SYNOPSIS
# get a Bio::Align::AlignI somehow - typically using Bio::AlignIO system
# some descriptors
print $aln->length, "\n";
print $aln->num_residues, "\n";
print $aln->is_flush, "\n";
print $aln->num_sequences, "\n";
print $aln->percentage_identity, "\n";
print $aln->consensus_string(50), "\n";
# find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;
# extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
$res = $seq->subseq($pos, $pos);
$count{$res}++;
}
foreach $res (keys %count) {
printf "Res: %s Count: %2d\n", $res, $count{$res};
}
DESCRIPTION
This interface describes the basis for alignment objects.FEEDBACK
Mailing Lists
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[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 of the bugs and their resolution. Bug reports can be submitted via the web:
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AUTHOR - Jason Stajich
Email [email protected]CONTRIBUTORS
Ewan Birney, [email protected] Heikki Lehvaslaiho, heikki-at-bioperl-dot-orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _Modifier methods
These methods modify the MSE by adding, removing or shuffling complete sequences.add_seq
Title : add_seq
Usage : $myalign->add_seq($newseq);
Function : Adds another sequence to the alignment. *Does not* align
it - just adds it to the hashes.
Returns : None
Argument : a Bio::LocatableSeq object
order (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 whatever %id.
This function will grind on large alignments. Beware!
(perhaps not ideally implemented)
Example :
Returns : An array of the removed sequences
Argument:
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 : an array
Argument :
Sequence selection methods
Methods returning one or more sequences objects.each_seq
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument :
each_alphabetically
Title : each_alphabetically
Usage : foreach $seq ( $ali->each_alphabetically() )
Function :
Returns an array of sequence object sorted alphabetically
by name and then by start point.
Does not change the order of the alignment
Returns :
Argument :
each_seq_with_id
Title : each_seq_with_id
Usage : foreach $seq ( $align->each_seq_with_id() )
Function :
Gets an array of Seq objects from the
alignment, the contents being those sequences
with the given name (there may be more than one)
Returns : an array
Argument : a seq name
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 Argument : positive integer for the sequence position
Create new alignments
The result of these methods are horizontal or vertical subsets of the current MSE.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
Argument : positive integer for the first sequence
positive integer for the last sequence to include (optional)
select_noncont
Title : select_noncont
Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences
Function :
Creates a new alignment from a subset of
sequences. Numbering starts from 1. Sequence positions
larger than num_sequences() will throw an error.
Returns : a Bio::SimpleAlign object
Args : array of integers 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. 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
Argument : positive integer for start column
positive integer for end column
Change sequences within the MSE
These methods affect characters in all sequences without changing the alignment.map_chars
Title : map_chars
Usage : $ali->map_chars('\.','-')
Function :
Does a s/$arg1/$arg2/ on the sequences. Useful for gap
characters
Notice that the from (arg1) is interpreted as a regex,
so be careful about quoting meta characters (eg
$ali->map_chars('.','-') wont do what you want)
Returns : None
Argument : 'from' rexexp
'to' string
uppercase
Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument :
match_line
Title : match_line()
Usage : $align->match_line()
Function : Generates a match line - much like consensus string
except that a line indicating the '*' for a match.
Argument : (optional) Match line characters ('*' by default)
(optional) Strong match char (':' by default)
(optional) Weak match char ('.' 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 MSE formats do not support match
characters in sequences, so this is mostly for output
only. NEXUS format (Bio::AlignIO::nexus) can handle
it.
Returns : 1
Argument : a match character, optional, defaults to '.'
unmatch
Title : unmatch()
Usage : $ali->unmatch()
Function :
Undoes the effect of method match. Unsets match_char.
Returns : 1
Argument : a match character, optional, defaults to '.'
MSE attibutes
Methods for setting and reading the MSE attributes.Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string ('').
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)
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 Argument: boolean to include the gap/missing/match characters
Alignment descriptors
These read only methods describe the MSE in various ways.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_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
is_flush
Title : is_flush
Usage : if( $ali->is_flush() )
:
:
Function : Tells you whether the alignment
: is flush, ie all of the same length
:
:
Returns : 1 or 0
Argument :
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 :
maxname_length
Title : maxname_length
Usage : $ali->maxname_length()
Function :
Gets the maximum length of the displayname in the
alignment. Used in writing out various MSE formats.
Returns : integer
Argument :
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
percentage_identity
Title : percentage_identity
Usage : $id = $align->percentage_identity
Function: The function calculates the percentage identity of the alignment
Returns : The percentage identity of the alignment (as defined by the
implementation)
Argument: None
overall_percentage_identity
Title : overall_percentage_identity
Usage : $id = $align->overall_percentage_identity
Function: The function calculates the percentage identity of
the conserved columns
Returns : The percentage identity of the conserved columns
Args : None
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
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.DDEFGHI
column_from_residue_number( "Seq1", 94 ) returns 6.
column_from_residue_number( "Seq2", 25 ) returns 2.
column_from_residue_number( "Seq3", 50 ) returns 9.
An exception is thrown if the residue number would lie
outside the length of the alignment
(e.g. column_from_residue_number( "Seq2", 22 )
Note: If 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 : None
Argument : None
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
Returns : 1
Argument : None
set_displayname_normal
Title : set_displayname_normal Usage : $ali->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end Returns : None Argument : None
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 : None Note : deprecated in favor of num_sequences()