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Manual Reference Pages  -  BIO::ALIGN::ALIGNI (3)

.ds Aq ’

NAME

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

CONTENTS

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:



  https://github.com/bioperl/bioperl-live/issues



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()



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