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.
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 Bio::LocatableSeq, a subclass of 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 "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 "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.
FEEDBACK
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting 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://github.com/bioperl/bioperl-live/issues
AUTHOR
Ewan Birney, [email protected]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.comAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _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)
Modifier methods
These methods modify the MSA by adding, removing or shuffling complete sequences.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 Bio::LocatableSeq for more information
remove_seq
Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object
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
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 :
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)
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
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
Sequence selection methods
Methods returning one or more sequences objects.each_seq
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets a Seq object from the alignment Returns : Seq object Argument :
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 :
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
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
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
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
Create new alignments
The result of these methods are horizontal or vertical subsets of the current MSA.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)
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.
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.
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)
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
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 remove_columns in most cases. Set gap character using gap_char().
Change sequences within the MSA
These methods affect characters in all sequences without changing the alignment.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
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
uppercase
Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : 1 on success Argument :
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)
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
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
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
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)
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 '.'
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 match and match_char
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 ('').
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)
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)
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)
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)
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)
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)
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
Alignment descriptors
These read only methods describe the MSA in various ways.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
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%)
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 :
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
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
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 :
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 :
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 :
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
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()
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()
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.
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
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.
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 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);
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)
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.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)
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 :
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 :
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 :
source
Title : source Usage : $obj->source($newval) Function: sets the Alignment source program Example : Returns : value of source Args : newvalue (optional)
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)
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".
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 :
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.
methods implementing Bio::FeatureHolderI
FeatureHolderI implementation to support labeled character sets like one would get from NEXUS represented data.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
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
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
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
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.
methods for Bio::AnnotatableI
AnnotatableI implementation to support sequence alignments which contain annotation (NEXUS, Stockholm).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 Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information
Deprecated methods
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()
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()
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)