Bio
SimpleAlign
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Summary
Bio::SimpleAlign - Multiple alignments held as a set of sequences
Package variables
No package variables defined.
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();
# 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.
Methods
Methods description
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) |
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 |
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 alignment to alphabetical on name
followed by numerical by number.
Returns :
Argument : |
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) |
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 |
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 |
Title : each_seq
Usage : foreach $seq ( $align->each_seq() )
Function : Gets a Seq object from the alignment
Returns : Seq object
Argument : |
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 : |
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 |
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 |
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 |
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 |
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) |
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. |
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. |
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) |
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 |
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(). |
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.
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 :
Argument : A regexp and a string |
Title : uppercase()
Usage : $ali->uppercase()
Function : Sets all the sequences to uppercase
Returns :
Argument : |
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) |
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 |
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 |
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 |
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) |
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
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 |
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 : accession
Usage : $myalign->accession("PF00244")
Function : Gets/sets the accession field of the alignment
Returns : An acc string
Argument : An acc string (optional) |
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) |
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 |
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 : 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%) |
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 : |
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_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 |
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 : |
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 : |
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 : |
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 |
Title : num_residues
Usage : $no = $ali->num_residues
Function : number of residues in total in the alignment
Returns : integer
Argument :
Note : replaces no_residues() |
Title : num_sequences
Usage : $depth = $ali->num_sequences
Function : number of sequence in the sequence alignment
Returns : integer
Argument : none
Note : replaces no_sequences() |
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 to average_percentage_identity)
Returns : The average percentage identity
Args : None |
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. |
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) |
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 : 1, on success
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 : 1, on success
Argument : |
Title : source
Usage : $obj->source($newval)
Function: sets the Alignment source program
Example :
Returns : value of source
Args : newvalue (optional) |
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) |
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". |
Title : sort_by_start
Usage : $ali->sort_by_start
Function : Changes the order of the alignment to the start position of each
subalignment
Returns :
Argument : |
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. |
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 |
Usage : $aln->add_SeqFeature($subfeat);
Function: Adds a SeqFeature into the SeqFeature array. The 'EXPAND' qualifier
(see Bio::FeatureHolderI) is supported, but has no effect.
Example :
Returns : true on success
Args : a Bio::SeqFeatureI object |
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 |
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 |
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 |
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() |
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() |
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 = $aln->mask_columns(20,30,'?')
Note : Masking must use a character that is not used for gaps or
frameshifts. These can be adjusted using the relevant global
variables, but be aware these may be (uncontrollably) modified
elsewhere within BioPerl (see bug 2715) |
Methods code
BEGIN {
%CONSERVATION_GROUPS = (
'strong' => [ qw(
STA
NEQK
NHQK
NDEQ
QHRK
MILV
MILF
HY
FYW )],
'weak' => [ qw(
CSA
ATV
SAG
STNK
STPA
SGND
SNDEQK
NDEQHK
NEQHRK
FVLIM
HFY )],); } | sub new
{ my($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);
$self->{'_seq'} = {};
$self->{'_order'} = {};
$self->{'_start_end_lists'} = {};
$self->{'_dis_name'} = {};
$self->{'_id'} = 'NoName';
$id && $self->id($id);
$acc && $self->accession($acc);
$desc && $self->description($desc);
$coll && $self->annotation($coll);
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);
if ($seqs && ref($seqs) eq 'ARRAY') {
for my $seq (@$seqs) {
$self->add_seq($seq);
}
}
return $self;
} | 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'}};
$order--;
if ($order < 0) {
$self->throw("User-specified value for ORDER must be >= 1");
}
$id = $seq->id() ||$seq->display_id || $seq->primary_id;
$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}) {
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;} | 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};
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 $id");
}
my %rev_order = reverse %{$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;} | 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 ) {
$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;} | 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;
$count++;
}
1;} | sub sort_by_list
{ my ($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);
my @sorted= map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$order{$_->id()}, $_] } @seq;
my $aln = $self->new;
foreach (@sorted) { $aln->add_seq($_) }
return $aln;} | sub set_new_reference
{ my ($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+$/) {
$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 {
$self->throw("The new reference sequence not in alignment ") unless &_in_aln($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 $aln;} | sub _in_aln
{
foreach (@$ref) {
return 1 if $str eq $_;
}
return 0; } | sub uniq_seq
{ my ($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();
$str =~ s/n/\?/gi if $str =~ /^[atcgn-]+$/i;
$str = &_convert_leading_ending_gaps($str, '-', '?');
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) {
my @memb = @{$member{$key}};
push @memb, $seq;
$member{$key} =\@ memb;
} else {
push @uniq_str, $key;
$order++;
$member{$key} = [ ($seq) ];
$order{$key} = $order;
}
}
foreach my $str (sort {$order{$a} <=> $order{$b}} keys %order) {
my $str2 = &_convert_leading_ending_gaps($str, '?', '-');
$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();
$self->debug($_->id(), "\t", "ST", $order{$str}, "\n");
}
}
return wantarray ? ($aln, $st) : $aln;} | sub _check_uniq
{
my @char1=split //, $str1;
my @array=@$ref;
return (0, $str1) if @array==0;
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;
}
return (0, $str1);
} | sub _convert_leading_ending_gaps
{ my $s=shift;
my $sym1=shift;
my $sym2=shift;
my @array=split //, $s;
for (my $i=0; $i<=$#array; $i++) {
($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last);
}
for (my $i = $#array; $i>= 0; $i--) {
($array[$i] eq $sym1) ? ($array[$i] = $sym2):(last);
}
my $s_new=join '', @array;
return $s_new;} | 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;} | 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;
}} | 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;} | 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};} | 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 $seq;
}
}
return;} | sub seq_with_features
{ my ($self,%arg) = @_;
$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();
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; } | 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);
return $aln;} | 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);
return $aln;} | sub select_noncont_by_name
{ my ($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;} | 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);
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);
return $aln;} | sub remove_columns
{ my ($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");
}
$aln;} | sub remove_gaps
{ my ($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 || $self->gap_char;
while ($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;
$start-=$length;
$end -=$length;
$length += ($end-$start+1);
push @remove, [$start,$end];
}
$aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
return $aln;} | sub _remove_col
{ my ($self,$aln,$remove) = @_;
my @new;
my $gap = $self->gap_char;
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;
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 + $start_adjust);
}
}
if (($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) {
$new_seq->start(0);
$new_seq->end(0);
}
$new_seq->seq($sequence) if $sequence;
push @new, $new_seq;
}
foreach my $new(@new){
$aln->add_seq($new);
}
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' => ''
);
my $del_char;
foreach my $type (@{$type}){
$del_char.= $matchchars{$type};
}
my $length = 0;
my $match_line = $self->match_line;
if($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;
$start-=$length;
$end -=$length;
$length += ($end-$start+1);
push @remove, [$start,$end];
}
}
$aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
$aln = $aln->remove_gaps() if $gap;
$aln = $aln->remove_gaps('', 1) if $all_gaps_columns;
$aln;} | sub _remove_columns_by_num
{ my ($self,$positions) = @_;
my $aln = $self->new;
@$positions = sort { $a->[0] <=> $b->[0] } @$positions;
my @remove;
my $length = 0;
foreach my $pos (@{$positions}) {
my ($start, $end) = @{$pos};
$start-=$length;
$end -=$length;
$length += ($end-$start+1);
push @remove, [$start,$end];
}
$aln = $#remove >= 0 ? $self->_remove_col($aln,\@remove) : $self;
$aln; } | sub splice_by_seq_pos
{ my ($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;} | 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;} | 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;} | 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;
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++;
}
}
}
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];
}
}
}
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;
}
}
for my $name (keys %cigars) {
my ($start,$end,$str) = "";
while ( ($start,$end) = splice @{$cigars{$name}}, 0, 2 ) {
$str .= ($start . "," . $end . ":");
}
$str =~ s/:$//;
$cigars{$name} = $str;
}
%cigars; } | sub match_line
{ my ($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;
my $matchline;
POS:
foreach my $pos ( 0..$self->length ) {
my $refchar = $refseq->[$pos];
my $char = $matchchars{'mismatch'};
unless( defined $refchar ) {
last if $pos == $self->length;
goto bottom;
}
my %col = ($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( $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 $f ( grep { index($_,$c) >= 0 } @{$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;
}
}
}
bottom:
$matchline .= $char;
}
return $matchline;} | sub gap_line
{ my ($self,$gapchar) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh;
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 $gap_line;} | sub all_gap_line
{ my ($self,$gapchar) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh;
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) {
$gap_line .= $self->gap_char;
} else {
$gap_line .= '.';
}
}
return $gap_line;} | sub gap_col_matrix
{ my ( $self, $gapchar ) = @_;
$gapchar = $gapchar || $self->gap_char;
my %gap_hsh;
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;} | 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 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);
}
$self->match_char('');
return 1;} | sub id
{ my ($self, $name) = @_;
if (defined( $name )) {
$self->{'_id'} = $name;
}
return $self->{'_id'};} | sub accession
{ my ($self, $acc) = @_;
if (defined( $acc )) {
$self->{'_accession'} = $acc;
}
return $self->{'_accession'};} | sub description
{ my ($self, $name) = @_;
if (defined( $name )) {
$self->{'_description'} = $name;
}
return $self->{'_description'};} | sub missing_char
{ my ($self, $char) = @_;
if (defined $char ) {
$self->throw("Single missing character, not [$char]!") if CORE::length($char) > 1;
$self->{'_missing_char'} = $char;
}
return $self->{'_missing_char'};} | sub match_char
{ my ($self, $char) = @_;
if (defined $char ) {
$self->throw("Single match character, not [$char]!") if CORE::length($char) > 1;
$self->{'_match_char'} = $char;
}
return $self->{'_match_char'};} | sub gap_char
{ my ($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 $self->{'_gap_char'};} | sub symbol_chars
{ my ($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;} | sub score
{ my $self = shift;
$self->{score} = shift if @_;
return $self->{score};} | 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;} | 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);
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 ) {
if( $hash{$key} > $count && $hash{$key} >= $threshold) {
$letter = $key;
$count = $hash{$key};
}
}
return $letter;
}
} | 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;} | 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 $out;} | sub _consensus_iupac
{ my ($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 $char;} | sub consensus_meta
{ my ($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 $self->{'_aln_meta'}} | sub is_flush
{ my ($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_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;} | 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;} | sub max_metaname_length
{ my $self = shift;
my $maxname = (-1);
my ($seq,$len);
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;
}
}
}
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;} | 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;} | sub num_sequences
{ my $self = shift;
return scalar($self->each_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 percentage_identity
{ my $self = shift;
return $self->average_percentage_identity();} | sub overall_percentage_identity
{ my ($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");
}
my $len;
my $total = 0;
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;
for my $column (0 .. $aln_len-1) {
my $char = uc( substr($seqstr, $column, 1) );
if ( exists $alphabet{$char} ) {
if ( defined $countHashes[$column]->{$char} ) {
$countHashes[$column]->{$char}++;
} else {
$countHashes[$column]->{$char} = 1;
}
if ( $countHashes[$column]->{$char} == $nof_seqs ) {
$total++;
}
}
}
if ($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 / $len ) * 100.0;
} | sub column_from_residue_number
{ my ($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 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.");
$self->displayname(@_);} | sub displayname
{ my ($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 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,$nse);
}
return 1;} | sub source
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'_source'} = $value;
}
return $self->{'_source'};} | 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);} | 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;} | 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'}} = ();
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 <=> $bstart;} | sub bracket_string
{ my ($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 = '';
for my $column ( 0 .. $len ) {
my $string;
my ($compres, $res1, $res2) =
map{substr($_->seq, $column, 1)} ($refseq, $allele1, $allele2);
$string = ($compres eq $res1 && $compres eq $res2) ? $compres :
$ld.$res1.$sep.$res2.$rd;
$bic .= $string;
}
return $bic;} | 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'}};} | 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 $feat eq 'EXPAND';
if( !$feat->isa("Bio::SeqFeatureI") ) {
$self->throw("Expected a Bio::SeqFeatureI object, but got a $feat.");
}
push @{$self->{'_as_feat'}}, $feat;
}
return 1;} | sub remove_SeqFeatures
{ my $self = shift;
return () unless $self->{'_as_feat'};
my @feats = @{$self->{'_as_feat'}};
$self->{'_as_feat'} = [];
return @feats;} | sub feature_count
{ my ($self) = @_;
if (defined($self->{'_as_feat'})) {
return ($#{$self->{'_as_feat'}} + 1);
} else {
return 0;
}} | sub annotation
{ my ($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'};} | 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(@_);} | 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(@_);} | sub mask_columns
{
my $self = shift;
my $nonres = $Bio::LocatableSeq::GAP_SYMBOLS.
$Bio::LocatableSeq::FRAMESHIFT_SYMBOLS;
my ($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);
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; } | General documentation
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
Please direct usage questions or support issues to the mailing list:
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.
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/
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
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
These methods modify the MSA 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 MSA.
| Change sequences within the MSA | Top |
These methods affect characters in all sequences without changing the
alignment.
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 ('').
These read only methods describe the MSA 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.
| methods implementing Bio::FeatureHolderI | Top |
FeatureHolderI implementation to support labeled character sets like one
would get from NEXUS represented data.
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 | Top |
AnnotatableI implementation to support sequence alignments which
contain annotation (NEXUS, Stockholm).