Bio::SimpleAlign man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

Bio::SimpleAlign(3)   User Contributed Perl Documentation  Bio::SimpleAlign(3)

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();

	 # Describe
	 print $aln->length;
	 print $aln->num_residues;
	 print $aln->is_flush;
	 print $aln->num_sequences;
	 print $aln->score;
	 print $aln->percentage_identity;
	 print $aln->consensus_string(50);

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

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

	 # Manipulate
	 $aln->remove_seq($seq);
	 $mini_aln = $aln->slice(20,30);  # get a block of columns
	 $mini_aln = $aln->select_noncont(1,3,5,7,11); # select certain sequences
	 $new_aln = $aln->remove_columns([20,30]); # remove by position
	 $new_aln = $aln->remove_columns(['mismatch']); # remove by property

	 # Analyze
	 $str = $aln->consensus_string($threshold_percent);
	 $str = $aln->match_line();
	 $str = $aln->cigar_line();
	 $id = $aln->percentage_identity;

	 # See the module documentation for details and more methods.

DESCRIPTION
       SimpleAlign is an object that handles a multiple sequence alignment
       (MSA). It is very permissive of types (it does not insist on sequences
       being all same length, for example). Think of it as a set of sequences
       with a whole series of built-in manipulations and methods for reading
       and writing alignments.

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

       SimpleAlign expects the combination of name, start, and end for a given
       sequence to be unique in the alignment, and this is the key for the
       internal hashes (name, start, end are abbreviated "nse" in the code).
       However, in some cases people do not want the name/start-end to be
       displayed: either multiple names in an alignment or names specific to
       the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called
       "displayname", and generally is what is used to print out the
       alignment. They default to name/start-end.

       The SimpleAlign Module is derived from the Align module by Ewan Birney.

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules.	 Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       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.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track
       the bugs and their resolution. Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR
       Ewan Birney, birney@ebi.ac.uk

CONTRIBUTORS
       Allen Day, allenday-at-ucla.edu, Richard Adams,
       Richard.Adams-at-ed.ac.uk, David J. Evans,
       David.Evans-at-vir.gla.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-
       dot-org, Allen Smith, allens-at-cpan.org, Jason Stajich,
       jason-at-bioperl.org, Anthony Underwood, aunderwood-at-phls.org.uk,
       Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu Brian Osborne,
       bosborne at alum.mit.edu Weigang Qiu, Weigang at GENECTR-HUNTER-CUNY-
       EDU Hongyu Zhang, forward at hongyu.org Jay Hannah, jay at jays.net
       Alexandr Bezginov, albezg at gmail.com

SEE ALSO
       Bio::LocatableSeq

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 = Bio::SimpleAlign->new();
	Function  : Creates a new simple align object
	Returns	  : Bio::SimpleAlign
	Args	  : -source	=> string representing the source program
				   where this alignment came from
		    -annotation => Bio::AnnotationCollectionI
		    -seq_annotation => Bio::AnnotationCollectionI for sequences (requires -annotation also be set)
		    -seqs	=> array ref containing Bio::LocatableSeq or Bio::Seq::Meta
		    -consensus	=> consensus string
		    -consensus_meta  => Bio::Seq::Meta object containing consensus met information (kludge)

Modifier methods
       These methods modify the MSA by adding, removing or shuffling complete
       sequences.

   add_seq
	Title	  : add_seq
	Usage	  : $myalign->add_seq($newseq);
		    $myalign->add_seq(-SEQ=>$newseq, -ORDER=>5);
	Function  : Adds another sequence to the alignment. *Does not* align
		    it - just adds it to the hashes.
		    If -ORDER is specified, the sequence is inserted at the
		    the position spec'd by -ORDER, and existing sequences
		    are pushed down the storage array.
	Returns	  : nothing
	Args	  : A Bio::LocatableSeq object
		    Positive integer for the sequence position (optional)

       See Bio::LocatableSeq for more information

   remove_seq
	Title	  : remove_seq
	Usage	  : $aln->remove_seq($seq);
	Function  : Removes a single sequence from an alignment
	Returns	  :
	Argument  : a Bio::LocatableSeq object

   purge
	Title	: purge
	Usage	: $aln->purge(0.7);
	Function: Removes sequences above given sequence similarity
		  This function will grind on large alignments. Beware!
	Example :
	Returns : An array of the removed sequences
	Args	: float, threshold for similarity

   sort_alphabetically
	Title	  : sort_alphabetically
	Usage	  : $ali->sort_alphabetically
	Function  : Changes the order of the alignment to alphabetical on name
		    followed by numerical by number.
	Returns	  :
	Argument  :

   sort_by_list
	Title	  : sort_by_list
	Usage	  : $aln_ordered=$aln->sort_by_list($list_file)
	Function  : Arbitrarily order sequences in an alignment
	Returns	  : A new Bio::SimpleAlign object
	Argument  : a file listing sequence names in intended order (one name per line)

   set_new_reference
	Title	  : set_new_reference
	Usage	  : $aln->set_new_reference(3 or 'B31'):  Select the 3rd sequence, or
		    the sequence whoes name is "B31" (full, exact, and case-sensitive),
		    as the reference (1st) sequence
	Function  : Change/Set a new reference (i.e., the first) sequence
	Returns	  : a new Bio::SimpleAlign object.
		    Throws an exception if designated sequence not found
	Argument  : a positive integer of sequence order, or a sequence name
		    in the original alignment

   uniq_seq
	Title	  : uniq_seq
	Usage	  : $aln->uniq_seq():  Remove identical sequences in
		    in the alignment.  Ambiguous base ("N", "n") and
		    leading and ending gaps ("-") are NOT counted as
		    differences.
	Function  : Make a new alignment of unique sequence types (STs)
	Returns	  : 1a. if called in a scalar context,
		       a new Bio::SimpleAlign object (all sequences renamed as "ST")
		    1b. if called in an array context,
		       a new Bio::SimpleAlign object, and a hashref whose keys
		       are sequence types, and whose values are arrayrefs to
		       lists of sequence ids within the corresponding sequence type
		    2. if $aln->verbose > 0, ST of each sequence is sent to
		       STDERR (in a tabular format)
	Argument  : None

Sequence selection methods
       Methods returning one or more sequences objects.

   each_seq
	Title	  : each_seq
	Usage	  : foreach $seq ( $align->each_seq() )
	Function  : Gets a Seq object from the alignment
	Returns	  : Seq object
	Argument  :

   each_alphabetically
	Title	  : each_alphabetically
	Usage	  : foreach $seq ( $ali->each_alphabetically() )
	Function  : Returns a sequence object, but the objects are returned
		    in alphabetically sorted order.
		    Does not change the order of the alignment.
	Returns	  : Seq object
	Argument  :

   each_seq_with_id
	Title	  : each_seq_with_id
	Usage	  : foreach $seq ( $align->each_seq_with_id() )
	Function  : Gets a Seq objects from the alignment, the contents
		    being those sequences with the given name (there may be
		    more than one)
	Returns	  : Seq object
	Argument  : a seq name

   get_seq_by_pos
	Title	  : get_seq_by_pos
	Usage	  : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment
	Function  : Gets a sequence based on its position in the alignment.
		    Numbering starts from 1.  Sequence positions larger than
		    num_sequences() will thow an error.
	Returns	  : a Bio::LocatableSeq object
	Args	  : positive integer for the sequence position

   get_seq_by_id
	Title	  : get_seq_by_id
	Usage	  : $seq = $aln->get_seq_by_id($name) # seq named $name
	Function  : Gets a sequence based on its name.
		    Sequences that do not exist will warn and return undef
	Returns	  : a Bio::LocatableSeq object
	Args	  : string for sequence name

   seq_with_features
	Title	: seq_with_features
	Usage	: $seq = $aln->seq_with_features(-pos => 1,
						 -consensus => 60
						 -mask =>
		  sub { my $consensus = shift;

			for my $i (1..5){
			   my $n = 'N' x $i;
			   my $q = '\?' x $i;
			   while($consensus =~ /[^?]$q[^?]/){
			      $consensus =~ s/([^?])$q([^?])/$1$n$2/;
			   }
			 }
			return $consensus;
		      }
						);
	Function: produces a Bio::Seq object by first splicing gaps from -pos
		  (by means of a splice_by_seq_pos() call), then creating
		  features using non-? chars (by means of a consensus_string()
		  call with stringency -consensus).
	Returns : a Bio::Seq object
	Args	: -pos : required. sequence from which to build the Bio::Seq
		    object
		  -consensus : optional, defaults to consensus_string()'s
		    default cutoff value
		  -mask : optional, a coderef to apply to consensus_string()'s
		    output before building features.  this may be useful for
		    closing gaps of 1 bp by masking over them with N, for
		    instance

Create new alignments
       The result of these methods are horizontal or vertical subsets of the
       current MSA.

   select
	Title	  : select
	Usage	  : $aln2 = $aln->select(1, 3) # three first sequences
	Function  : Creates a new alignment from a continuous subset of
		    sequences.	Numbering starts from 1.  Sequence positions
		    larger than num_sequences() will 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	  : # 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.

   slice
	Title	  : slice
	Usage	  : $aln2 = $aln->slice(20,30)
	Function  : Creates a slice from the alignment inclusive of start and
		    end columns, and the first column in the alignment is denoted 1.
		    Sequences with no residues in the slice are excluded from the
		    new alignment and a warning is printed. Slice beyond the length of
		    the sequence does not do padding.
	Returns	  : A Bio::SimpleAlign object
	Args	  : Positive integer for start column, positive integer for end column,
		    optional boolean which if true will keep gap-only columns in the newly
		    created slice. Example:

		    $aln2 = $aln->slice(20,30,1)

   remove_columns
	Title	  : remove_columns
	Usage	  : $aln2 = $aln->remove_columns(['mismatch','weak']) or
		    $aln2 = $aln->remove_columns([0,0],[6,8])
	Function  : Creates an aligment with columns removed corresponding to
		    the specified type or by specifying the columns by number.
	Returns	  : Bio::SimpleAlign object
	Args	  : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'|
		    'all_gaps_columns') or array ref where the referenced array
		    contains a pair of integers that specify a range.
		    The first column is 0

   remove_gaps
	Title	  : remove_gaps
	Usage	  : $aln2 = $aln->remove_gaps
	Function  : Creates an aligment with gaps removed
	Returns	  : a Bio::SimpleAlign object
	Args	  : a gap character(optional) if none specified taken
		       from $self->gap_char,
		    [optional] $all_gaps_columns flag (1 or 0, default is 0)
			       indicates that only all-gaps columns should be deleted

       Used from method remove_columns in most cases. Set gap character using
       gap_char().

Change sequences within the MSA
       These methods affect characters in all sequences without changing the
       alignment.

   splice_by_seq_pos
	Title	: splice_by_seq_pos
	Usage	: $status = splice_by_seq_pos(1);
	Function: splices all aligned sequences where the specified sequence
		  has gaps.
	Example :
	Returns : 1 on success
	Args	: position of sequence to splice by

   map_chars
	Title	  : map_chars
	Usage	  : $ali->map_chars('\.','-')
	Function  : Does a s/$arg1/$arg2/ on the sequences. Useful for gap
		    characters

		    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	 : %cigars = $align->cigar_line()
	Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment
		   Report) line for each sequence in the alignment. Examples are
		   "1,60" or "5,10:12,58", where the numbers refer to conserved
		   positions within the alignment. The keys of the hash are the
		   NSEs (name/start/end) assigned to each sequence.
	Args	 : threshold (optional, defaults to 100)
	Returns	 : Hash of strings (cigar lines)

   match_line
	Title	 : match_line()
	Usage	 : $line = $align->match_line()
	Function : Generates a match line - much like consensus string
		   except that a line indicating the '*' for a match.
	Args	 : (optional) Match line characters ('*' by default)
		   (optional) Strong match char (':' by default)
		   (optional) Weak match char ('.' by default)
	Returns	 : String

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

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

   gap_col_matrix
	Title	 : gap_col_matrix()
	Usage	 : my $cols = $align->gap_col_matrix()
	Function : Generates an array of hashes where
		   each entry in the array is a hash reference
		   with keys of all the sequence names and
		   and value of 1 or 0 if the sequence has a gap at that column
	Args	 : (optional) gap line characters ($aln->gap_char or '-' by default)

   match
	Title	  : match()
	Usage	  : $ali->match()
	Function  : Goes through all columns and changes residues that are
		    identical to residue in first sequence to match '.'
		    character. Sets match_char.

		    USE WITH CARE: Most MSA formats do not support match
		    characters in sequences, so this is mostly for output
		    only. NEXUS format (Bio::AlignIO::nexus) can handle
		    it.
	Returns	  : 1
	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

MSA attributes
       Methods for setting and reading the MSA attributes.

       Note that the methods defining character semantics depend on the user
       to set them sensibly.  They are needed only by certain input/output
       methods. Unset them by setting to an empty string ('').

   id
	Title	  : id
	Usage	  : $myalign->id("Ig")
	Function  : Gets/sets the id field of the alignment
	Returns	  : An id string
	Argument  : An id string (optional)

   accession
	Title	  : accession
	Usage	  : $myalign->accession("PF00244")
	Function  : Gets/sets the accession field of the alignment
	Returns	  : An acc string
	Argument  : An acc string (optional)

   description
	Title	  : description
	Usage	  : $myalign->description("14-3-3 proteins")
	Function  : Gets/sets the description field of the alignment
	Returns	  : An description string
	Argument  : An description string (optional)

   missing_char
	Title	  : missing_char
	Usage	  : $myalign->missing_char("?")
	Function  : Gets/sets the missing_char attribute of the alignment
		    It is generally recommended to set it to 'n' or 'N'
		    for nucleotides and to 'X' for protein.
	Returns	  : An missing_char string,
	Argument  : An missing_char string (optional)

   match_char
	Title	  : match_char
	Usage	  : $myalign->match_char('.')
	Function  : Gets/sets the match_char attribute of the alignment
	Returns	  : An match_char string,
	Argument  : An match_char string (optional)

   gap_char
	Title	  : gap_char
	Usage	  : $myalign->gap_char('-')
	Function  : Gets/sets the gap_char attribute of the alignment
	Returns	  : An gap_char string, defaults to '-'
	Argument  : An gap_char string (optional)

   symbol_chars
	Title	: symbol_chars
	Usage	: my @symbolchars = $aln->symbol_chars;
	Function: Returns all the seen symbols (other than gaps)
	Returns : array of characters that are the seen symbols
	Args	: boolean to include the gap/missing/match characters

Alignment descriptors
       These read only methods describe the MSA in various ways.

   score
	Title	  : score
	Usage	  : $str = $ali->score()
	Function  : get/set a score of the alignment
	Returns	  : a score for the alignment
	Argument  : an optional score to set

   consensus_string
	Title	  : consensus_string
	Usage	  : $str = $ali->consensus_string($threshold_percent)
	Function  : Makes a strict consensus
	Returns	  : Consensus string
	Argument  : Optional 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

   consensus_meta
	Title	  : consensus_meta
	Usage	  : $seqmeta = $ali->consensus_meta()
	Function  : Returns a Bio::Seq::Meta object containing the consensus
		    strings derived from meta data analysis.
	Returns	  : Bio::Seq::Meta
	Argument  : Bio::Seq::Meta
	Throws	  : non-MetaI object

   is_flush
	Title	  : is_flush
	Usage	  : if ( $ali->is_flush() )
	Function  : Tells you whether the alignment
		  : is flush, i.e. all of the same length
	Returns	  : 1 or 0
	Argument  :

   length
	Title	  : length()
	Usage	  : $len = $ali->length()
	Function  : Returns the maximum length of the alignment.
		    To be sure the alignment is a block, use is_flush
	Returns	  : Integer
	Argument  :

   maxdisplayname_length
	Title	  : maxdisplayname_length
	Usage	  : $ali->maxdisplayname_length()
	Function  : Gets the maximum length of the displayname in the
		    alignment. Used in writing out various MSA formats.
	Returns	  : integer
	Argument  :

   max_metaname_length
	Title	  : max_metaname_length
	Usage	  : $ali->max_metaname_length()
	Function  : Gets the maximum length of the meta name tags in the
		    alignment for the sequences and for the alignment.
		    Used in writing out various MSA formats.
	Returns	  : integer
	Argument  : None

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

   num_sequences
	Title	  : num_sequences
	Usage	  : $depth = $ali->num_sequences
	Function  : number of sequence in the sequence alignment
	Returns	  : integer
	Argument  : none
	Note	  : replaces no_sequences()

   average_percentage_identity
	Title	: average_percentage_identity
	Usage	: $id = $align->average_percentage_identity
	Function: The function uses a fast method to calculate the average
		  percentage identity of the alignment
	Returns : The average percentage identity of the alignment
	Args	: None
	Notes	: This method implemented by Kevin Howe calculates a figure that is
		  designed to be similar to the average pairwise identity of the
		  alignment (identical in the absence of gaps), without having to
		  explicitly calculate pairwise identities proposed by Richard Durbin.
		  Validated by Ewan Birney ad Alex Bateman.

   percentage_identity
	Title	: percentage_identity
	Usage	: $id = $align->percentage_identity
	Function: The function calculates the average percentage identity
		  (aliased to average_percentage_identity)
	Returns : The average percentage identity
	Args	: None

   overall_percentage_identity
	Title	: overall_percentage_identity
	Usage	: $id = $align->overall_percentage_identity
		  $id = $align->overall_percentage_identity('short')
	Function: The function calculates the percentage identity of
		  the conserved columns
	Returns : The percentage identity of the conserved columns
	Args	: length value to use, optional defaults to alignment length
			possible values: 'align', 'short', 'long'

       The argument values 'short' and 'long' refer to shortest and longest
       sequence in the alignment. Method modification code by Hongyu Zhang.

Alignment positions
       Methods to map a sequence position into an alignment column and back.
       column_from_residue_number() does the former. The latter is really a
       property of the sequence object and can done using
       Bio::LocatableSeq::location_from_column:

	   # select somehow a sequence from the alignment, e.g.
	   my $seq = $aln->get_seq_by_pos(1);
	   #$loc is undef or Bio::LocationI object
	   my $loc = $seq->location_from_column(5);

   column_from_residue_number
	Title	: column_from_residue_number
	Usage	: $col = $ali->column_from_residue_number( $seqname, $resnumber)
	Function: This function gives the position in the alignment
		  (i.e. column number) of the given residue number in the
		  sequence with the given name. For example, for the
		  alignment

		    Seq1/91-97 AC..DEF.GH.
		    Seq2/24-30 ACGG.RTY...
		       Seq3/43-51 AC.DDEF.GHI

		  column_from_residue_number( "Seq1", 94 ) returns 6.
		  column_from_residue_number( "Seq2", 25 ) returns 2.
		  column_from_residue_number( "Seq3", 50 ) returns 10.

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

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

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

Sequence names
       Methods to manipulate the display name. The default name based on the
       sequence id and subsequence positions can be overridden in various
       ways.

   displayname
	Title	  : displayname
	Usage	  : $myalign->displayname("Ig", "IgA")
	Function  : Gets/sets the display name of a sequence in the alignment
	Returns	  : A display name string
	Argument  : name of the sequence
		    displayname of the sequence (optional)

   set_displayname_count
	Title	  : set_displayname_count
	Usage	  : $ali->set_displayname_count
	Function  : Sets the names to be name_# where # is the number of
		    times this name has been used.
	Returns	  : 1, on success
	Argument  :

   set_displayname_flat
	Title	  : set_displayname_flat
	Usage	  : $ali->set_displayname_flat()
	Function  : Makes all the sequences be displayed as just their name,
		    not name/start-end
	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	  : 1, on success
	Argument  :

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

   set_displayname_safe
	Title	  : set_displayname_safe
	Usage	  : ($new_aln, $ref_name)=$ali->set_displayname_safe(4)
	Function  : Assign machine-generated serial names to sequences in input order.
		    Designed to protect names during PHYLIP runs. Assign 10-char string
		    in the form of "S000000001" to "S999999999". Restore the original
		    names using "restore_displayname".
	Returns	  : 1. a new $aln with system names;
		    2. a hash ref for restoring names
	Argument  : Number for id length (default 10)

   restore_displayname
	Title	  : restore_displayname
	Usage	  : $aln_name_restored=$ali->restore_displayname($hash_ref)
	Function  : Restore original sequence names (after running
		    $ali->set_displayname_safe)
	Returns	  : a new $aln with names restored.
	Argument  : a hash reference of names from "set_displayname_safe".

   sort_by_start
	Title	  : sort_by_start
	Usage	  : $ali->sort_by_start
	Function  : Changes the order of the alignment to the start position of each
		    subalignment
	Returns	  :
	Argument  :

   bracket_string
	Title	  : bracket_string
	Usage	  : my @params = (-refseq     => 'testseq',
				  -allele1    => 'allele1',
				  -allele2    => 'allele2',
				  -delimiters => '{}',
				  -separator  => '/');
		    $str = $aln->bracket_string(@params)

	Function :  When supplied with a list of parameters (see below), returns a
		    string in BIC format. This is used for allelic comparisons.
		    Briefly, if either allele contains a base change when compared to
		    the refseq, the base or gap for each allele is represented in
		    brackets in the order present in the 'alleles' parameter.

		    For the following data:

		    >testseq
		    GGATCCATTGCTACT
		    >allele1
		    GGATCCATTCCTACT
		    >allele2
		    GGAT--ATTCCTCCT

		    the returned string with parameters 'refseq => testseq' and
		    'alleles => [qw(allele1 allele2)]' would be:

		    GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
	Returns	  : BIC-formatted string
	Argument  : Required args
		       refseq	 : string (ID) of the reference sequence used
				   as basis for comparison
		       allele1	 : string (ID) of the first allele
		       allele2	 : string (ID) of the second allele
		    Optional args
		       delimiters: two symbol string of left and right delimiters.
				   Only the first two symbols are used
				   default = '[]'
		       separator : string used as a separator.	Only the first
				   symbol is used
				   default = '/'
	Throws	  : On no refseq/alleles, or invalid refseq/alleles.

   methods implementing Bio::FeatureHolderI
       FeatureHolderI implementation to support labeled character sets like
       one would get from NEXUS represented data.

   get_SeqFeatures
	Usage	: @features = $aln->get_SeqFeatures
	Function: Get the feature objects held by this feature holder.
	Example :
	Returns : an array of Bio::SeqFeatureI implementing objects
	Args	: optional filter coderef, taking a Bio::SeqFeatureI
		: as argument, returning TRUE if wanted, FALSE if
		: unwanted

   add_SeqFeature
	Usage	: $aln->add_SeqFeature($subfeat);
	Function: adds a SeqFeature into the SeqFeature array.
	Example :
	Returns : true on success
	Args	: a Bio::SeqFeatureI object
	Note	: This implementation is not compliant
		  with Bio::FeatureHolderI

   remove_SeqFeatures
	Usage	: $obj->remove_SeqFeatures
	Function: Removes all SeqFeatures.  If you want to remove only a subset,
		  remove that subset from the returned array, and add back the rest.
	Returns : The array of Bio::SeqFeatureI features that was
		  deleted from this alignment.
	Args	: none

   feature_count
	Title	: feature_count
	Usage	: $obj->feature_count()
	Function: Return the number of SeqFeatures attached to the alignment
	Returns : integer representing the number of SeqFeatures
	Args	: None

   get_all_SeqFeatures
	Title	: get_all_SeqFeatures
	Usage	:
	Function: Get all SeqFeatures.
	Example :
	Returns : an array of Bio::SeqFeatureI implementing objects
	Args	: none
	Note	: Falls through to Bio::FeatureHolderI implementation.

   methods for Bio::AnnotatableI
       AnnotatableI implementation to support sequence alignments which
       contain annotation (NEXUS, Stockholm).

   annotation
	Title	: annotation
	Usage	: $ann = $aln->annotation or
		  $aln->annotation($ann)
	Function: Gets or sets the annotation
	Returns : Bio::AnnotationCollectionI object
	Args	: None or Bio::AnnotationCollectionI object

       See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more
       information

Deprecated methods
   no_residues
	Title	  : no_residues
	Usage	  : $no = $ali->no_residues
	Function  : number of residues in total in the alignment
	Returns	  : integer
	Argument  :
	Note	  : deprecated in favor of num_residues()

   no_sequences
	Title	  : no_sequences
	Usage	  : $depth = $ali->no_sequences
	Function  : number of sequence in the sequence alignment
	Returns	  : integer
	Argument  :
	Note	  : deprecated in favor of num_sequences()

   mask_columns
	Title	  : mask_columns
	Usage	  : $aln2 = $aln->mask_columns(20,30)
	Function  : Masks a slice of the alignment inclusive of start and
		    end columns, and the first column in the alignment is denoted 1.
		    Mask beyond the length of the sequence does not do padding.
	Returns	  : A Bio::SimpleAlign object
	Args	  : Positive integer for start column, positive integer for end column,
		    optional string value use for the mask. Example:

		    $aln2 = $aln->mask_columns(20,30,'?')
	Note	  : Masking must use a character that is not used for gaps or
		    frameshifts.  These can be adjusted using the relevant global
		    variables, but be aware these may be (uncontrollably) modified
		    elsewhere within BioPerl (see bug 2715)

perl v5.14.1			  2011-07-22		   Bio::SimpleAlign(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net