class FastaReader

Public Class Methods

new(fn, regex = nil) click to toggle source

Initalize the reader of FASTA file fn. Options can be :regex and :index (true/false)

# File lib/bio-table/parsers/fastareader.rb, line 19
def initialize fn, regex = nil
  @logger = Bio::Log::LoggerPlus['bio-table']
  @f = File.open(fn)
  @fread_once = false
  @regex = regex
  @regex = '^(\S+)' if @regex == nil
  @regex = '('+regex+')' if regex !~ /\(/
  @logger.info "Parsing FASTA with ID regex '"+@regex+"'"
end

Public Instance Methods

close() click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 126
def close
  @f.close
end
digest_tag(tag) click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 106
def digest_tag tag
  if tag =~ /^>/
    descr = $'.strip
    matches = /#{@regex}/.match(descr).captures
    if matches.size > 0
      # p matches
      return matches.join("\t"), descr
    end
    p descr  # do not remove these
    p @regex
  end
  raise "Can not digest '#{tag}' using '"+@regex+"'"
end
each() { |fasta_record| ... } click to toggle source

returns a FastaRecord for every item (invokes parse_each)

# File lib/bio-table/parsers/fastareader.rb, line 64
def each
  parse_each { | id, descr, seq | yield FastaRecord.new(id, descr, seq) }
end
first() click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 68
def first
  parse_each { | id, descr, seq | 
    return FastaRecord.new(id, descr, seq) 
  }
end
get(id) click to toggle source

Return a record by its id, nil when not found

# File lib/bio-table/parsers/fastareader.rb, line 75
def get id
  indexed?
  if fpos = indexer_get(id)
    get_rec(fpos)
  else
    nil
  end
end
get_by_index(idx) click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 97
def get_by_index idx
  indexed?
  if fpos = indexer_get_by_index(idx)[1]
    ret = get_rec(fpos)
    return ret
  end
  nil
end
get_rec(fpos) click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 84
def get_rec fpos
  @f.seek fpos
  tag = @f.gets
  seq = ""
  begin
    line = @f.gets
    break if line =~ /^>/
    seq += line.strip 
  end while !@f.eof
  id, descr = digest_tag(tag)
  FastaRecord.new(id,descr,seq)
end
parse_each() { |id, descr, seq| ... } click to toggle source

Parse the FASTA file and yield id, descr, sequence. When the indexer is on it will index the records the first time. Note that, with indexing, when you don’t complete parsing there will be an error the second time. This is a # trade-off, otherwise one would always have to index the file and read it twice.

# File lib/bio-table/parsers/fastareader.rb, line 34
def parse_each
  @f.seek 0    # force file rewind
  @rec_fpos = 0
  @rec_line = @f.gets
  fpos = 0
  @count = 0
  begin
    # digest id from record description
    id, descr = digest_tag(@rec_line)
    id_fpos = @rec_fpos
    # parse the sequence
    seq = ""
    begin
      fpos = @f.tell
      line = @f.gets
      break if line =~ /^>/
      seq += line.strip 
    end while !@f.eof 
    # new record
    @count += 1
    @rec_fpos = fpos
    @rec_line = line
    # p [@rec_line, id, id_fpos]
    # indexer_set(id, id_fpos) if @indexer and not @fread_once
    yield id, descr, seq
  end while !@f.eof
  @fread_once = true
end
size() click to toggle source

Returns the size of the dataset - as read. After the final record the size represents the number of items in the FASTA file

# File lib/bio-table/parsers/fastareader.rb, line 122
def size
  @count
end

Private Instance Methods

indexed?() click to toggle source
# File lib/bio-table/parsers/fastareader.rb, line 132
def indexed?
  if @indexer and not @fread_once
    # force indexer
    # $stderr.print "Force indexer"
    parse_each { | x, y, z | nil }
  end
  true
end