Class: Bio::GFF::FastaReader

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/gff/file/gfffasta.rb

Overview

Read FASTA records from file and store seek positions, which are used to retrieve the records. Note, this implementation merely retains records in memory (FIXME)

Instance Method Summary collapse

Constructor Details

#initialize(fh, io_seek = nil) ⇒ FastaReader

Returns a new instance of FastaReader.



18
19
20
21
22
 
# File 'lib/bio/db/gff/file/gfffasta.rb', line 18

def initialize fh, io_seek=nil
  @fh = fh
  @h = {}
  parse
end

Instance Method Details

#[](index) ⇒ Object 



42
43
44
 
# File 'lib/bio/db/gff/file/gfffasta.rb', line 42

def [] index
  @h[index]
end

#each ⇒ Object 



46
47
48
49
50
 
# File 'lib/bio/db/gff/file/gfffasta.rb', line 46

def each 
  @h.each do | k,v |
    yield k, v
  end
end

#parse ⇒ Object 



24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
 
# File 'lib/bio/db/gff/file/gfffasta.rb', line 24

def parse
  # read FASTA records
  header = nil
  seqs   = []
  @fh.each_line do | line |
    line = line.strip
    next if line =~ /^#/
    if line =~ /^>/  # FASTA record header
      add(header,seqs)
      header = line
      seqs   = []
    else
      seqs << line.gsub(/\s+/,'')
    end
  end
  add(header,seqs)
end