ulla 0.9.9.1 → 0.9.9.2
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- checksums.yaml +7 -0
- data/History.txt +1 -1
- data/Manifest.txt +4 -0
- data/PostInstall.txt +1 -1
- data/README.rdoc +6 -7
- data/Rakefile +2 -2
- data/lib/narray_extensions.rb +0 -3
- data/lib/nmatrix_extensions.rb +0 -11
- data/lib/ulla.rb +45 -1
- data/lib/ulla/cli.rb +192 -89
- data/lib/ulla/esst.rb +32 -0
- data/lib/ulla/essts.rb +84 -0
- data/lib/ulla/heatmap_array.rb +0 -12
- data/lib/ulla/joy_tem.rb +63 -0
- data/lib/ulla/sequence.rb +7 -0
- data/script/txt2html +5 -5
- data/ulla.gemspec +3 -3
- data/website/index.html +286 -19
- data/website/stylesheets/screen.css +80 -81
- metadata +109 -71
data/lib/ulla/esst.rb
ADDED
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@@ -0,0 +1,32 @@
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1
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+
module Ulla
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2
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+
class Esst
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3
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+
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4
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+
attr_accessor :type, :label, :no, :colnames, :rownames, :matrix
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5
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+
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6
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+
def initialize(type, label, no, colnames=[], rownames=[], matrix = nil)
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7
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+
@type = type
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8
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+
@label = label
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9
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+
@no = no
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10
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+
@colnames = colnames
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11
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+
@rownames = rownames
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12
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+
@matrix = matrix
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13
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+
end
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14
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+
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15
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+
def scores_from(aa)
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16
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+
i = colnames.index(aa)
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17
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+
@matrix[i, 0..-1]
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18
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+
end
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19
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+
|
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20
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+
def scores_to(aa)
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21
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+
j = rownames.index(aa)
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22
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+
@matrix[0..-1, j]
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23
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+
end
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24
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+
|
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25
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+
def score(from_aa, to_aa)
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26
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+
i = colnames.index(from_aa)
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27
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+
j = rownames.index(to_aa)
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28
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+
@matrix[i, j]
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29
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+
end
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30
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+
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31
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+
end
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32
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+
end
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data/lib/ulla/essts.rb
ADDED
|
@@ -0,0 +1,84 @@
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1
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+
module Ulla
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2
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+
class Essts
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3
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+
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4
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+
attr_reader :file, :type, :aa_symbols,
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5
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+
:environments, :essts, :total_table,
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6
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+
:number_of_environments, :number_of_alignments
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7
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+
|
|
8
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+
def initialize(file, type = :logo)
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9
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+
@file = file
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10
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+
@type = type
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11
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+
@environments = []
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12
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+
@essts = []
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13
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+
@total_table = nil
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14
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+
parse_tag = nil
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15
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+
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16
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+
IO.readlines(@file).each_with_index do |line, li|
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17
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+
line.chomp!
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18
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+
if line =~ /^#\s+(ACDEFGHIKLMNPQRSTV\w+)/
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19
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+
@aa_symbols = $1.split('')
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20
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+
elsif line =~ /^#\s+(.*;\w+;\w+;[T|F];[T|F])/
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21
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+
elems = $1.split(';')
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22
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+
@environments << (env = OpenStruct.new)
|
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23
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+
@environments[-1].name = elems[0]
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24
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+
@environments[-1].values = elems[1].split('')
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25
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+
@environments[-1].labels = elems[2].split('')
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26
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+
@environments[-1].constraind = elems[3] == 'T' ? true : false
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27
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+
@environments[-1].silent = elems[4] == 'T' ? true : false
|
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28
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+
elsif line =~ /^#\s+Total\s+number\s+of\s+environments:\s+(\d+)/
|
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29
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+
@number_of_environments = Integer($1)
|
|
30
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+
elsif line =~ /^#\s+Number\s+of\s+alignments:\s+(\d+)/
|
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31
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+
@number_of_alignments = Integer($1)
|
|
32
|
+
elsif line =~ /^#/ # skip other comments!
|
|
33
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+
next
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34
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+
elsif line =~ /^>Total/i
|
|
35
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+
@total_table = Esst.new(type, 'total', @essts.size, @aa_symbols)
|
|
36
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+
parse_tag = :tot_row
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|
37
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+
elsif line =~ /^>Total\s+(\S+)/i
|
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38
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+
@total_table = Esst.new(type, 'total', Integer($1), @aa_symbols)
|
|
39
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+
parse_tag = :tot_row
|
|
40
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+
elsif line =~ /^>(\S+)\s+(\S+)/
|
|
41
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+
break if parse_tag == :tot_row
|
|
42
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+
@essts << Esst.new(type, $1, Integer($2), @aa_symbols)
|
|
43
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+
parse_tag = :esst_row
|
|
44
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+
elsif line =~ /^(\S+)\s+(\S+.*)$/ && (parse_tag == :esst_row || parse_tag == :tot_row)
|
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45
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+
row_name = $1
|
|
46
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+
row_values = $2.strip.split(/\s+/).map { |v| Float(v) }
|
|
47
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+
if parse_tag == :esst_row
|
|
48
|
+
@essts[-1].rownames << row_name
|
|
49
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+
@essts[-1].matrix = NMatrix[*(@essts[-1].matrix.to_a << row_values)]
|
|
50
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+
elsif parse_tag == :tot_row
|
|
51
|
+
@total_table.rownames << row_name
|
|
52
|
+
@total_table.matrix = NMatrix[*(@total_table.matrix.to_a << row_values)]
|
|
53
|
+
else
|
|
54
|
+
$logger.error "Something wrong at line #{li}: #{line}"
|
|
55
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+
exit 1
|
|
56
|
+
end
|
|
57
|
+
else
|
|
58
|
+
raise "Something wrong at line, #{li}: #{line}"
|
|
59
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+
end
|
|
60
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+
end
|
|
61
|
+
end
|
|
62
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+
|
|
63
|
+
def colnames
|
|
64
|
+
@essts[0].colnames
|
|
65
|
+
end
|
|
66
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+
|
|
67
|
+
def rownames
|
|
68
|
+
@essts[0].rownames
|
|
69
|
+
end
|
|
70
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+
|
|
71
|
+
def [](index)
|
|
72
|
+
case index
|
|
73
|
+
when Integer
|
|
74
|
+
@essts[index]
|
|
75
|
+
when String
|
|
76
|
+
@essts.find { |e| e.label == index }
|
|
77
|
+
else
|
|
78
|
+
$logger.error "#{index} is not available for indexing ESSTs"
|
|
79
|
+
exit
|
|
80
|
+
end
|
|
81
|
+
end
|
|
82
|
+
|
|
83
|
+
end
|
|
84
|
+
end
|
data/lib/ulla/heatmap_array.rb
CHANGED
|
@@ -1,15 +1,3 @@
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1
|
-
require 'rubygems'
|
|
2
|
-
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|
3
|
-
begin
|
|
4
|
-
require 'RMagick'
|
|
5
|
-
include Magick
|
|
6
|
-
rescue Exception => e
|
|
7
|
-
$logger.warn "#{e.to_s.chomp} For this reason, heat maps cannot be generated."
|
|
8
|
-
$no_rmagick = true
|
|
9
|
-
end
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
13
1
|
module Ulla
|
|
14
2
|
class HeatmapArray < Array
|
|
15
3
|
|
data/lib/ulla/joy_tem.rb
ADDED
|
@@ -0,0 +1,63 @@
|
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|
1
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+
module Ulla
|
|
2
|
+
class JoyTem
|
|
3
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+
|
|
4
|
+
attr_reader :file, :entries
|
|
5
|
+
|
|
6
|
+
def initialize(file)
|
|
7
|
+
@file = file
|
|
8
|
+
io = File.exist?(file) ? File.open(file, 'r') : StringIO.new(file)
|
|
9
|
+
@entries = {}
|
|
10
|
+
ent_code = nil
|
|
11
|
+
ent_desc = nil
|
|
12
|
+
ent_data = nil
|
|
13
|
+
parse_tag = nil
|
|
14
|
+
|
|
15
|
+
io.each_with_index do |line, li|
|
|
16
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+
line.chomp!
|
|
17
|
+
if line =~ /^#/ || line =~ /^\s*$/
|
|
18
|
+
next
|
|
19
|
+
elsif line =~ /^>\S+;(\S+)/
|
|
20
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+
parse_tag = :desc
|
|
21
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+
ent_code = $1
|
|
22
|
+
@entries[ent_code] = {} unless @entries.has_key?(ent_code)
|
|
23
|
+
elsif line =~ /^(\S+.*)/ && parse_tag == :desc
|
|
24
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+
parse_tag = :data
|
|
25
|
+
ent_desc = $1.strip
|
|
26
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+
@entries[ent_code][ent_desc] = ''
|
|
27
|
+
elsif line =~ /^\s*(\S+.*)/ && parse_tag == :data
|
|
28
|
+
ent_data = $1.strip.gsub('*', '')
|
|
29
|
+
@entries[ent_code][ent_desc] += ent_data
|
|
30
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+
else
|
|
31
|
+
$logger.error "Cannot parse line #{li+1}: #{line}"
|
|
32
|
+
exit 1
|
|
33
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+
end
|
|
34
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+
end
|
|
35
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+
end
|
|
36
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+
|
|
37
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+
def entry_codes
|
|
38
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+
@entries.keys
|
|
39
|
+
end
|
|
40
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+
|
|
41
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+
def entry_descriptions
|
|
42
|
+
@entries[entry_codes[0]].keys
|
|
43
|
+
end
|
|
44
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+
|
|
45
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+
def alignment_length
|
|
46
|
+
@entries[entry_codes[0]][entry_descriptions[0]].length
|
|
47
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+
end
|
|
48
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+
|
|
49
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+
def sequences
|
|
50
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+
seqs = []
|
|
51
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+
@entries.keys.each do |code|
|
|
52
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+
if @entries[code].has_key?('sequence')
|
|
53
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+
seqs << Sequence.new(@entries[code]['sequence'], code)
|
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54
|
+
else
|
|
55
|
+
$logger.error "Cannot find 'sequence' data for #{code} in JOY template: #{@file}"
|
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56
|
+
exit 1
|
|
57
|
+
end
|
|
58
|
+
end
|
|
59
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+
seqs
|
|
60
|
+
end
|
|
61
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+
|
|
62
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+
end
|
|
63
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+
end
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data/script/txt2html
CHANGED
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@@ -1,17 +1,17 @@
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1
1
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#!/usr/bin/env ruby
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2
2
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3
3
|
load File.dirname(__FILE__) + "/../Rakefile"
|
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4
|
-
require 'rubyforge'
|
|
4
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+
#require 'rubyforge'
|
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5
5
|
require 'redcloth'
|
|
6
6
|
require 'syntax/convertors/html'
|
|
7
7
|
require 'erb'
|
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8
8
|
|
|
9
|
-
download = "http://rubyforge.org/projects/#{$hoe.rubyforge_name}"
|
|
9
|
+
#download = "http://rubyforge.org/projects/#{$hoe.rubyforge_name}"
|
|
10
10
|
version = $hoe.version
|
|
11
11
|
|
|
12
|
-
def rubyforge_project_id
|
|
13
|
-
RubyForge.new.configure.autoconfig["group_ids"][$hoe.rubyforge_name]
|
|
14
|
-
end
|
|
12
|
+
#def rubyforge_project_id
|
|
13
|
+
#RubyForge.new.configure.autoconfig["group_ids"][$hoe.rubyforge_name]
|
|
14
|
+
#end
|
|
15
15
|
|
|
16
16
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class Fixnum
|
|
17
17
|
def ordinal
|
data/ulla.gemspec
CHANGED
|
@@ -2,7 +2,7 @@
|
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|
2
2
|
|
|
3
3
|
Gem::Specification.new do |s|
|
|
4
4
|
s.name = %q{ulla}
|
|
5
|
-
s.version = "0.9.9.
|
|
5
|
+
s.version = "0.9.9.2"
|
|
6
6
|
|
|
7
7
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
|
8
8
|
s.authors = ["Semin Lee"]
|
|
@@ -12,12 +12,12 @@ Gem::Specification.new do |s|
|
|
|
12
12
|
s.email = ["seminlee@gmail.com"]
|
|
13
13
|
s.executables = ["ulla"]
|
|
14
14
|
s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
|
|
15
|
-
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/array_extensions.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
|
|
15
|
+
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/array_extensions.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "lib/ulla/esst.rb", "lib/ulla/essts.rb", "lib/ulla/joy_tem.rb", "lib/ulla/sequence.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
|
|
16
16
|
s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
|
|
17
17
|
s.post_install_message = %q{PostInstall.txt}
|
|
18
18
|
s.rdoc_options = ["--main", "README.rdoc"]
|
|
19
19
|
s.require_paths = ["lib"]
|
|
20
|
-
s.rubyforge_project = %q{ulla}
|
|
20
|
+
#s.rubyforge_project = %q{ulla}
|
|
21
21
|
s.rubygems_version = %q{1.3.5}
|
|
22
22
|
s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
|
|
23
23
|
s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
|
data/website/index.html
CHANGED
|
@@ -1,26 +1,293 @@
|
|
|
1
1
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
|
|
2
2
|
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
|
3
3
|
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
4
|
-
<head>
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
4
|
+
<head>
|
|
5
|
+
<link rel="stylesheet" href="stylesheets/screen.css" type="text/css" media="screen" />
|
|
6
|
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
7
|
+
<title>
|
|
8
|
+
ULLA
|
|
9
|
+
</title>
|
|
10
|
+
<script src="javascripts/rounded_corners_lite.inc.js" type="text/javascript"></script>
|
|
11
|
+
<style>
|
|
12
|
+
|
|
13
|
+
</style>
|
|
14
|
+
<script type="text/javascript">
|
|
15
|
+
window.onload = function() {
|
|
16
|
+
settings = {
|
|
17
|
+
tl: { radius: 10 },
|
|
18
|
+
tr: { radius: 10 },
|
|
19
|
+
bl: { radius: 10 },
|
|
20
|
+
br: { radius: 10 },
|
|
21
|
+
antiAlias: true,
|
|
22
|
+
autoPad: true,
|
|
23
|
+
validTags: ["div"]
|
|
24
|
+
}
|
|
25
|
+
var versionBox = new curvyCorners(settings, document.getElementById("version"));
|
|
26
|
+
versionBox.applyCornersToAll();
|
|
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<h1>ULLA</h1>
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<hr />
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<div class="sidebar">
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<div id="version" class="clickable" onclick='document.location = "http://rubygems.org/gems/ulla"; return false'>
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<p>Get Version</p>
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<a href="http://rubygems.org/gems/ulla" class="numbers">0.9.9.1</a>
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</div>
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<h2>* Description</h2>
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<p>‘ULLA’ is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.</p>
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<h2>* Features</h2>
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<ul>
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<li>Environment-specific substitution table generation based on user providing environmental class definition</li>
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<li>Entropy-based smoothing procedures to cope with sparse data problem</li>
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<li><span class="caps">BLOSUM</span>-like weighting procedures using <span class="caps">PID</span> threshold</li>
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<li>Heat Map generation for substitution tables</li>
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</ul>
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<h2>* Requirements</h2>
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<ul>
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<li>ruby 1.9.1 or above (<a href="http://www.ruby-lang.org">http://www.ruby-lang.org</a>)</li>
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<li>rubygems 1.3.4 or above (<a href="http://rubygems.org/">http://rubygems.org/</a>)</li>
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</ul>
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<p>Following RubyGems will be automatically installed if you have rubygems installed on your machine</p>
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<li><a href="http://narray.rubyforge.org">narray</a></li>
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<li><a href="http://bioruby.open-bio.org">bio</a></li>
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<li><a href="http://rmagick.rubyforge.org">RMagick</a></li>
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</ul>
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<h2>* Installation</h2>
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<pre>
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~user $ sudo gem install ulla
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</pre>
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<h2>* Basic Usage</h2>
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<p>It’s pretty much the same as Kenji’s <a href="http://mordred.bioc.cam.ac.uk/~kenji/subst/">subst</a>, so in most cases, you can swap ‘subst’ with ‘ulla’.</p>
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<pre>
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~user $ ulla -l TEMLIST-file -c classdef.dat
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or
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~user $ ulla -f TEM-file -c classdef.dat
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</pre>
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<h2>* Options</h2>
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<pre>
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--tem-file (-f) FILE: a tem file
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--tem-list (-l) FILE: a list for tem files
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--classdef (-c) FILE: a file for the defintion of environmental class
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if no definition file provided, --cys (-y) 2 and --nosmooth options automatcially applied
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--outfile (-o) FILE: output filename (default 'allmat.dat')
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--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
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--noweight: calculate substitution counts with no weights
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--environment (-e) INTEGER:
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0 for considering only substituted amino acids' environments (default)
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1 for considering both substituted and substituting amino acids' environments
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--smooth (-s) INTEGER:
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0 for partial smoothing (default)
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1 for full smoothing
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--p1smooth: perform smoothing for p1 probability calculation when partial smoothing
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--nosmooth: perform no smoothing operation
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--cys (-y) INTEGER:
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0 for using C and J only for structure (default)
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1 for both structure and sequence
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2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
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--output INTEGER:
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0 for raw counts (no smoothing performed)
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1 for probabilities
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2 for log-odds (default)
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--noroundoff: do not round off log odds ratio
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--scale INTEGER: log-odds matrices in 1/n bit units (default 3)
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--sigma DOUBLE: change the sigma value for smoothing (default 5.0)
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--autosigma: automatically adjust the sigma value for smoothing
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--add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 0)
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--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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--heatmap INTEGER:
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0 create a heat map file for each substitution table
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1 create one big file containing all heat maps from substitution tables
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2 do both 0 and 1
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--heatmap-format INTEGER:
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0 for Portable Network Graphics (PNG) Format (default)
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1 for Graphics Interchange Format (GIF)
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2 for Joint Photographic Experts Group (JPEG) Format
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3 for Microsoft Windows bitmap (BMP) Format
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4 for Portable Document Format (PDF)
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--heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
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--heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
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--heatmap-values: print values in the cells when generating heat maps
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--verbose (-v) INTEGER
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1 for WARN or above level (default)
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2 for INFO or above level
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3 for DEBUG or above level
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--version: print version
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--help (-h): show help
|
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</pre>
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<h2>* Usage</h2>
|
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<p>1. Prepare an environmental class definition file. For more details, please check this <a href="http://mordred.bioc.cam.ac.uk/~kenji/subst/NOTES">notes</a>. You can download a sample environmental class definition file from <a href="http://mordred.bioc.cam.ac.uk/~kenji/subst/classdef.dat">here</a>.</p>
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<pre>
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~user $ cat classdef.dat
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#
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# name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
|
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# constrained or not (T or F); silent (used as masks)? (T or F)
|
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#
|
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143
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+
secondary structure and phi angle;HEPC;HEPC;T;F
|
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solvent accessibility;TF;Aa;F;F
|
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</pre>
|
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|
+
<p>2. Prepare structural alignments and their annotations of above environmental classes in <span class="caps">PIR</span> format. You can download sample alignments from <a href="http://mordred.bioc.cam.ac.uk/~kenji/subst/alltem-allmask.tar.gz">http://mordred.bioc.cam.ac.uk/~kenji/subst/alltem-allmask.tar.gz</a> or <a href="http://www-cryst.bioc.cam.ac.uk/ESST">http://www-cryst.bioc.cam.ac.uk/ESST</a></p>
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<pre>
|
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~user $ cat sample1.tem
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|
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>P1;1mnma
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sequence
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QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
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IQACLNAPDD*
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>P1;1egwa
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sequence
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--GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
|
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+
----------*
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157
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>P1;1mnma
|
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158
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secondary structure and phi angle
|
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159
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CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
|
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160
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+
HHHHHCCCCP*
|
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161
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>P1;1egwa
|
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162
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+
secondary structure and phi angle
|
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163
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--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
|
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|
+
----------*
|
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165
|
+
>P1;1mnma
|
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166
|
+
solvent accessibility
|
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167
|
+
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
|
|
168
|
+
TTTTTTTTTT*
|
|
169
|
+
>P1;1egwa
|
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170
|
+
solvent accessibility
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171
|
+
--TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
|
|
172
|
+
----------*
|
|
173
|
+
...
|
|
174
|
+
</pre>
|
|
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|
+
<p>3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.</p>
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|
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<pre>
|
|
177
|
+
~user $ ls -1 *.tem > TEMLIST
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178
|
+
~user $ cat TEMLIST
|
|
179
|
+
sample1.tem
|
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180
|
+
sample2.tem
|
|
181
|
+
...
|
|
182
|
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</pre>
|
|
183
|
+
<p>4. To produce substitution count matrices,</p>
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184
|
+
<pre>
|
|
185
|
+
~user $ ulla -l TEMLIST --output 0 -o substcount.mat
|
|
186
|
+
</pre>
|
|
187
|
+
<p>5. To produce substitution probability matrices,</p>
|
|
188
|
+
<pre>
|
|
189
|
+
~user $ ulla -l TEMLIST --output 1 -o substprob.mat
|
|
190
|
+
</pre>
|
|
191
|
+
<p>6. To produce log odds ratio matrices,</p>
|
|
192
|
+
<pre>
|
|
193
|
+
~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
|
|
194
|
+
</pre>
|
|
195
|
+
<p>7. To produce substitution probability matrices from the sequence pairs within a certain <span class="caps">PID</span> range (if you don’t provide any name for output, ‘allmat.dat’ will be used.),</p>
|
|
196
|
+
<pre>
|
|
197
|
+
~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
|
|
198
|
+
</pre>
|
|
199
|
+
<p>8. To change the clustering level (default 60) to <span class="caps">PID</span> 80,</p>
|
|
200
|
+
<pre>
|
|
201
|
+
~user $ ulla -l TEMLIST --weight 80 --output 1
|
|
202
|
+
</pre>
|
|
203
|
+
<p>9. In case positions are masked with the character ‘X’ in any environmental features, all mutations from/to the position will be excluded from substitution counts.</p>
|
|
204
|
+
<p>10. Then, it will produce a file containing all the matrices, which will look like the one below. For more details, please check this <a href="http://mordred.bioc.cam.ac.uk/~kenji/subst/NOTES">notes</a>.</p>
|
|
205
|
+
<pre>
|
|
206
|
+
# Environment-specific amino acid substitution matrices
|
|
207
|
+
# Creator: ulla version 0.0.5
|
|
208
|
+
# Creation Date: 05/02/2009 17:29
|
|
209
|
+
#
|
|
210
|
+
# Definitions for structural environments:
|
|
211
|
+
# 2 features used
|
|
212
|
+
#
|
|
213
|
+
# secondary structure and phi angle;HEPC;HEPC;F;F
|
|
214
|
+
# solvent accessibility;TF;Aa;F;F
|
|
215
|
+
# (read in from classdef.dat)
|
|
216
|
+
#
|
|
217
|
+
# Number of alignments: 1187
|
|
218
|
+
# (list of .tem files read in from TEMLIST)
|
|
219
|
+
#
|
|
220
|
+
# Total number of environments: 8
|
|
221
|
+
#
|
|
222
|
+
# There are 21 amino acids considered.
|
|
223
|
+
# ACDEFGHIKLMNPQRSTVWYJ
|
|
224
|
+
#
|
|
225
|
+
# C: Cystine (the disulfide-bonded form)
|
|
226
|
+
# J: Cysteine (the free thiol form)
|
|
227
|
+
#
|
|
228
|
+
# Weighting scheme: clustering at PID 60 level
|
|
229
|
+
# ...
|
|
230
|
+
#
|
|
231
|
+
>HA 0
|
|
232
|
+
# A C D E F G H I K L M N P Q R S T V W Y J
|
|
233
|
+
A 3 -5 0 0 -1 2 0 0 1 0 0 0 1 1 0 1 1 1 -1 0 2
|
|
234
|
+
C -16 19 -16 -18 -11 -14 -13 -13 -14 -14 -14 -11 -17 -16 -13 -16 -14 -12 -12 -10 -4
|
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235
|
+
D 1 -7 6 3 -3 1 0 -3 1 -3 -2 2 1 2 0 1 0 -2 -3 -2 -2
|
|
236
|
+
E 3 -7 5 7 -1 2 2 0 3 0 0 3 2 4 3 3 2 1 -1 0 -1
|
|
237
|
+
F -4 -4 -6 -6 7 -5 -1 0 -4 1 0 -5 -5 -4 -4 -4 -3 -1 3 3 0
|
|
238
|
+
G -2 -6 -3 -4 -5 5 -4 -5 -4 -5 -4 -2 -3 -4 -4 -2 -3 -5 -6 -4 -3
|
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239
|
+
H 0 -6 0 0 1 0 8 -1 0 0 0 1 -2 1 1 0 0 0 1 3 0
|
|
240
|
+
I -3 -7 -6 -5 0 -5 -3 4 -4 1 1 -5 -4 -4 -3 -5 -2 2 -2 -1 0
|
|
241
|
+
K 2 -6 2 2 -1 1 2 0 5 1 1 2 0 3 4 2 2 0 -2 0 -1
|
|
242
|
+
L -2 -6 -5 -4 1 -4 -2 2 -3 4 2 -3 -4 -3 -2 -4 -2 1 0 0 1
|
|
243
|
+
M -2 -7 -4 -3 1 -2 -1 2 -2 2 6 -3 -4 -2 -1 -2 -1 1 0 0 1
|
|
244
|
+
N 0 -5 1 0 -3 1 1 -3 0 -2 -2 6 -2 0 0 1 1 -2 -3 -1 -1
|
|
245
|
+
P -1 -7 -1 -2 -4 -1 -3 -3 -2 -3 -4 -2 9 -2 -3 0 -1 -2 -4 -4 -4
|
|
246
|
+
Q 2 -7 2 2 -1 1 2 -1 2 0 0 2 0 5 2 1 1 0 -2 -1 0
|
|
247
|
+
R 1 -6 1 1 -1 0 2 0 3 0 1 1 -1 2 6 1 1 0 -1 0 0
|
|
248
|
+
S 0 -6 -1 -1 -3 0 -2 -3 -1 -3 -3 0 0 -1 -1 3 1 -2 -4 -3 0
|
|
249
|
+
T -1 -7 -2 -2 -3 -2 -2 -2 -2 -2 -2 -1 -2 -2 -2 0 3 -1 -3 -3 0
|
|
250
|
+
V -3 -6 -6 -5 -1 -4 -3 1 -4 0 0 -5 -3 -4 -4 -4 -2 2 -2 -2 0
|
|
251
|
+
W -4 -6 -6 -5 2 -6 -2 -2 -5 -1 -2 -5 -5 -4 -4 -5 -4 -2 12 2 -3
|
|
252
|
+
Y -3 -5 -5 -5 3 -4 1 -1 -3 -1 -1 -3 -5 -3 -3 -4 -3 -2 3 7 -1
|
|
253
|
+
J -2 0 -4 -5 0 -2 -1 0 -3 0 0 -3 -6 -2 -2 -1 -1 0 -1 0 9
|
|
254
|
+
U -5 16 -7 -8 -3 -5 -4 -3 -6 -3 -3 -5 -9 -6 -5 -4 -4 -3 -4 -3 6
|
|
255
|
+
...
|
|
256
|
+
</pre>
|
|
257
|
+
<p>11. To generate a heat map for each table with values in it,</p>
|
|
258
|
+
<pre>
|
|
259
|
+
~user $ ulla -l TEMLIST --heatmap 0 --heatmap-values
|
|
260
|
+
</pre>
|
|
261
|
+
which will look like this,<br/>
|
|
262
|
+
<img src="http://mordred.bioc.cam.ac.uk/~semin/images/0.HA.png" alt="" />
|
|
263
|
+
<p>12. To generate one big figure, ‘myheatmaps.gif’ containing all the heat maps (4 maps in a row),</p>
|
|
264
|
+
<pre>
|
|
265
|
+
~user $ ulla -l TEMLIST --heatmap 1 --heatmap-stem myheatmaps --heatmap-format 1 --heatmap-columns 4
|
|
266
|
+
</pre>
|
|
267
|
+
which will look like this,<br/>
|
|
268
|
+
<img src="http://mordred.bioc.cam.ac.uk/~semin/images/myheatmaps.gif" alt="" />
|
|
269
|
+
<h2>* Repository</h2>
|
|
270
|
+
<p>You can download a pre-built RubyGems package from</p>
|
|
271
|
+
<ul>
|
|
272
|
+
<li>rubygems: <a href="http://rubygems.org/gems/ulla">http://rubygems.org/gems/ulla</a></li>
|
|
273
|
+
</ul>
|
|
274
|
+
<h2>* Reference</h2>
|
|
275
|
+
<ul>
|
|
276
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<li><a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/25/15/1976">Lee S., Blundell T.L. (2009) Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinformatics. 25(15):1976-1977; doi:10.1093/bioinformatics/btp300</a></li>
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<p>Comments are welcome, please send an email to me (seminlee at gmail dot com).</p>
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<h2>* License</h2>
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<p><img src="http://i.creativecommons.org/l/by-nc/2.0/uk/88x31.png" alt="" /><br />
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This work is licensed under a <a href="http://creativecommons.org/licenses/by-nc/2.0/uk/">Creative Commons Attribution-Noncommercial 2.0 UK: England & Wales License</a>.</p>
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Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
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