $len > $maxname ) {
$maxname = $len;
}
}
}
return $maxname;
}
=head2 num_residues
Title : num_residues
Usage : $no = $ali->num_residues
Function : number of residues in total in the alignment
Returns : integer
Argument :
Note : replaces no_residues()
=cut
sub num_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 num_sequences
Title : num_sequences
Usage : $depth = $ali->num_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument : none
Note : replaces no_sequences()
=cut
sub num_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 to 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 : overall_percentage_identity
Usage : $id = $align->overall_percentage_identity
$id = $align->overall_percentage_identity('short')
Function: The function calculates the percentage identity of
the conserved columns
Returns : The percentage identity of the conserved columns
Args : length value to use, optional defaults to alignment length
possible values: 'align', 'short', 'long'
The argument values 'short' and 'long' refer to shortest and longest
sequence in the alignment. Method modification code by Hongyu Zhang.
=cut
sub overall_percentage_identity{
my ($self, $length_measure) = @_;
my %alphabet = map {$_ => undef} qw (A C G T U B D E F H I J K L M N O P Q R S V W X Y Z);
my %enum = map {$_ => undef} qw (align short long);
$self->throw("Unknown argument [$length_measure]")
if $length_measure and not exists $enum{$length_measure};
$length_measure ||= 'align';
if (! $self->is_flush()) {
$self->throw("All sequences in the alignment must be the same length");
}
# Count the residues seen at each position
my $len;
my $total = 0; # number of positions with identical residues
my @countHashes;
my @seqs = $self->each_seq;
my $nof_seqs = scalar @seqs;
my $aln_len = $self->length();
for my $seq (@seqs) {
my $seqstr = $seq->seq;
# Count residues for given sequence
for my $column (0 .. $aln_len-1) {
my $char = uc( substr($seqstr, $column, 1) );
if ( exists $alphabet{$char} ) {
# This is a valid char
if ( defined $countHashes[$column]->{$char} ) {
$countHashes[$column]->{$char}++;
} else {
$countHashes[$column]->{$char} = 1;
}
if ( $countHashes[$column]->{$char} == $nof_seqs ) {
# All sequences have this same residue
$total++;
}
}
}
# Sequence length
if ($length_measure eq 'short' || $length_measure eq 'long') {
my $seq_len = $seqstr =~ tr/[A-Za-z]//;
if ($length_measure eq 'short') {
if ( (not defined $len) || ($seq_len < $len) ) {
$len = $seq_len;
}
} elsif ($length_measure eq 'long') {
if ( (not defined $len) || ($seq_len > $len) ) {
$len = $seq_len;
}
}
}
}
if ($length_measure eq 'align') {
$len = $aln_len;
}
return ($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.DDEF.GHI
column_from_residue_number( "Seq1", 94 ) returns 6.
column_from_residue_number( "Seq2", 25 ) returns 2.
column_from_residue_number( "Seq3", 50 ) returns 10.
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 displayname {
my ( $self, $name, $disname ) = @_;
$self->throw("No sequence with name [$name]")
unless defined $self->{'_seq'}->{$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;
}
}
sub get_displayname {
my $self = shift;
$self->deprecated("get_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);
}
sub set_displayname {
my $self = shift;
$self->deprecated("set_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);
}
=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 : 1, on success
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 (NSE)
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 (NSE)
Returns : 1, on success
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 $self->{'_source'};
}
=head2 set_displayname_safe
Title : set_displayname_safe
Usage : ($new_aln, $ref_name)=$ali->set_displayname_safe(4)
Function : Assign machine-generated serial names to sequences in input order.
Designed to protect names during PHYLIP runs. Assign 10-char string
in the form of "S000000001" to "S999999999". Restore the original
names using "restore_displayname".
Returns : 1. a new $aln with system names;
2. a hash ref for restoring names
Argument : Number for id length (default 10)
=cut
sub set_displayname_safe {
my $self = shift;
my $idlength = shift || 10;
my ( $seq, %phylip_name );
my $ct = 0;
my $new = Bio::SimpleAlign->new();
foreach $seq ( $self->each_seq() ) {
$ct++;
my $pname = "S" . sprintf "%0" . ( $idlength - 1 ) . "s", $ct;
$phylip_name{$pname} = $seq->id();
my $new_seq = Bio::LocatableSeq->new(
-id => $pname,
-seq => $seq->seq(),
-alphabet => $seq->alphabet,
-start => $seq->{_start},
-end => $seq->{_end}
);
$new->add_seq($new_seq);
}
$self->debug(
"$ct seq names changed. Restore names by using restore_displayname.");
return ( $new, \%phylip_name );
}
=head2 restore_displayname
Title : restore_displayname
Usage : $aln_name_restored=$ali->restore_displayname($hash_ref)
Function : Restore original sequence names (after running
$ali->set_displayname_safe)
Returns : a new $aln with names restored.
Argument : a hash reference of names from "set_displayname_safe".
=cut
sub restore_displayname {
my $self = shift;
my $ref=shift;
my %name=%$ref;
my $new=Bio::SimpleAlign->new();
foreach my $seq ( $self->each_seq() ) {
$self->throw("No sequence with name") unless defined $name{$seq->id()};
my $new_seq= Bio::LocatableSeq->new(-id => $name{$seq->id()},
-seq => $seq->seq(),
-alphabet => $seq->alphabet,
-start => $seq->{_start},
-end => $seq->{_end}
);
$new->add_seq($new_seq);
}
return $new;
}
=head2 sort_by_start
Title : sort_by_start
Usage : $ali->sort_by_start
Function : Changes the order of the alignment to the start position of each
subalignment
Returns : 1 on success
Argument :
=cut
sub sort_by_start {
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 _startend keys %hash) {
$self->{'_order'}->{$count} = $nse;
$count++;
}
1;
}
sub _startend {
my ($aname,$arange) = split (/[\/]/,$a);
my ($bname,$brange) = split (/[\/]/,$b);
my ($astart,$aend) = split(/\-/,$arange);
my ($bstart,$bend) = split(/\-/,$brange);
return $astart <=> $bstart;
}
=head2 bracket_string
Title : bracket_string
Usage : my @params = (-refseq => 'testseq',
-allele1 => 'allele1',
-allele2 => 'allele2',
-delimiters => '{}',
-separator => '/');
$str = $aln->bracket_string(@params)
Function : When supplied with a list of parameters (see below), returns a
string in BIC format. This is used for allelic comparisons.
Briefly, if either allele contains a base change when compared to
the refseq, the base or gap for each allele is represented in
brackets in the order present in the 'alleles' parameter.
For the following data:
>testseq
GGATCCATTGCTACT
>allele1
GGATCCATTCCTACT
>allele2
GGAT--ATTCCTCCT
the returned string with parameters 'refseq => testseq' and
'alleles => [qw(allele1 allele2)]' would be:
GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
Returns : BIC-formatted string
Argument : Required args
refseq : string (ID) of the reference sequence used
as basis for comparison
allele1 : string (ID) of the first allele
allele2 : string (ID) of the second allele
Optional args
delimiters: two symbol string of left and right delimiters.
Only the first two symbols are used
default = '[]'
separator : string used as a separator. Only the first
symbol is used
default = '/'
Throws : On no refseq/alleles, or invalid refseq/alleles.
=cut
sub bracket_string {
my ($self, @args) = @_;
my ($ref, $a1, $a2, $delim, $sep) =
$self->_rearrange([qw(refseq allele1 allele2 delimiters separator)], @args);
$self->throw('Missing refseq/allele1/allele2') if (!$a1 || !$a2 || !$ref);
my ($ld, $rd);
($ld, $rd) = split('', $delim, 2) if $delim;
$ld ||= '[';
$rd ||= ']';
$sep ||= '/';
my ($refseq, $allele1, $allele2) =
map {( $self->each_seq_with_id($_) )} ($ref, $a1, $a2);
if (!$refseq || !$allele1 || !$allele2) {
$self->throw("One of your refseq/allele IDs is invalid!");
}
my $len = $self->length-1;
my $bic = '';
# loop over the alignment columns
for my $column ( 0 .. $len ) {
my $string;
my ($compres, $res1, $res2) =
map{substr($_->seq, $column, 1)} ($refseq, $allele1, $allele2);
# are any of the allele symbols different from the refseq?
$string = ($compres eq $res1 && $compres eq $res2) ? $compres :
$ld.$res1.$sep.$res2.$rd;
$bic .= $string;
}
return $bic;
}
=head2 methods implementing Bio::FeatureHolderI
FeatureHolderI implementation to support labeled character sets like one
would get from NEXUS represented data.
=head2 get_SeqFeatures
Usage : @features = $aln->get_SeqFeatures
Function: Get the feature objects held by this feature holder.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args : optional filter coderef, taking a Bio::SeqFeatureI
: as argument, returning TRUE if wanted, FALSE if
: unwanted
=cut
sub get_SeqFeatures {
my $self = shift;
my $filter_cb = shift;
$self->throw("Arg (filter callback) must be a coderef")
unless !defined($filter_cb)
or ref($filter_cb) eq 'CODE';
if ( !defined $self->{'_as_feat'} ) {
$self->{'_as_feat'} = [];
}
if ($filter_cb) {
return grep { $filter_cb->($_) } @{ $self->{'_as_feat'} };
}
return @{ $self->{'_as_feat'} };
}
=head2 add_SeqFeature
Usage : $aln->add_SeqFeature($subfeat);
Function: Adds a SeqFeature into the SeqFeature array. The 'EXPAND' qualifier
(see L<Bio::FeatureHolderI>) is supported, but has no effect.
Example :
Returns : 1 on success
Args : a Bio::SeqFeatureI object
=cut
sub add_SeqFeature {
my ($self, @feat) = @_;
$self->{'_as_feat'} = [] unless $self->{'_as_feat'};
if (scalar @feat > 1) {
$self->deprecated(
-message => 'Providing an array of features to Bio::SimpleAlign add_SeqFeature()'.
' is deprecated and will be removed in a future version. '.
'Add a single feature at a time instead.',
-warn_version => 1.007,
-throw_version => 1.009,
);
}
for my $feat ( @feat ) {
next if $feat eq 'EXPAND'; # Need to support it for FeatureHolderI compliance
if( !$feat->isa("Bio::SeqFeatureI") ) {
$self->throw("Expected a Bio::SeqFeatureI object, but got a $feat.");
}
push @{$self->{'_as_feat'}}, $feat;
}
return 1;
}
=head2 remove_SeqFeatures
Usage : $obj->remove_SeqFeatures
Function: Removes all SeqFeatures. If you want to remove only a subset,
remove that subset from the returned array, and add back the rest.
Returns : The array of Bio::SeqFeatureI features that was
deleted from this alignment.
Args : none
=cut
sub remove_SeqFeatures {
my $self = shift;
return () unless $self->{'_as_feat'};
my @feats = @{$self->{'_as_feat'}};
$self->{'_as_feat'} = [];
return @feats;
}
=head2 feature_count
Title : feature_count
Usage : $obj->feature_count()
Function: Return the number of SeqFeatures attached to the alignment
Returns : integer representing the number of SeqFeatures
Args : None
=cut
sub feature_count {
my ($self) = @_;
if (defined($self->{'_as_feat'})) {
return ($#{$self->{'_as_feat'}} + 1);
} else {
return 0;
}
}
=head2 get_all_SeqFeatures
Title : get_all_SeqFeatures
Usage :
Function: Get all SeqFeatures.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args : none
Note : Falls through to Bio::FeatureHolderI implementation.
=cut
=head2 methods for Bio::AnnotatableI
AnnotatableI implementation to support sequence alignments which
contain annotation (NEXUS, Stockholm).
=head2 annotation
Title : annotation
Usage : $ann = $aln->annotation or
$aln->annotation($ann)
Function: Gets or sets the annotation
Returns : Bio::AnnotationCollectionI object
Args : None or Bio::AnnotationCollectionI object
See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
for more information
=cut
sub annotation {
my ($obj,$value) = @_;
if( defined $value ) {
$obj->throw("object of class ".ref($value)." does not implement ".
"Bio::AnnotationCollectionI. Too bad.")
unless $value->isa("Bio::AnnotationCollectionI");
$obj->{'_annotation'} = $value;
} elsif( ! defined $obj->{'_annotation'}) {
$obj->{'_annotation'} = Bio::Annotation::Collection->new();
}
return $obj->{'_annotation'};
}
=head1 Deprecated methods
=cut
=head2 no_residues
Title : no_residues
Usage : $no = $ali->no_residues
Function : number of residues in total in the alignment
Returns : integer
Argument :
Note : deprecated in favor of num_residues()
=cut
sub no_residues {
my $self = shift;
$self->deprecated(-warn_version => 1.0069,
-throw_version => 1.0075,
-message => 'Use of method no_residues() is deprecated, use num_residues() instead');
$self->num_residues(@_);
}
=head2 no_sequences
Title : no_sequences
Usage : $depth = $ali->no_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument :
Note : deprecated in favor of num_sequences()
=cut
sub no_sequences {
my $self = shift;
$self->deprecated(-warn_version => 1.0069,
-throw_version => 1.0075,
-message => 'Use of method no_sequences() is deprecated, use num_sequences() instead');
$self->num_sequences(@_);
}
=head2 mask_columns
Title : mask_columns
Usage : $aln2 = $aln->mask_columns(20,30)
Function : Masks a slice of the alignment inclusive of start and
end columns, and the first column in the alignment is denoted 1.
Mask 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,
optional string value use for the mask. Example:
$aln2 = $aln->mask_columns(20,30,'?')
Note : Masking must use a character that is not used for gaps or
frameshifts. These can be adjusted using the relevant global
variables, but be aware these may be (uncontrollably) modified
elsewhere within BioPerl (see bug 2715)
=cut
sub mask_columns {
#based on slice(), but did not include the Bio::Seq::Meta sections as I was not sure what it is doing
my $self = shift;
my $nonres = $Bio::LocatableSeq::GAP_SYMBOLS.
$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
# coordinates are alignment-based, not sequence-based
my ($start, $end, $mask_char) = @_;
unless (defined $mask_char) { $mask_char = 'N' }
$self->throw("Mask start has to be a positive integer and less than ".
"alignment length, not [$start]")
unless $start =~ /^\d+$/ && $start > 0 && $start <= $self->length;
$self->throw("Mask end has to be a positive integer and less than ".
"alignment length, not [$end]")
unless $end =~ /^\d+$/ && $end > 0 && $end <= $self->length;
$self->throw("Mask start [$start] has to be smaller than or equal to ".
"end [$end]") unless $start <= $end;
$self->throw("Mask character $mask_char has to be a single character ".
"and not a gap or frameshift symbol")
unless CORE::length($mask_char) == 1 && $mask_char !~ m{$nonres};
my $aln = $self->new;
$aln->id($self->id);
foreach my $seq ( $self->each_seq() ) {
my $new_seq = Bio::LocatableSeq->new(-id => $seq->id,
-alphabet => $seq->alphabet,
-strand => $seq->strand,
-verbose => $self->verbose);
# convert from 1-based alignment coords!
my $masked_string = substr($seq->seq, $start - 1, $end - $start + 1);
$masked_string =~ s{[^$nonres]}{$mask_char}g;
my $new_dna_string = substr($seq->seq,0,$start-1) . $masked_string . substr($seq->seq,$end);
$new_seq->seq($new_dna_string);
$aln->add_seq($new_seq);
}
return $aln;
}
1;