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
|
#!/usr/bin/env ruby
require 'ostruct'
require 'optparse'
require "scripts/evalseedhash.rb"
def usage(opts,msg)
STDERR.puts "#{$0}: #{msg}\n#{opts.to_s}"
exit 1
end
def checkrange(val,tag,from,to)
if val < from or val > to
STDERR.puts "#{$0}: #{tag} must be value in range [#{from}..#{to}]"
exit(1)
end
return val
end
def parseargs(argv)
options = OpenStruct.new
options.inputfile = nil
options.seedlength = 20
options.minidentity = 90
options.maxalilendiff = 30
options.history = 60
options.silent = false
options.percmathistory = 55
options.xdropbelow = 5
opts = OptionParser.new
opts.on("--inputfile STRING","specify input file") do |x|
options.inputfile = x
end
opts.on("--seedlength NUM","specify seedlength") do |x|
options.seedlength = x.to_i
end
opts.on("--minid NUM","specify minimum identity of matches",
"default: #{options.minidentity}") do |x|
options.minid = checkrange(x.to_i,"minid",70,99)
end
opts.on("--maxalilendiff NUM",
"specify maximum difference of aligned length",
"default: #{options.maxalilendiff}") do |x|
options.maxalilendiff = x.to_i
end
opts.on("--history NUM",
"specify size of history in range [1..64]",
"default #{options.history}") do |x|
options.history = checkrange(x.to_i,"history",1,64)
end
opts.on("--percmathistory NUM",
"percentage of matches required in history",
"default #{options.percmathistory}") do |x|
options.percmathistory = checkrange(x.to_i,"percmathhistory",1,100)
end
opts.on("--xdropbelow NUM",
"specify xdrop cutoff score",
"default #{options.xdropbelow}") do |x|
options.xdropbelow = checkrange(x.to_i,"xdropbelow",1,100)
end
opts.on("--silent","do not show differences") do |x|
options.silent = true
end
rest = opts.parse(argv)
if not rest.empty?
STDERR.puts "#{$0}: superfluous arguments: #{rest}"
exit 1
end
if options.inputfile.nil?
STDERR.puts "#{$0}: option -inputfile is mandatory"
exit 1
end
return options
end
options = parseargs(ARGV)
indexname = preprocess_index(options.inputfile)
taglist = ["greedy","xdrop"]
seedhash1 = makeseedhash(indexname,options.seedlength,"extend#{taglist[0]}",
["-minid #{options.minid}",
"-maxalilendiff #{options.maxalilendiff}",
"-history #{options.history}",
"-percmathistory #{options.percmathistory}"])
puts "# seedhash1: size = #{seedhash1.length}"
seedhash2 = makeseedhash(indexname,options.seedlength,"extend#{taglist[1]}",
["-minid #{options.minidentity}"])
puts "# seedhash2: size = #{seedhash2.length}"
minidentity = 100 - options.minidentity
seqnumpair_set1 = seedhash2seqnum_pairs(seedhash1)
seqnumpair_set2 = seedhash2seqnum_pairs(seedhash2)
result = calcdifference(seqnumpair_set1,seqnumpair_set2).join("\t")
puts "#{options.seedlength}\t#{result}"
if options.silent
cmpextendedlength(minidentity,seedhash1,seedhash2)
else
cmpseedhashes(true,minidentity,taglist,seedhash1,seedhash2)
cmpseedhashes(false,minidentity,taglist.reverse,seedhash2,seedhash1)
end
|
