1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
|
module Fasta
require 'zlib'
# require 'codon2aa.rb'
class SequenceEntry
def initialize(headline)
h = headline.match(/^>(.*)\n/)
if h
@header = h[1]
else
STDERR.puts "#{$0}: illegal header #{header}"
exit 1
end
@comment = Array.new()
@seqoflines = Array.new()
end
def add_comment_line(line)
@comment.push(line)
end
def add_sequence_line(line)
@seqoflines.push(line.chomp.gsub(/\s/,""))
end
def set_header(s)
@header = s
end
def write(rc, io, seq_line_width = 70)
io.print ">#{@header}"
@comment.each do |c|
io.print c
end
s = @seqoflines.join("")
if rc
s = s.reverse
s.tr!("ACGTacgt","TGCAtgca")
end
b = 0
while b < s.size
io.puts(s[b..b + seq_line_width - 1])
b += seq_line_width
end
end
def get_seqlength()
lensum = 0
@seqoflines.each do |line|
lensum += line.length
end
return lensum
end
def get_sequence()
return @seqoflines.join("")
end
def get_header()
return @header
end
end
=begin
def write_open_reading_frame( offset, io, reverse=false )
s = @seqoflines.join("")
if reverse
s = s.reverse
end
aaSequence = ""
position = offset
while position+3 < s.length # enough bases for a codon
begin
codon = s[ position, 3 ]
aa = codon2aa_11( codon )
aaSequence += aa
rescue => text
io.puts text
return
end
position += 3
end
puts aaSequence
end
=end
def Fasta.read_multi_file(fname) # function for module Fasta
begin
if fname.match(/\.gz$/)
infp = Zlib::GzipReader.open(fname)
else
infp = File.open(fname,"r")
end
rescue => err
STDERR.print "Could not open file \"#{fname}\": #{err}\n"
exit 1
end
curr_entry = nil
infp.each_line do |line|
if line.match(/^>/)
if not curr_entry.nil?
yield curr_entry # deliver current entry to iterator
end
curr_entry = SequenceEntry.new(line) # create new sequence entry
elsif line.match(/^;/) # comment line
curr_entry.add_comment_line(line)
else
curr_entry.add_sequence_line(line)
end
end
if curr_entry.nil?
STDERR.puts "#{$0}: assertion in f. #{__FILE__}, l. #{__LINE__} failed"
end
yield curr_entry
infp.close
end
end # module Fasta
|
