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
|
require 'fileutils'
Name "arg passing test 1"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/arg.lua"
grep(last_stdout, /^arg\[0\]=.*gt.*arg\.lua/)
end
Name "arg passing test 2"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/arg.lua foo"
grep(last_stdout, /^arg\[0\]=.*gt.*arg\.lua/)
grep(last_stdout, /^arg\[1\]=foo$/)
end
Name "bittab bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/bittab.lua"
end
1.upto(4) do |i|
Name "csa_stream bindings #{i}"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/csa_stream.lua " +
"#{$testdata}gt_csa_prob_#{i}.in"
run "diff #{last_stdout} #{$testdata}gt_csa_prob_#{i}.out"
end
end
1.upto(14) do |i|
Name "cds_stream bindings #{i}"
Keywords "gt_scripts"
Test do
FileUtils.copy "#{$testdata}gt_cds_test_#{i}.fas", "."
run_test "#{$bin}gt #{$testdata}gtscripts/cds_stream.lua " +
"gt_cds_test_#{i}.fas " +
"#{$testdata}gt_cds_test_#{i}.in"
run "sed 's/gtscript/gt cds/' #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gt_cds_test_#{i}.out"
end
end
Name "genome_node bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/genome_node.lua"
end
Name "genome node required methods for all node types"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/required_methods.lua #{$testdata}/all_node_types.gff3"
end
Name "genome_stream bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/genome_stream.lua #{$testdata}"
end
Name "genome_stream bindings (output stream)"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/gff3.lua #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
run_test "#{$bin}gt #{$testdata}gtscripts/genome_stream_outfile.lua outfile < #{$testdata}eden.gff3"
run_test "#{$bin}gt gff3 -sort -retainids -tidy outfile > 1"
run_test "#{$bin}gt gff3 -sort -retainids -tidy #{$testdata}eden.gff3 > 2"
run "diff 1 2"
run_test "#{$bin}gt #{$testdata}gtscripts/genome_stream_outfile.lua /nonexist < #{$testdata}eden.gff3", :retval => 1
end
Name "genome_stream bindings (input stream stdin)"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/genome_stream_stdin.lua #{$testdata}eden.gff3 < #{$testdata}eden.gff3"
run "diff #{last_stdout} #{$testdata}genome_stream_stdin.gff3"
end
Name "genome_visitor bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/genome_visitor.lua #{$testdata}gff3_file_1_short.txt"
run "env LC_ALL=C sort #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end
Name "range bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/range.lua"
end
Name "memleak.lua"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/memleak.lua #{$testdata}standard_gene_as_tree.gff3"
end
Name "scorematrix2c"
Keywords "gt_scripts scorematrix"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/scorematrix2c.lua #{$testdata}BLOSUM62"
run "diff #{last_stdout} #{$testdata}blosum62.c"
end
Name "scorematrix2stdout"
Keywords "gt_scripts scorematrix"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/scorematrix2stdout.lua " +
"#{$testdata}BLOSUM62.gth"
run "diff #{last_stdout} #{$testdata}BLOSUM62.out"
end
Name "require 'gtlua'"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/require_gtlua.lua"
end
Name "LPeg library"
Keywords "gt_scripts lpeg"
Test do
run "cp #{$cur}/src/external/lpeg-0.10.2/test.lua ."
run "cp #{$cur}/src/external/lpeg-0.10.2/re.lua ."
run_test "#{$bin}gt test.lua"
end
Name "MD5 library"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$cur}/src/external/md5-1.2/tests/test.lua"
end
Name "gtdoc"
Keywords "gt_scripts gtdoc"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua #{$cur}"
end
Name "gtdoc -v"
Keywords "gt_scripts gtdoc"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -v #{$cur}"
end
Name "gtdoc -html"
Keywords "gt_scripts gtdoc"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -html #{$cur}"
end
Name "gtdoc -html -v"
Keywords "gt_scripts gtdoc"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -html -v #{$cur}"
end
Name "feature_index and feature_stream bindings"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/feature_stuff.lua #{$testdata}"
run "env LC_ALL=C sort #{last_stdout}"
run "grep -v '^##sequence-region' #{$testdata}gff3_file_1_short_sorted.txt | diff #{last_stdout} -"
end
if not $arguments["nocairo"] then
Name "AnnotationSketch (general bindings)"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/sketch.lua test.png " +
"#{$testdata}gff3_file_1_short.txt"
end
Name "AnnotationSketch (recmaps)"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}gtscripts/recmap.lua #{$testdata}gff3_file_1_short.txt"
run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.recmaps"
end
Name "AnnotationSketch (invalid ImageInfo object)"
Keywords "gt_scripts"
Test do
run_test("#{$bin}gt #{$testdata}gtscripts/ii_fail.lua #{$testdata}gff3_file_1_short.txt", :retval => 1)
end
Name "show_seqids"
Keywords "gt_scripts"
Test do
run_test("#{$bin}gt #{$testdata}gtscripts/show_seqids.lua #{$testdata}encode_known_genes_Mar07.gff3", :maxtime => 100)
run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
end
Name "evalviz.lua test 1"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/evalviz.lua png_files #{$testdata}gt_eval_test_1.in #{$testdata}gt_eval_test_1.in"
run "grep -v seqid #{last_stdout}"
run "diff #{last_stdout} #{$testdata}gt_eval_test_1.out"
end
=begin XXX: takes too long
Name "evalviz.lua test 2"
Keywords "gt_scripts"
Test do
run_test "#{$bin}gt #{$testdata}../gtscripts/evalviz.lua png_files #{$testdata}gt_evalviz_test.reality #{$testdata}gt_evalviz_test.prediction"
run "diff #{last_stdout} #{$testdata}gt_evalviz_test.out"
end
=end
end
|
