Bio::SimpleAlign - Multiple alignments held as a set of sequences
# 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->score, "\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};
}
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.
SimpleAlign is being slowly converted to bioperl coding standards, mainly by Ewan.
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/
Ewan Birney, birney@sanger.ac.uk
Allen Day, allenday@ucla.edu, Richard Adams, Richard.Adams@ed.ac.uk, David J. Evans, David.Evans@vir.gla.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk, Allen Smith, allens@cpan.org, Jason Stajich, jason@bioperl.org, Anthony Underwood, aunderwood@phls.org.uk, Xintao Wei & Giri Narasimhan, giri@cs.fiu.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
These methods modify the MSE by adding, removing or shuffling complete sequences.
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 : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object
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 : sort_alphabetically
Usage : $ali->sort_alphabetically
Function :
Changes the order of the alignemnt to alphabetical on name
followed by numerical by number.
Returns :
Argument :
Methods returning one or more sequences objects.
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_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_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 : 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 : 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 1bp by glossing over them with N, for
instance
The result of these methods are horizontal or vertical subsets of the current MSE.
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 : 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 : remove_column
Usage : $aln2 = $aln->remove_columns(['mismatch','weak'])
Function :
Creates an aligment with columns removed corresponding to
the specified criteria.
Returns : a L<Bio::SimpleAlign> object
Args : array ref of types, 'match'|'weak'|'strong'|'mismatch'|'gaps'
Title : remove_gaps
Usage : $aln2 = $aln->remove_gaps('-')
Function :
Creates an aligment with gaps removed
Returns : a L<Bio::SimpleAlign> object
Args : a gap character(optional) if no specified,
taken from $self->gap_char
These methods affect characters in all sequences without changeing the alignment.
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
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 : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument :
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 : 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 : gap_line()
Usage : $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)
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 : 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
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 ('').
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 : 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 : 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 : 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 : 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
These read only methods describe the MSE in various ways.
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
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 : 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 : 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 : 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 : 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 : 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 : 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 : 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
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);
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)
Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways.
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 : 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 : source Usage : $obj->source($newval) Function: sets the Alignment source program Example : Returns : value of source Args : newvalue (optional)
