Class Bio::MAFFT
In: lib/bio/appl/mafft/report.rb
lib/bio/appl/mafft.rb
Parent: Object

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.

Methods

fftns   fftnsi   log   new   new2   nwap   nwns   nwnsi   option   query   query_align   query_alignment   query_by_filename   query_string   reset  

Classes and Modules

Class Bio::MAFFT::Report

Attributes

command  [R]  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.
data_stdout  [RW]  Last output to the stdout.
exit_status  [R]  Last exit status
options  [RW]  options
output  [R]  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  [RW]  program name (usually ‘mafft’ in UNIX)
report  [R]  Shows last alignment result (instance of Bio::MAFFT::Report class) performed by the factory.

Public Class methods

fftns(n = nil)

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, line 47
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
fftnsi()

Creates a new alignment factory. Performs ‘fftnsi’.

[Source]

    # File lib/bio/appl/mafft.rb, line 59
59:     def self.fftnsi
60:       self.new2(nil, 'fftnsi')
61:     end
new(program = 'mafft', opt = [])

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, line 108
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
new2(dir, prog, *opt)

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, line 98
 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
nwap(n = nil)

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, line 90
90:     def self.nwap(n = nil)
91:       self.nwns(n, true)
92:     end
nwns(n = nil, ap = nil)

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, line 67
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
nwnsi(all_positive = nil)

Creates a new alignment factory. Performs ‘nwnsi’. If all_positive is true, add option ’—all-positive’.

[Source]

    # File lib/bio/appl/mafft.rb, line 81
81:     def self.nwnsi(all_positive = nil)
82:       opt = []
83:       opt << '--all-positive' if all_positive
84:       self.new2(nil, 'nwnsi', *opt)
85:     end

Public Instance methods

log()

log is deprecated (no replacement) and returns empty string.

[Source]

     # File lib/bio/appl/mafft.rb, line 141
141:     def log
142:       warn "Bio::MAFFT#log is deprecated (no replacement) and returns empty string."
143:       ''
144:     end
option()

option is deprecated. Instead, please use options.

[Source]

     # File lib/bio/appl/mafft.rb, line 125
125:     def option
126:       warn "Bio::MAFFT#option is deprecated. Please use options."
127:       options
128:     end
query(seqs)

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, line 179
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
query_align(seqs, *arg)

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, line 194
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
query_alignment(seqs)

Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.

[Source]

     # File lib/bio/appl/mafft.rb, line 206
206:     def query_alignment(seqs)
207:       query_align(seqs)
208:     end
query_by_filename(fn, *arg)

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, line 232
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
query_string(str, *arg)

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, line 214
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
reset()

Clear the internal data and status, except program and options.

[Source]

     # File lib/bio/appl/mafft.rb, line 164
164:     def reset
165:       @command = nil
166:       @output = nil
167:       @report = nil
168:       @exit_status = nil
169:       @data_stdout = nil
170:     end

[Validate]