Bio::Align::AlignI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Align::AlignI - An interface for describing sequence alignments.

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

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Ewan Birney, birney@ebi.ac.uk Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

APPENDIX

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()