/ 
bioperl-1.4
/ Bio::SimpleAlign

NAME

Bio::SimpleAlign - Multiple alignments held as a set of sequences

SYNOPSIS

# use Bio::AlignIO to read in the alignment
$str = Bio::AlignIO->new('-file' => 't/data/testaln.pfam');
$aln = $str->next_aln();

# some descriptors
print $aln->length, "\n";
print $aln->no_residues, "\n";
print $aln->is_flush, "\n";
print $aln->no_sequences, "\n";
print $aln->score, "\n";
print $aln->percentage_identity, "\n";
print $aln->consensus_string(50), "\n";

# find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;

# extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
    $res = $seq->subseq($pos, $pos);
    $count{$res}++;
}
foreach $res (keys %count) {
    printf "Res: %s  Count: %2d\n", $res, $count{$res};
}

DESCRIPTION

SimpleAlign handles multiple alignments of sequences. It is very permissive of types (it won't insist on things being all same length etc): really it is a SequenceSet explicitly held in memory with a whole series of built in manipulations and especially file format systems for read/writing alignments.

SimpleAlign basically views an alignment as an immutable block of text. SimpleAlign *is not* the object to be using if you want to perform complex alignment manipulations.

However for lightweight display/formatting and minimal manipulation (e.g. removing all-gaps columns) - this is the one to use.

SimpleAlign uses a subclass of Bio::PrimarySeq class Bio::LocatableSeq to store its sequences. These are subsequences with a start and end positions in the parent reference sequence.

Tricky concepts. SimpleAlign expects name,start,end to be 'unique' in the alignment, and this is the key for the internal hashes. (name,start,end is abbreviated nse in the code). However, in many cases people don't want the name/start-end to be displayed: either multiple names in an alignment or names specific to the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called 'displayname', and generally is what is used to print out the alignment. They default to name/start-end.

The SimpleAlign Module came from Ewan Birney's Align module.

PROGRESS

SimpleAlign is being slowly converted to bioperl coding standards, mainly by Ewan.

Use Bio::Root::Object - done
Use proper exceptions - done
Use hashed constructor - not done!

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.

bioperl-l@bioperl.org             - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR

Ewan Birney, birney@sanger.ac.uk

CONTRIBUTORS

Allen Day, allenday@ucla.edu, Richard Adams, Richard.Adams@ed.ac.uk, David J. Evans, David.Evans@vir.gla.ac.uk, Heikki Lehvaslaiho, heikki@ebi.ac.uk, Allen Smith, allens@cpan.org, Jason Stajich, jason@bioperl.org, Anthony Underwood, aunderwood@phls.org.uk, Xintao Wei & Giri Narasimhan, giri@cs.fiu.edu

SEE ALSO

Bio::LocatableSeq.pm

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title     : new
Usage     : my $aln = new Bio::SimpleAlign();
Function  : Creates a new simple align object
Returns   : Bio::SimpleAlign
Args      : -source => string representing the source program
                       where this alignment came from

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   : nothing
Args      : 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 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 alignemnt to alphabetical on name
            followed by numerical by number.

Returns   : 
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
            no_sequences() will thow an error.

Returns   : a Bio::LocatableSeq object
Args      : positive integer for the sequence osition

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 1bp by glossing over them with N, for
            instance

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 no_sequences() will thow an error.

Returns   : a Bio::SimpleAlign object
Args      : positive integer for the first sequence
            positive integer for the last sequence to include (optional)

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 no_sequences() will thow 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
Args      : positive integer for start column
            positive integer for end column

remove_columns

Title     : remove_column
Usage     : $aln2 = $aln->remove_columns(['mismatch','weak'])
Function  :
            Creates an aligment with columns removed corresponding to
            the specified criteria.
Returns   : a L<Bio::SimpleAlign> object
Args      : array ref of types, 'match'|'weak'|'strong'|'mismatch'|'gaps'

remove_gaps

Title     : remove_gaps
Usage     : $aln2 = $aln->remove_gaps('-')
Function  :
            Creates an aligment with gaps removed 
Returns   : a L<Bio::SimpleAlign> object
Args      : a gap character(optional) if no specified, 
            taken from $self->gap_char

Change sequences within the MSE

These methods affect characters in all sequences without changeing 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

            Notice that the from (arg1) is interpretted as a regex,
            so be careful about quoting meta characters (eg
            $ali->map_chars('.','-') wont do what you want)

Returns   : 
Argument  : 'from' rexexp
            'to' string

uppercase

Title     : uppercase()
Usage     : $ali->uppercase()
Function  : Sets all the sequences to uppercase
Returns   : 
Argument  :

cigar_line

Title    : cigar_line()
Usage    : $align->cigar_line()
Function : Generates a "cigar" line for each sequence in the alignment
           The format is simply A-1,60;B-1,1:4,60;C-5,10:12,58
           where A,B,C,etc. are the sequence identifiers, and the numbers
           refer to conserved positions within the alignment
Args     : none

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.
Args     : (optional) Match line characters ('*' by default)
           (optional) Strong match char (':' by default)
           (optional) Weak match char ('.' by default)

gap_line

Title    : gap_line()
Usage    : $align->gap_line()
Function : Generates a gap line - much like consensus string
           except that a line where '-' represents gap  
Args     : (optional) gap line characters ('-' by default)

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 '.'

See match and match_char

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
Args    : boolean to include the gap/missing/match characters

Alignment descriptors

These read only methods describe the MSE 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   : 
Argument  : Optional treshold ranging from 0 to 100.
            The consensus residue has to appear at least threshold %
            of the sequences at a given location, otherwise a '?'
            character will be placed at that location.
            (Default value = 0%)

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   : 
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 MSE formats.

Returns   : integer
Argument  :

no_residues

Title     : no_residues
Usage     : $no = $ali->no_residues
Function  : number of residues in total in the alignment
Returns   : integer
Argument  :

no_sequences

Title     : no_sequences
Usage     : $depth = $ali->no_sequences
Function  : number of sequence in the sequence alignment
Returns   : integer
Argument  :

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 for average_percentage_identity)
Returns : The average percentage identity
Args    : None

overall_percentage_identity

Title   : percentage_identity
Usage   : $id = $align->percentage_identity
Function: The function calculates the percentage identity of
          the conserved columns
Returns : The percentage identity of the conserved columns
Args    : None

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 5.
           column_from_residue_number( "Seq2", 25 ) returns 2.
           column_from_residue_number( "Seq3", 50 ) returns 9.

           An exception is thrown if the residue number would lie
           outside the length of the aligment
           (e.g. column_from_residue_number( "Seq2", 22 )

	  Note: If the the parent sequence is represented by more than
	  one alignment sequence and the residue number is present in
	  them, this method finds only the first one.

 Returns : A column number for the position in the alignment of the
           given residue in the given sequence (1 = first column)
 Args    : A sequence id/name (not a name/start-end)
           A residue number in the whole sequence (not just that
           segment of it in the alignment)

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   : 
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
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
Returns   : 
Argument  :

source

Title   : source
Usage   : $obj->source($newval)
Function: sets the Alignment source program
Example : 
Returns : value of source
Args    : newvalue (optional)