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
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
|
#
# = sample/demo_blast_report.rb - demonstration of Bio::Blast::Report, Bio::Blast::Default::Report, and Bio::Blast::WU::Report
#
# Copyright:: Copyright (C) 2003 Toshiaki Katayama <k@bioruby.org>
# Copyright:: Copyright (C) 2003-2006,2008-2009 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::Blast::Report (NCBI BLAST XML format parser),
# Bio::Blast::Default::Report (NCBI BLAST default (-m 0) format parser),
# and Bio::Blast::WU::Report (WU-BLAST default format parser).
#
# == Usage
#
# Specify files containing BLAST results.
#
# $ ruby demo_blast_report.rb files...
#
# Example usage using test data:
#
# $ ruby -Ilib sample/demo_blast_report.rb test/data/blast/b0002.faa.m7
# $ ruby -Ilib sample/demo_blast_report.rb test/data/blast/b0002.faa.m0
#
# == Development information
#
# The code was moved from lib/bio/appl/blast/report.rb,
# lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb,
# and modified.
#
require 'bio'
# dummpy class to return specific object
class Dummy
def initialize(obj)
@obj = obj
end
def size
@obj
end
def inspect
@obj.inspect
end
end #class Dummy
# wrapper class to ignore error
class Wrapper
def initialize(obj)
@obj = obj
end
def class
@obj.class
end
def respond_to?(*arg)
@obj.respond_to?(*arg)
end
def method_missing(meth, *arg, &block)
begin
@obj.__send__(meth, *arg, &block)
rescue NoMethodError => evar
Dummy.new(evar)
end
end
end #class Wrapper
def wrap(obj)
Wrapper.new(obj)
end
# -m0: not defined in Bio::Blast::Default::Report ???
# +m0: newly added in Bio::Blast::Default::Report ???
# -WU: not defined in Bio::Blast::WU::Report ???
# +WU: newly added in Bio::Blast::WU::Report ???
Bio::FlatFile.open(ARGF) do |ff|
puts "Detected file format: #{ff.dbclass}"
unless ff.dbclass then
ff.dbclass = Bio::Blast::Report
puts "Input data may be tab-delimited format (-m 8)."
end
ff.each do |rep|
rep = wrap(rep)
#print "# === Bio::Blast::Default::Report\n"
print "# === #{rep.class}\n"
puts
print " rep.program #=> "; p rep.program
print " rep.version #=> "; p rep.version
print " rep.reference #=> "; p rep.reference
print " rep.notice [WU] #=> "; p rep.notice #+WU
print " rep.db #=> "; p rep.db
print " rep.query_id #=> "; p rep.query_id #-m0,-WU
print " rep.query_def #=> "; p rep.query_def
print " rep.query_len #=> "; p rep.query_len
#puts
print " rep.version_number #=> "; p rep.version_number #+m0,+WU
print " rep.version_date #=> "; p rep.version_date #+m0,+WU
puts
print "# === Parameters\n"
#puts
print " rep.parameters #=> "; p rep.parameters #-m0
puts
print " rep.matrix #=> "; p rep.matrix #-WU
print " rep.expect #=> "; p rep.expect
print " rep.inclusion #=> "; p rep.inclusion #-m0,-WU
print " rep.sc_match #=> "; p rep.sc_match #-WU
print " rep.sc_mismatch #=> "; p rep.sc_mismatch #-WU
print " rep.gap_open #=> "; p rep.gap_open #-WU
print " rep.gap_extend #=> "; p rep.gap_extend #-WU
print " rep.filter #=> "; p rep.filter #-m0,-WU
print " rep.pattern #=> "; p rep.pattern #-WU
print " rep.entrez_query #=> "; p rep.entrez_query #-m0
#puts
print " rep.pattern_positions #=> "; p rep.pattern_positions #+m0
puts
print "# === Statistics (last iteration's)\n"
#puts
print " rep.statistics #=> "; p rep.statistics #-m0,-WU
puts
print " rep.db_num #=> "; p rep.db_num
print " rep.db_len #=> "; p rep.db_len
print " rep.hsp_len #=> "; p rep.hsp_len #-m0,-WU
print " rep.eff_space #=> "; p rep.eff_space #-WU
print " rep.kappa #=> "; p rep.kappa #-WU
print " rep.lambda #=> "; p rep.lambda #-WU
print " rep.entropy #=> "; p rep.entropy #-WU
puts
print " rep.num_hits #=> "; p rep.num_hits #+m0
print " rep.gapped_kappa #=> "; p rep.gapped_kappa #+m0
print " rep.gapped_lambda #=> "; p rep.gapped_lambda #+m0
print " rep.gapped_entropy #=> "; p rep.gapped_entropy #+m0
print " rep.posted_date #=> "; p rep.posted_date #+m0
puts
print "# === Message (last iteration's)\n"
puts
print " rep.message #=> "; p rep.message #-WU
#puts
print " rep.converged? #=> "; p rep.converged? #+m0
puts
print "# === Warning messages\n"
print " rep.warnings [WU] #=> "; p rep.warnings #+WU
print "# === Iterations\n"
puts
print " rep.itrerations.each do |itr|\n"
puts
rep.iterations.each do |itr|
itr = wrap(itr)
#print "# --- Bio::Blast::Default::Report::Iteration\n"
print "# --- #{itr.class}\n"
puts
print " itr.num #=> "; p itr.num
print " itr.statistics #=> "; p itr.statistics #-m0,-WU
print " itr.warnings [WU] #=> "; p itr.warnings #+WU
print " itr.message #=> "; p itr.message
print " itr.hits.size #=> "; p itr.hits.size
#puts
print " itr.hits_newly_found.size #=> "; p((itr.hits_newly_found.size rescue nil)); #+m0
print " itr.hits_found_again.size #=> "; p((itr.hits_found_again.size rescue nil)); #+m0
if itr.respond_to?(:hits_for_pattern) and itr.hits_for_pattern then #+m0
itr.hits_for_pattern.each_with_index do |hp, hpi|
print " itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
end
end
print " itr.converged? #=> "; p itr.converged? #+m0,+WU
puts
print " itr.hits.each do |hit|\n"
puts
itr.hits.each_with_index do |hit, i|
hit = wrap(hit)
#print "# --- Bio::Blast::Default::Report::Hit"
print "# --- #{hit.class}"
print " ([#{i}])\n"
puts
print " hit.num #=> "; p hit.num #-m0,-WU
print " hit.hit_id #=> "; p hit.hit_id #-m0,-WU
print " hit.len #=> "; p hit.len
print " hit.definition #=> "; p hit.definition
print " hit.accession #=> "; p hit.accession #-m0,-WU
#puts
print " hit.found_again? #=> "; p hit.found_again? #+m0,+WU
print " hit.score [WU] #=> "; p hit.score #+WU
print " hit.pvalue [WU] #=> "; p hit.pvalue #+WU
print " hit.n_number [WU] #=> "; p hit.n_number #+WU
print " --- compatible/shortcut ---\n"
print " hit.query_id #=> "; p hit.query_id #-m0,-WU
print " hit.query_def #=> "; p hit.query_def #-m0,-WU
print " hit.query_len #=> "; p hit.query_len #-m0,-WU
print " hit.target_id #=> "; p hit.target_id #-m0,-WU
print " hit.target_def #=> "; p hit.target_def
print " hit.target_len #=> "; p hit.target_len
print " --- first HSP's values (shortcut) ---\n"
print " hit.evalue #=> "; p hit.evalue
print " hit.bit_score #=> "; p hit.bit_score
print " hit.identity #=> "; p hit.identity
print " hit.overlap #=> "; p hit.overlap #-m0,-WU
print " hit.query_seq #=> "; p hit.query_seq
print " hit.midline #=> "; p hit.midline
print " hit.target_seq #=> "; p hit.target_seq
print " hit.query_start #=> "; p hit.query_start
print " hit.query_end #=> "; p hit.query_end
print " hit.target_start #=> "; p hit.target_start
print " hit.target_end #=> "; p hit.target_end
print " hit.lap_at #=> "; p hit.lap_at
print " --- first HSP's vaules (shortcut) ---\n"
print " --- compatible/shortcut ---\n"
puts
print " hit.hsps.size #=> "; p hit.hsps.size
if hit.hsps.size == 0 then
puts " (HSP not found: please see blastall's -b and -v options)"
puts
else
puts
print " hit.hsps.each do |hsp|\n"
puts
hit.hsps.each_with_index do |hsp, j|
hsp = wrap(hsp)
#print "# --- Bio::Blast::Default::Report::Hsp"
print "# --- #{hsp.class}"
print " ([#{j}])\n"
puts
print " hsp.num #=> "; p hsp.num #-m0,-WU
print " hsp.bit_score #=> "; p hsp.bit_score
print " hsp.score #=> "; p hsp.score
print " hsp.evalue #=> "; p hsp.evalue
print " hsp.identity #=> "; p hsp.identity
print " hsp.gaps #=> "; p hsp.gaps
print " hsp.positive #=> "; p hsp.positive
print " hsp.align_len #=> "; p hsp.align_len
print " hsp.density #=> "; p hsp.density #-m0,-WU
print " hsp.pvalue [WU]#=> "; p hsp.pvalue #+WU
print " hsp.p_sum_n [WU]#=> "; p hsp.p_sum_n #+WU
print " hsp.query_frame #=> "; p hsp.query_frame
print " hsp.query_from #=> "; p hsp.query_from
print " hsp.query_to #=> "; p hsp.query_to
print " hsp.hit_frame #=> "; p hsp.hit_frame
print " hsp.hit_from #=> "; p hsp.hit_from
print " hsp.hit_to #=> "; p hsp.hit_to
print " hsp.pattern_from#=> "; p hsp.pattern_from #-m0,-WU
print " hsp.pattern_to #=> "; p hsp.pattern_to #-m0,-WU
print " hsp.qseq #=> "; p hsp.qseq
print " hsp.midline #=> "; p hsp.midline
print " hsp.hseq #=> "; p hsp.hseq
puts
print " hsp.percent_identity #=> "; p hsp.percent_identity
print " hsp.mismatch_count #=> "; p hsp.mismatch_count #-m0,-WU
#
print " hsp.query_strand #=> "; p hsp.query_strand #+m0,+WU
print " hsp.hit_strand #=> "; p hsp.hit_strand #+m0,+WU
print " hsp.percent_positive #=> "; p hsp.percent_positive #+m0,+WU
print " hsp.percent_gaps #=> "; p hsp.percent_gaps #+m0,+WU
puts
end #each
end #if hit.hsps.size == 0
end
end
end #ff.each
end #Bio::FlatFile.open
|
