Bio
SimpleAlign
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Summary
Bio::SimpleAlign - Multiple alignments held as a set of sequences
Package variables
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Included modules
Inherit
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};
}
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
Bio::PrimarySeq class
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.
Methods
Methods description
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 Bio::LocatableSeq for more information |
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. |
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 |
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) |
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 |
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%) |
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) |
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 : |
Title : each_seq
Usage : foreach $seq ( $align->each_seq() )
Function : Gets an array of Seq objects from the alignment
Returns : an array
Argument : |
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 |
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) |
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 |
Title : id
Usage : $myalign->id("Ig")
Function : Gets/sets the id field of the alignment
Returns : An id string
Argument : An id string (optional) |
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 : |
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 : |
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 |
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 '.' |
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) |
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) |
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 : |
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) |
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 |
Title : no_residues
Usage : $no = $ali->no_residues
Function : number of residues in total in the alignment
Returns : integer
Argument : |
Title : no_sequences
Usage : $depth = $ali->no_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument : |
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 |
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 |
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 |
Title : remove_column
Usage : $aln2 = $aln->remove_columns(['mismatch','weak'])
Function :
Creates an aligment with columns removed corresponding to
the specified criteria.
Returns : a Bio::SimpleAlign object
Args : array ref of types, 'match'|'weak'|'strong'|'mismatch' |
Title : remove_seq
Usage : $aln->remove_seq($seq);
Function : Removes a single sequence from an alignment
Returns :
Argument : a Bio::LocatableSeq object |
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) |
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 |
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 : |
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 : |
Title : set_displayname_normal
Usage : $ali->set_displayname_normal()
Function : Makes all the sequences be displayed as name/start-end
Returns :
Argument : |
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 |
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 : |
Title : source
Usage : $obj->source($newval)
Function: sets the Alignment source program
Example :
Returns : value of source
Args : newvalue (optional) |
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 |
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 match and match_char |
Title : uppercase()
Usage : $ali->uppercase()
Function : Sets all the sequences to uppercase
Returns :
Argument : |
Methods code
BEGIN {
%CONSERVATION_GROUPS = ( 'strong' => [ qw(STA
NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW)
],
'weak' => [ qw(CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY) ],
); } | | _alpha_startend | description | prev | next | Top |
sub _alpha_startend
{ my ($aname,$astart,$bname,$bstart);
($aname,$astart) = split (/-/,$a);
($bname,$bstart) = split (/-/,$b);
if( $aname eq $bname ) {
return $astart <=> $bstart;
}
else {
return $aname cmp $bname;
}} | 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;
$hash{$letter}++;
}
my $number_of_sequences = $self->no_sequences();
my $threshold = $number_of_sequences * $threshold_percent / 100. ;
$count = -1;
$letter = '?';
foreach $key ( sort keys %hash ) {
if( $hash{$key} > $count && $hash{$key} >= $threshold) {
$letter = $key;
$count = $hash{$key};
}
}
return $letter;} | sub _consensus_iupac
{ my ($self, $column) = @_;
my ($string, $char, $rna);
foreach my $seq ( $self->each_seq() ) {
$string .= substr($seq->seq, $column, 1);
}
$string = uc $string;
if ($string =~ /N/) {
$string =~ /\W/ ? return 'n' : return 'N';
}
return '-' if $string =~ /^\W+$/;
if ($string =~ /U/) {
$string =~ s/U/T/;
$rna = 1;
}
if ($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/;
$string =~ s/M/AC/;
}
if ($string =~ /A/) {
$char = 'A';
if ($string =~ /G/) {
$char = 'R';
if ($string =~ /C/) {
$char = 'V';
if ($string =~ /T/) {
$char = 'N';
}
} elsif ($string =~ /T/) {
$char = 'D';
}
} elsif ($string =~ /C/) {
$char = 'M';
if ($string =~ /T/) {
$char = 'H';
}
} elsif ($string =~ /T/) {
$char = 'W';
}
} elsif ($string =~ /C/) {
$char = 'C';
if ($string =~ /T/) {
$char = 'Y';
if ($string =~ /G/) {
$char = 'B';
}
} elsif ($string =~ /G/) {
$char = 'S';
}
} elsif ($string =~ /G/) {
$char = 'G';
if ($string =~ /C/) {
$char = 'S';
} elsif ($string =~ /T/) {
$char = 'K';
}
} elsif ($string =~ /T/) {
$char = 'T';
}
$char = 'U' if $rna and $char eq 'T';
$char = lc $char if $string =~ /\W/;
return $char;} | sub _remove_col
{ my ($self,$aln,$remove) = @_;
my @new;
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( $seq->start);
}
if($end >= $seq->end){
$new_seq->end( $start);
}
else {
$new_seq->end($seq->end);
}
}
$new_seq->seq($sequence);
push @new, $new_seq;
}
foreach my $new(@new){
$aln->add_seq($new);
}
return $aln;} | 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();
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 {
$self->{'_order'}->{$order} = $name;
unless( exists( $self->{'_start_end_lists'}->{$id})) {
$self->{'_start_end_lists'}->{$id} = [];
}
push @{$self->{'_start_end_lists'}->{$id}}, $seq;
}
$self->{'_seq'}->{$name} = $seq;} | sub average_percentage_identity
{ my ($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();
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 / $divisor )*100.0 : 0;
} | sub cigar_line
{ my ($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 ) {
$i++;
if ($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{$i}."\n";
}
return %clines;} | sub column_from_residue_number
{ my ($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");} | sub consensus_iupac
{ my $self = shift;
my $out = "";
my $len = $self->length-1;
foreach my $seq ( $self->each_seq() ) {
$self->throw("Seq [". $seq->get_nse. "] is a protein")
if $seq->alphabet eq 'protein';
}
foreach my $count ( 0 .. $len ) {
$out .= $self->_consensus_iupac($count);
}
return $out;} | 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 $out;} | sub displayname
{ my ($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;
}} | sub eachSeq
{ my $self = shift;
$self->warn(ref($self). "::eachSeq - deprecated method. Use each_seq() instead.");
$self->each_seq();} | 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_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 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;} | 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'}->{$id}};
}
return @arr;} | sub gap_char
{ my ($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'};} | sub get_displayname
{ my $self = shift;
$self->warn(ref($self). "::get_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);} | 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};} | sub id
{ my ($self, $name) = @_;
if (defined( $name )) {
$self->{'_id'} = $name;
}
return $self->{'_id'};} | sub is_flush
{ my ($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;} | 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;} | sub length_aln
{ my $self = shift;
$self->warn(ref($self). "::length_aln - deprecated method. Use length() instead.");
$self->length(@_);} | 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;} | 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;} | 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 $self->{'_match_char'};} | sub match_line
{ my ($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;
my $matchline;
POS: foreach my $pos ( 0..$self->length ) {
my $refchar = $refseq->[$pos];
next unless $refchar;
my %col = ($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( $dash ) { $char = $matchchars{'mismatch'} }
elsif( @colresidues == 1 ) { $char = $matchchars{'match'} }
elsif( $alphabet eq 'protein' ) {
TYPE: foreach my $type ( qw(strong weak) ) {
my %groups;
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 @$cols;
next if( scalar @$cols != scalar @colresidues );
for($_=0;$_ < (scalar @$cols);$_++ ) {
next GRP if( $cols->[$_] ne $colresidues[$_] );
}
$char = $matchchars{$type};
last TYPE;
}
}
}
$matchline .= $char;
}
return $matchline;} | 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;} | 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.");
$self->maxdisplayname_length();} | sub missing_char
{ my ($self, $char) = @_;
if (defined $char ) {
$self->throw("Single missing character, not [$char]!") if CORE::length($char) > 1;
$self->{'_missing_char'} = $char;
}
return $self->{'_missing_char'};} | sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($src) = $self->_rearrange([qw(SOURCE)], @args);
$src && $self->source($src);
$self->{'_seq'} = {};
$self->{'_order'} = {};
$self->{'_start_end_lists'} = {};
$self->{'_dis_name'} = {};
$self->{'_id'} = 'NoName';
$self->{'_symbols'} = {};
return $self;
} | 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;} | sub no_sequences
{ my $self = shift;
return scalar($self->each_seq);} | 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();
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;
} | sub percentage_identity
{ my $self = shift;
return $self->average_percentage_identity();} | sub purge
{ my ($self,$perc) = @_;
my (%duplicate, @dups);
my @seqs = $self->each_seq();
for (my $i=0;$i< @seqs - 1;$i++ ) {
my $seq = $seqs[$i];
next if exists $duplicate{$seq->display_id} ;
my $one = $seq->seq();
my @one = split '', $one;
for (my $j=$i+1;$j < @seqs;$j++) {
my $seq2 = $seqs[$j];
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 ( $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;} | sub removeSeq
{ my $self = shift;
$self->warn(ref($self). "::removeSeq - deprecated method. Use remove_seq() instead.");
$self->remove_seq(@_);} | sub remove_columns
{ my ($self,$type) = @_;
my %matchchars = ( 'match' => '\*',
'weak' => '\.',
'strong' => ':',
'mismatch'=> ' ',
);
my $del_char;
foreach my $type(@{$type}){
$del_char.= $matchchars{$type};
}
my $match_line = $self->match_line;
my $aln = new $self;
my @remove;
my $length = 0;
while($match_line=~m/[$del_char]/g){
my $start = pos($match_line)-1;
$match_line=~/\G[$del_char]+/gc;
my $end = pos($match_line)-1;
$start-=$length;
$end -=$length;
$length += ($end-$start+1);
push @remove, [$start,$end];
}
$aln = $self->_remove_col($aln,\@remove);
return $aln;} | 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};
if (exists $self->{'_start_end_lists'}->{$id}) {
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;
} | 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;} | 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;} | sub set_displayname
{ my $self = shift;
$self->warn(ref($self). "::set_displayname - deprecated method. Use displayname() instead.");
$self->displayname(@_);} | sub set_displayname_count
{ my $self= shift;
my (@arr,$name,$seq,$count,$temp,$nse);
foreach $seq ( $self->each_alphabetically() ) {
$nse = $seq->get_nse();
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;} | 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;} | 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;} | 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);
my $seq_end = $end;
$seq_end = $seq->length if $end > $seq->length;
my $slice_seq = $seq->subseq($start, $seq_end);
$new_seq->seq( $slice_seq );
if ($start > 1) {
my $pre_start_seq = $seq->subseq(1, $start - 1);
$pre_start_seq =~ s/\W//g;
$new_seq->start( $seq->start + CORE::length($pre_start_seq) );
} else {
$new_seq->start( $seq->start);
}
$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;} | 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'}} = ();
foreach $nse ( sort _alpha_startend keys %hash) {
$self->{'_order'}->{$count} = $nse;
$count++;
}
1;} | sub source
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'_source'} = $value;
}
return $self->{'_source'};
}
1;} | sub symbol_chars
{ my ($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 $char );
}
}
return keys %copy;} | sub unmatch
{ my ($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;} | 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;} | General documentation
SimpleAlign is being slowly converted to bioperl coding standards,
mainly by Ewan.
Use Bio::Root::Object - done
Use proper exceptions - done
Use hashed constructor - not done!
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
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/
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.eduThe rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
These methods modify the MSE by adding, removing or shuffling complete
sequences.
| Sequence selection methods | Top |
Methods returning one or more sequences objects.
The result of these methods are horizontal or vertical subsets of the
current MSE.
| Change sequences within the MSE | Top |
These methods affect characters in all sequences without changeing the
alignment.
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 ('').
These read only methods describe the MSE in various ways.
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
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);
Methods to manipulate the display name. The default name based on the
sequence id and subsequence positions can be overridden in various
ways.