Class: Bio::FlatFile
- Includes:
- Enumerable
- Defined in:
- lib/bio/io/flatfile.rb
Overview
Bio::FlatFile is a helper and wrapper class to read a biological data file. It acts like a IO object. It can automatically detect data format, and users do not need to tell the class what the data is.
Defined Under Namespace
Modules: Splitter Classes: AutoDetect, BufferedInputStream, UnknownDataFormatError
Instance Attribute Summary collapse
-
#dbclass ⇒ Object
Returns database class which is automatically detected or given in FlatFile#initialize.
-
#entry ⇒ Object
readonly
Returns the value of attribute entry.
-
#raw ⇒ Object
If true, raw mode.
-
#skip_leader_mode ⇒ Object
The mode how to skip leader of the data.
Class Method Summary collapse
-
.auto(*arg, &block) ⇒ Object
Same as Bio::FlatFile.open(nil, filename_or_stream, mode, perm, options).
-
.autodetect(text) ⇒ Object
Detects database class (== file format) of given string.
-
.autodetect_file(filename) ⇒ Object
Detects database class (== file format) of given file.
-
.autodetect_io(io) ⇒ Object
Detects database class (== file format) of given input stream.
-
.autodetect_stream(io) ⇒ Object
This is OBSOLETED.
-
.foreach(*arg) ⇒ Object
Executes the block for every entry in the stream.
-
.open(*arg, &block) ⇒ Object
Bio::FlatFile.open(file, *arg) Bio::FlatFile.open(dbclass, file, *arg).
-
.open_file(filename, *arg) ⇒ Object
Same as FlatFile.auto(filename, *arg), except that it only accept filename and doesn’t accept IO object.
-
.open_uri(uri, *arg) ⇒ Object
Opens URI specified as uri.
-
.to_a(*arg) ⇒ Object
Same as FlatFile.auto(filename_or_stream, *arg).to_a.
Instance Method Summary collapse
-
#autodetect(lines = 31, ad = AutoDetect.default) ⇒ Object
Performs determination of database class (file format).
-
#close ⇒ Object
Closes input stream.
-
#each_entry ⇒ Object
(also: #each)
Iterates over each entry in the flatfile.
-
#entry_ended_pos ⇒ Object
(end position of the last entry) + 1.
-
#entry_pos_flag ⇒ Object
a flag to write down entry start and end positions.
-
#entry_pos_flag=(x) ⇒ Object
Sets flag to write down entry start and end positions.
-
#entry_raw ⇒ Object
Returns the last raw entry as a string.
-
#entry_start_pos ⇒ Object
start position of the last entry.
-
#eof? ⇒ Boolean
Returns true if input stream is end-of-file.
-
#gets(*arg) ⇒ Object
Similar to IO#gets.
-
#initialize(dbclass, stream) ⇒ FlatFile
constructor
Same as FlatFile.open, except that ‘stream’ should be a opened stream object (IO, File, …, who have the ‘gets’ method).
-
#io ⇒ Object
(DEPRECATED) IO object in the flatfile object.
-
#next_entry ⇒ Object
Get next entry.
-
#path ⇒ Object
Pathname, filename or URI (or nil).
-
#pos ⇒ Object
Returns current position of input stream.
-
#pos=(p) ⇒ Object
(Not recommended to use it.) Sets position of input stream.
-
#rewind ⇒ Object
Resets file pointer to the start of the flatfile.
-
#to_io ⇒ Object
IO object in the flatfile object.
Constructor Details
#initialize(dbclass, stream) ⇒ FlatFile
Same as FlatFile.open, except that ‘stream’ should be a opened stream object (IO, File, …, who have the ‘gets’ method).
-
Example 1
Bio::FlatFile.new(Bio::GenBank, ARGF)
-
Example 2
Bio::FlatFile.new(Bio::GenBank, IO.popen("gzip -dc nc1101.flat.gz"))
Compatibility Note: Now, you cannot specify “:raw => true” or “:raw => false”. Below styles are DEPRECATED.
-
Example 3 (deprecated)
# Bio::FlatFile.new(nil, $stdin, :raw=>true) # => ERROR # Please rewrite as below. ff = Bio::FlatFile.new(nil, $stdin) ff.raw = true
-
Example 3 in old style (deprecated)
# Bio::FlatFile.new(nil, $stdin, true) # => ERROR # Please rewrite as below. ff = Bio::FlatFile.new(nil, $stdin) ff.raw = true
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# File 'lib/bio/io/flatfile.rb', line 548 def initialize(dbclass, stream) # 2nd arg: IO object if stream.kind_of?(BufferedInputStream) @stream = stream else @stream = BufferedInputStream.for_io(stream) end # 1st arg: database class (or file format autodetection) if dbclass then self.dbclass = dbclass else autodetect end # @skip_leader_mode = :firsttime @firsttime_flag = true # default raw mode is false self.raw = false end |
Instance Attribute Details
#dbclass ⇒ Object
Returns database class which is automatically detected or given in FlatFile#initialize.
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# File 'lib/bio/io/flatfile.rb', line 735 def dbclass @dbclass end |
#entry ⇒ Object (readonly)
Returns the value of attribute entry.
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# File 'lib/bio/io/flatfile.rb', line 618 def entry @entry end |
#raw ⇒ Object
If true, raw mode.
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# File 'lib/bio/io/flatfile.rb', line 710 def raw @raw end |
#skip_leader_mode ⇒ Object
The mode how to skip leader of the data.
- :firsttime
-
(DEFAULT) only head of file (= first time to read)
- :everytime
-
everytime to read entry
- nil
-
never skip
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# File 'lib/bio/io/flatfile.rb', line 572 def skip_leader_mode @skip_leader_mode end |
Class Method Details
.auto(*arg, &block) ⇒ Object
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# File 'lib/bio/io/flatfile.rb', line 445 def self.auto(*arg, &block) self.open(nil, *arg, &block) end |
.autodetect(text) ⇒ Object
Detects database class (== file format) of given string. If fails to determine, returns false or nil.
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# File 'lib/bio/io/flatfile.rb', line 774 def self.autodetect(text) AutoDetect.default.autodetect(text) end |
.autodetect_file(filename) ⇒ Object
Detects database class (== file format) of given file. If fails to determine, returns nil.
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# File 'lib/bio/io/flatfile.rb', line 754 def self.autodetect_file(filename) self.open_file(filename).dbclass end |
.autodetect_io(io) ⇒ Object
Detects database class (== file format) of given input stream. If fails to determine, returns nil. Caution: the method reads some data from the input stream, and the data will be lost.
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# File 'lib/bio/io/flatfile.rb', line 762 def self.autodetect_io(io) self.new(nil, io).dbclass end |
.autodetect_stream(io) ⇒ Object
This is OBSOLETED. Please use autodetect_io(io) instead.
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# File 'lib/bio/io/flatfile.rb', line 767 def self.autodetect_stream(io) $stderr.print "Bio::FlatFile.autodetect_stream will be deprecated." if $VERBOSE self.autodetect_io(io) end |
.foreach(*arg) ⇒ Object
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# File 'lib/bio/io/flatfile.rb', line 517 def self.foreach(*arg) self.open(*arg) do |flatfileobj| flatfileobj.each do |entry| yield entry end end end |
.open(*arg, &block) ⇒ Object
Bio::FlatFile.open(file, *arg)
Bio::FlatFile.open(dbclass, file, *arg)
Creates a new Bio::FlatFile object to read a file or a stream which contains dbclass data.
dbclass should be a class (or module) or nil. e.g. Bio::GenBank, Bio::FastaFormat.
If file is a filename (which doesn’t have gets method), the method opens a local file named file with File.open(filename, *arg)
.
When dbclass is omitted or nil is given to dbclass, the method tries to determine database class (file format) automatically. When it fails to determine, dbclass is set to nil and FlatFile#next_entry would fail. You can still set dbclass using FlatFile#dbclass= method.
-
Example 1
Bio::FlatFile.open(Bio::GenBank, "genbank/gbest40.seq")
-
Example 2
Bio::FlatFile.open(nil, "embl/est_hum17.dat")
-
Example 3
Bio::FlatFile.open("genbank/gbest40.seq")
-
Example 4
Bio::FlatFile.open(Bio::GenBank, $stdin)
If it is called with a block, the block will be executed with a new Bio::FlatFile object. If filename is given, the file is automatically closed when leaving the block.
-
Example 5
Bio::FlatFile.open(nil, 'test4.fst') do |ff| ff.each { |e| print e.definition, "\n" } end
-
Example 6
Bio::FlatFile.open('test4.fst') do |ff| ff.each { |e| print e.definition, "\n" } end
Compatibility Note: *arg is completely passed to the File.open
and you cannot specify “:raw => true” or “:raw => false”.
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# File 'lib/bio/io/flatfile.rb', line 403 def self.open(*arg, &block) # FlatFile.open(dbclass, file, mode, perm) # FlatFile.open(file, mode, perm) if arg.size <= 0 raise ArgumentError, 'wrong number of arguments (0 for 1)' end x = arg.shift if x.is_a?(Module) then # FlatFile.open(dbclass, filename_or_io, ...) dbclass = x elsif x.nil? then # FlatFile.open(nil, filename_or_io, ...) dbclass = nil else # FlatFile.open(filename, ...) dbclass = nil arg.unshift(x) end if arg.size <= 0 raise ArgumentError, 'wrong number of arguments (1 for 2)' end file = arg.shift # check if file is filename or IO object unless file.respond_to?(:gets) # 'file' is a filename _open_file(dbclass, file, *arg, &block) else # 'file' is a IO object ff = self.new(dbclass, file) block_given? ? (yield ff) : ff end end |
.open_file(filename, *arg) ⇒ Object
Same as FlatFile.auto(filename, *arg), except that it only accept filename and doesn’t accept IO object. File format is automatically determined.
It can accept a block. If a block is given, it returns the block’s return value. Otherwise, it returns a new FlatFile object.
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# File 'lib/bio/io/flatfile.rb', line 467 def self.open_file(filename, *arg) _open_file(nil, filename, *arg) end |
.open_uri(uri, *arg) ⇒ Object
Opens URI specified as uri. uri must be a String or URI object. *arg is passed to OpenURI.open_uri or URI#open.
Like FlatFile#open, it can accept a block.
Note that you MUST explicitly require ‘open-uri’. Because open-uri.rb modifies existing class, it isn’t required by default.
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# File 'lib/bio/io/flatfile.rb', line 500 def self.open_uri(uri, *arg) if block_given? then BufferedInputStream.open_uri(uri, *arg) do |stream| yield self.new(nil, stream) end else stream = BufferedInputStream.open_uri(uri, *arg) self.new(nil, stream) end end |
.to_a(*arg) ⇒ Object
Same as FlatFile.auto(filename_or_stream, *arg).to_a
(This method might be OBSOLETED in the future.)
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# File 'lib/bio/io/flatfile.rb', line 452 def self.to_a(*arg) self.auto(*arg) do |ff| raise 'cannot determine file format' unless ff.dbclass ff.to_a end end |
Instance Method Details
#autodetect(lines = 31, ad = AutoDetect.default) ⇒ Object
Performs determination of database class (file format). Pre-reads lines
lines for format determination (default 31 lines). If fails, returns nil or false. Otherwise, returns database class.
The method can be called anytime if you want (but not recommended). This might be useful if input file is a mixture of muitiple format data.
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# File 'lib/bio/io/flatfile.rb', line 743 def autodetect(lines = 31, ad = AutoDetect.default) if r = ad.autodetect_flatfile(self, lines) self.dbclass = r else self.dbclass = nil unless self.dbclass end r end |
#close ⇒ Object
Closes input stream. (similar to IO#close)
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# File 'lib/bio/io/flatfile.rb', line 670 def close @stream.close end |
#each_entry ⇒ Object Also known as: each
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# File 'lib/bio/io/flatfile.rb', line 653 def each_entry while e = self.next_entry yield e end end |
#entry_ended_pos ⇒ Object
(end position of the last entry) + 1
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# File 'lib/bio/io/flatfile.rb', line 641 def entry_ended_pos @splitter.entry_ended_pos end |
#entry_pos_flag ⇒ Object
a flag to write down entry start and end positions
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# File 'lib/bio/io/flatfile.rb', line 626 def entry_pos_flag @splitter.entry_pos_flag end |
#entry_pos_flag=(x) ⇒ Object
Sets flag to write down entry start and end positions
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# File 'lib/bio/io/flatfile.rb', line 631 def entry_pos_flag=(x) @splitter.entry_pos_flag = x end |
#entry_raw ⇒ Object
Returns the last raw entry as a string.
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# File 'lib/bio/io/flatfile.rb', line 621 def entry_raw @splitter.entry end |
#entry_start_pos ⇒ Object
start position of the last entry
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# File 'lib/bio/io/flatfile.rb', line 636 def entry_start_pos @splitter.entry_start_pos end |
#eof? ⇒ Boolean
Returns true if input stream is end-of-file. Otherwise, returns false. (Similar to IO#eof?, but may not be equal to io.eof?, because FlatFile has its own internal buffer.)
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# File 'lib/bio/io/flatfile.rb', line 699 def eof? @stream.eof? end |
#gets(*arg) ⇒ Object
Similar to IO#gets. Internal use only. Users should not call it directly.
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# File 'lib/bio/io/flatfile.rb', line 714 def gets(*arg) @stream.gets(*arg) end |
#io ⇒ Object
(DEPRECATED) IO object in the flatfile object.
Compatibility Note: Bio::FlatFile#io is deprecated. Please use Bio::FlatFile#to_io instead.
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# File 'lib/bio/io/flatfile.rb', line 578 def io warn "Bio::FlatFile#io is deprecated." @stream.to_io end |
#next_entry ⇒ Object
Get next entry.
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# File 'lib/bio/io/flatfile.rb', line 600 def next_entry raise UnknownDataFormatError, 'file format auto-detection failed?' unless @dbclass if @skip_leader_mode and ((@firsttime_flag and @skip_leader_mode == :firsttime) or @skip_leader_mode == :everytime) @splitter.skip_leader end r = @splitter.get_entry @firsttime_flag = false return nil unless r if raw then r else @entry = @dbclass.new(r) @entry end end |
#path ⇒ Object
Pathname, filename or URI (or nil).
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# File 'lib/bio/io/flatfile.rb', line 591 def path @stream.path end |
#pos ⇒ Object
Returns current position of input stream. If the input stream is not a normal file, the result is not guaranteed. It is similar to IO#pos. Note that it will not be equal to io.pos, because FlatFile has its own internal buffer.
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# File 'lib/bio/io/flatfile.rb', line 680 def pos @stream.pos end |
#pos=(p) ⇒ Object
(Not recommended to use it.) Sets position of input stream. If the input stream is not a normal file, the result is not guaranteed. It is similar to IO#pos=. Note that it will not be equal to io.pos=, because FlatFile has its own internal buffer.
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# File 'lib/bio/io/flatfile.rb', line 691 def pos=(p) @stream.pos=(p) end |
#rewind ⇒ Object
Resets file pointer to the start of the flatfile. (similar to IO#rewind)
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# File 'lib/bio/io/flatfile.rb', line 662 def rewind r = @stream.rewind @firsttime_flag = true r end |
#to_io ⇒ Object
IO object in the flatfile object.
Compatibility Note: Bio::FlatFile#io is deprecated.
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# File 'lib/bio/io/flatfile.rb', line 586 def to_io @stream.to_io end |