class Bio::MAFFT
Bio::MAFFT is a wrapper class to execute MAFFT. MAFFT is a very fast multiple sequence alignment software.
Though Bio::MAFFT class currently supports only MAFFT version 3, you can use MAFFT version 5 because the class is a wrapper class.
Attributes
Shows last command-line string. Returns nil or an array of String. Note that filenames described in the command-line may already be removed because they are temporary files.
Last output to the stdout.
Last exit status
options
Shows latest raw alignment result. Return a string. (Changed in bioruby-1.1.0). Compatibility note: If you want an array of Bio::FastaFormat instances, you should use report.data instead.
program name (usually ‘mafft’ in UNIX)
Shows last alignment result (instance of Bio::MAFFT::Report class) performed by the factory.
Public Class Methods
Source
# File lib/bio/appl/mafft.rb 47 def self.fftns(n = nil) 48 opt = [] 49 if n.to_s == 'i' then 50 self.new2(nil, 'fftnsi', *opt) 51 else 52 opt << n.to_s if n 53 self.new2(nil, 'fftns', *opt) 54 end 55 end
Creates a new alignment factory. When n is a number (1,2,3, …), performs ‘fftns n’. When n is :i or ‘i’, performs ‘fftnsi’.
Source
# File lib/bio/appl/mafft.rb 59 def self.fftnsi 60 self.new2(nil, 'fftnsi') 61 end
Creates a new alignment factory. Performs ‘fftnsi’.
Source
# File lib/bio/appl/mafft.rb 108 def initialize(program = 'mafft', opt = []) 109 @program = program 110 @options = opt 111 @command = nil 112 @output = nil 113 @report = nil 114 @data_stdout = nil 115 @exit_status = nil 116 end
Creates a new alignment factory. program is the name of the program. opt is options of the program.
Source
# File lib/bio/appl/mafft.rb 98 def self.new2(dir, prog, *opt) 99 if dir then 100 prog = File.join(dir, prog) 101 end 102 self.new(prog, opt) 103 end
Creates a new alignment factory. dir is the path of the MAFFT program. prog is the name of the program. opt is options of the program.
Source
# File lib/bio/appl/mafft.rb 90 def self.nwap(n = nil) 91 self.nwns(n, true) 92 end
Creates a new alignment factory. Performs ‘nwns –all-positive n’ or ‘nwnsi –all-positive’. Same as Bio::MAFFT.nwap(n, true).
Source
# File lib/bio/appl/mafft.rb 67 def self.nwns(n = nil, ap = nil) 68 opt = [] 69 opt << '--all-positive' if ap 70 if n.to_s == 'i' then 71 self.new2(nil, 'nwnsi', *opt) 72 else 73 opt << n.to_s if n 74 self.new2(nil, 'nwns', *opt) 75 end 76 end
Creates a new alignment factory. When n is a number (1,2,3, …), performs ‘nwns n’. When n is :i or ‘i’, performs ‘nwnsi’. In both case, if all_positive is true, add option ‘–all-positive’.
Source
# File lib/bio/appl/mafft.rb 81 def self.nwnsi(all_positive = nil) 82 opt = [] 83 opt << '--all-positive' if all_positive 84 self.new2(nil, 'nwnsi', *opt) 85 end
Creates a new alignment factory. Performs ‘nwnsi’. If all_positive is true, add option ‘–all-positive’.
Public Instance Methods
Source
# File lib/bio/appl/mafft.rb 141 def log 142 warn "Bio::MAFFT#log is deprecated (no replacement) and returns empty string." 143 '' 144 end
log is deprecated (no replacement) and returns empty string.
Source
# File lib/bio/appl/mafft.rb 125 def option 126 warn "Bio::MAFFT#option is deprecated. Please use options." 127 options 128 end
option is deprecated. Instead, please use options.
Source
# File lib/bio/appl/mafft.rb 179 def query(seqs) 180 if seqs then 181 query_align(seqs) 182 else 183 exec_local(@options) 184 @exit_status.exitstatus == 0 ? true : false 185 end 186 end
Executes the program. If seqs is not nil, perform alignment for seqs. If seqs is nil, simply executes the program.
Compatibility note: When seqs is nil, returns true if the program exits normally, and returns false if the program exits abnormally.
Source
# File lib/bio/appl/mafft.rb 194 def query_align(seqs, *arg) 195 if arg.size > 0 then 196 warn '2nd and other arguments of Bio::MAFFT#query_align is ignored' 197 end 198 unless seqs.is_a?(Bio::Alignment) 199 seqs = Bio::Alignment.new(seqs) 200 end 201 query_string(seqs.output_fasta(:width => 70)) 202 end
Note that this method will be renamed to query_alignment.
Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.
Compatibility Note: arg is deprecated and ignored.
Source
# File lib/bio/appl/mafft.rb 206 def query_alignment(seqs) 207 query_align(seqs) 208 end
Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.
Source
# File lib/bio/appl/mafft.rb 232 def query_by_filename(fn, *arg) 233 if arg.size > 0 then 234 warn '2nd argument of Bio::MAFFT#query_filename is ignored' 235 end 236 opt = @options + [ fn ] 237 exec_local(opt) 238 @report = Report.new(@output) 239 @report 240 end
Performs alignment of sequences in the file named fn.
Compatibility Note: 2nd argument (seqtype) is deprecated and ignored.
Source
# File lib/bio/appl/mafft.rb 214 def query_string(str, *arg) 215 if arg.size > 0 then 216 warn '2nd and other arguments of Bio::MAFFT#query_string is ignored' 217 end 218 begin 219 tf_in = Tempfile.open('align') 220 tf_in.print str 221 ensure 222 tf_in.close(false) 223 end 224 r = query_by_filename(tf_in.path, *arg) 225 tf_in.close(true) 226 r 227 end
Performs alignment for str. Str should be a string that can be recognized by the program.
Compatibility Note: arg is deprecated and ignored.
Source
# File lib/bio/appl/mafft.rb 164 def reset 165 @command = nil 166 @output = nil 167 @report = nil 168 @exit_status = nil 169 @data_stdout = nil 170 end
Clear the internal data and status, except program and options.