/
BEDTools.t
380 lines (358 loc) · 15.7 KB
/
BEDTools.t
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
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
#-*-perl-*-
#$Id: BEDTools.t kortsch $
use strict;
use warnings;
no warnings qw(once);
our $home;
my $v = 0; # private verbosity - this module only
BEGIN {
$home = '.'; # set to '.' for Build use,
# '..' for debugging from .t file
unshift @INC, $home;
use Bio::Root::Test;
test_begin(-tests => 423,
-requires_modules => [qw(IPC::Run Bio::Tools::Run::BEDTools)]);
}
use Bio::Tools::Run::WrapperBase;
use Bio::SeqIO;
use Bio::Tools::GuessSeqFormat;
# test command functionality
ok my $bedtoolsfac = Bio::Tools::Run::BEDTools->new, "make a default factory";
is $bedtoolsfac->command, 'bam_to_bed', "default to command 'bam_to_bed'";
my @commands = qw(
annotate fasta_from_bed overlap
bam_to_bed genome_coverage pair_to_pair
bed_to_bam graph_union pair_to_bed
bed_to_IGV group_by shuffle
b12_to_b6 intersect slop
closest links sort
complement mask_fasta_from_bed subtract
coverage merge window
);
my %p = (
'annotate' => 0,
'bam_to_bed' => 2,
'bed_to_bam' => 1,
'bed_to_IGV' => 5,
'b12_to_b6' => 0,
'closest' => 1,
'complement' => 0,
'coverage' => 0,
'fasta_from_bed' => 0,
'genome_coverage' => 2,
'graph_union' => 2,
'group_by' => 3,
'intersect' => 1,
'links' => 3,
'mask_fasta_from_bed' => 0,
'merge' => 1,
'overlap' => 1,
'pair_to_bed' => 2,
'pair_to_pair' => 3,
'shuffle' => 2,
'slop' => 3,
'sort' => 0,
'subtract' => 1,
'window' => 3
);
my %s = (
'annotate' => 4,
'bam_to_bed' => 6,
'bed_to_bam' => 2,
'bed_to_IGV' => 2,
'b12_to_b6' => 0,
'closest' => 2,
'complement' => 0,
'coverage' => 4,
'fasta_from_bed' => 3,
'genome_coverage' => 4,
'graph_union' => 2,
'group_by' => 0,
'intersect' => 11,
'links' => 0,
'mask_fasta_from_bed' => 1,
'merge' => 3,
'overlap' => 0,
'pair_to_bed' => 4,
'pair_to_pair' => 3,
'shuffle' => 1,
'slop' => 1,
'sort' => 6,
'subtract' => 1,
'window' => 5
);
my $bam_file = test_input_file('Ft.bam');
my $bed_file = test_input_file('Ft.bed');
my $bed12_file = test_input_file('Ft.bed12');
my $fas_file = test_input_file('Ft.frag.fas');
my $bedpe1_file = test_input_file('e_coli_1.bedpe');
my $bedpe2_file = test_input_file('e_coli_2.bedpe');
my $bed3_file = test_input_file('e_coli.bed3');
my $bg1_file = test_input_file('1.bg');
my $bg2_file = test_input_file('2.bg');
my $bg3_file = test_input_file('3.bg');
my %format_lookup = (
'annotate' => 'bed',
'bam_to_bed' => 'bed',
'bed_to_bam' => 'bam',
'bed_to_IGV' => 'igv',
'b12_to_b6' => 'bed',
'closest' => 'bedpe',
'complement' => 'bed',
'coverage' => 'bed',
'fasta_from_bed' => 'fasta',
'genome_coverage' => 'tab',
'graph_union' => 'bg',
'group_by' => 'bed',
'intersect' => 'bed|bam',
'links' => 'html',
'mask_fasta_from_bed' => 'fasta',
'merge' => 'bed',
'overlap' => 'bed',
'pair_to_bed' => 'bedpe|bam',
'pair_to_pair' => 'bedpe',
'slop' => 'bed',
'shuffle' => 'bed',
'sort' => 'bed',
'subtract' => 'bed',
'window' => 'bedpe'
);
my %result_lookup = (
'annotate' => 1385, # OK
'bam_to_bed' => 1385, # OK
'fasta_from_bed' => 1385, # OK
'mask_fasta_from_bed' => 1, # OK
'shuffle' => 828, # OK
'window' => 74998, # OK
'closest' => 845, # OK
'genome_coverage' => 38, # OK
'merge' => 242, # OK
'slop' => 828, # OK
'complement' => 291, # OK - change in data provided by BEDTools or behaviour of complementBed? was 243
'intersect' => 72534, # OK
'pair_to_bed' => 2, # OK
'sort' => 828, # OK
'coverage' => 57261, # OK
'links' => 11603, # OK
'pair_to_pair' => 497, # OK
'subtract' => 57959, # OK
'group_by' => 1, # OK
'b12_to_b6' => 1385, # OK
'overlap' => 500 # OK
);
SKIP : {
test_skip( -requires_executable => $bedtoolsfac,
-tests => 421 );
# Sorry to all those out there who don't have a find command
# - perhaps someone can add an alternative
my $rmsk_bed;
my $gene_bed;
my $mm8_genome;
my $mm9_genome;
my $hg18_genome;
my $hg19_genome;
if ($^O =~ m/mswin/i) {
use Cwd 'getcwd';
my $dir = getcwd;
# Assume files are in drive C:\, change location if this is not true
chdir 'C:\\'; # Search in all C:
($rmsk_bed) = `cmd.exe /C dir /B /S rmsk.hg18.chr21.bed 2>NUL`;
($gene_bed) = `cmd.exe /C dir /B /S knownGene.hg18.chr21.bed 2>NUL`;
($mm8_genome) = `cmd.exe /C dir /B /S mouse.mm8.genome 2>NUL`;
($mm9_genome) = `cmd.exe /C dir /B /S mouse.mm9.genome 2>NUL`;
($hg18_genome) = `cmd.exe /C dir /B /S human.hg18.genome 2>NUL`;
($hg19_genome) = `cmd.exe /C dir /B /S human.hg19.genome 2>NUL`;
chdir $dir; # Go back to $dir;
}
else {
($rmsk_bed) = `find /usr -name 'rmsk.hg18.chr21.bed' 2>/dev/null`;
($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`;
($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`;
($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`;
($hg18_genome) = `find /usr -name 'human.hg18.genome' 2>/dev/null`;
($hg19_genome) = `find /usr -name 'human.hg19.genome' 2>/dev/null`;
}
chomp $rmsk_bed if $rmsk_bed;
chomp $gene_bed if $gene_bed;
chomp $mm8_genome if $mm8_genome;
chomp $mm9_genome if $mm9_genome;
chomp $hg18_genome if $hg18_genome;
chomp $hg19_genome if $hg19_genome;
COMMAND : for (@commands) {
$v && diag("Testing command: '$_'");
ok( my $bedtoolsfac = Bio::Tools::Run::BEDTools->new(-command => $_),
"make a factory using command '$_'" );
$v && diag(" return command");
is( my $command = $bedtoolsfac->command, $_, "factory command for '$_' is correct" );
$v && diag(" return switches and params");
is( scalar $bedtoolsfac->available_parameters, $p{$_}+1+$s{$_}, "all available options for '$_'" );
is( scalar $bedtoolsfac->available_parameters('params'), $p{$_}+1, "available parameters for '$_'" );
is( scalar $bedtoolsfac->available_parameters('switches'), $s{$_}, "available switches for '$_'" );
$v && diag(" return executable version");
ok( $bedtoolsfac->version, "get version for '$_'" );
for ($command) {
$v && diag(" run command as default");
m/^annotate$/ && do {
ok( my $result = $bedtoolsfac->run( -bgv => $bed_file,
-ann => [$bed3_file] ),
"can run command '$command'" );
last;
};
m/^bam_to_bed$/ && do {
ok( my $result = $bedtoolsfac->run( -bam => $bam_file ),
"can run command '$command'" );
last;
};
m/^(?:fasta_from_bed|mask_fasta_from_bed)$/ && do {
ok( my $result = $bedtoolsfac->run( -seq => $fas_file,
-bgv => $bed_file ),
"can run command '$command'" );
last;
};
m/^(?:bed_to_IGV|merge|sort|links)$/ && do {
ok( my $result = $bedtoolsfac->run( -bgv => $gene_bed ),
"can run command '$command'" );
last;
};
m/^(?:bed_to_bam|shuffle|slop|complement)$/ && do {
is( $bedtoolsfac->add_bidirectional(100), 100,
"can set parameter -add_bidirectional => 100 " ) if $command eq 'slop';
ok( my $result = $bedtoolsfac->run( -bgv => $gene_bed,
-genome => $hg18_genome ),
"can run command '$command'" );
last;
};
m/^genome_coverage$/ && do {
ok( my $result = $bedtoolsfac->run( -bed => $gene_bed,
-genome => $hg18_genome ),
"can run command '$command'" );
last;
};
m/^(?:window|closest|coverage|subtract|intersect)$/ && do {
ok( my $result = $bedtoolsfac->run( -bgv1 => $gene_bed,
-bgv2 => $rmsk_bed ),
"can run command '$command'" );
last;
};
m/^pair_to_pair$/ && do {
is( $bedtoolsfac->type('neither'), 'neither',
"can set parameter -type => 'neither'" );
ok( my $result = $bedtoolsfac->run( -bedpe1 => $bedpe1_file,
-bedpe2 => $bedpe2_file ),
"can run command '$command'" );
last;
};
m/^pair_to_bed$/ && do {
ok( my $result = $bedtoolsfac->run( -bedpe => $bedpe1_file,
-bgv => $bed3_file ),
"can run command '$command'" );
last;
};
m/^overlap$/ && do {
is( $bedtoolsfac->columns('2,3,5,6'), '2,3,5,6',
"can set parameter -columns => '2,3,5,6' " );
ok( my $result = $bedtoolsfac->run( -bed => $bedpe1_file, ),
"can run command '$command'" );
last;
};
m/^b12_to_b6$/ && do {
ok( my $result = $bedtoolsfac->run( -bed => $bed12_file, ),
"can run command '$command'" );
last;
};
m/^group_by$/ && do {
is( $bedtoolsfac->group(1), 1,
"can set parameter -group => 1 " );
is( $bedtoolsfac->columns('2,2,3,3'), '2,2,3,3',
"can set parameter -columns => '2,2,3,3' " );
is( $bedtoolsfac->operations('min,max,min,max'), 'min,max,min,max',
"can set parameter -operations => 'min,max,min,max' " );
ok( my $result = $bedtoolsfac->run( -bed => $bed3_file ),
"can run command '$command'" );
last;
};
m/^graph_union$/ && do {
ok( my $result = $bedtoolsfac->run( -bg => [$bg1_file, $bg2_file, $bg2_file] ),
"can run command '$command'" );
last;
};
do {
# we should never get here - internal test
fail( "all commands tested - missed '$_'");
};
}
$v && diag(" check file has been written");
ok( eval { (-e $bedtoolsfac->result && -r _) }, "result files exists for command '$command'");
$v && diag(" check can get internal result format description and confirm it");
ok( my $format = $bedtoolsfac->result( -want => 'format' ),
"can return output format for command '$command'" );
like( $format, qr/(?:$format_lookup{$command})/,
"result claims to be in correct format for command '$command'" );
$v && diag(" check can get internal result file name value");
ok( my $file = $bedtoolsfac->result(-want=>'raw'),
"can return output file for command '$command'" );
if ($command eq 'links') {
$v && diag(" check result file is html and correct size");
ok eval { (-e $file)&&(-r _) }, "make readable output";
open (FILE, $file);
my $lines =(my $first_line)= <FILE>;
close FILE;
like( $first_line, qr/\<html\>/, " - html tag line");
is( $lines, $result_lookup{$command}, " - number of lines");
} elsif ($command eq 'genome_coverage') {
$v && diag(" check result file is correct size");
ok eval { (-e $file)&&(-r _) }, "make readable output";
open (FILE, $file);
my $lines =()= <FILE>;
close FILE;
is( $lines, $result_lookup{$command}, " - number of lines");
} else {
$v && diag(" check can get internal result format matches result file");
my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file );
for ($format_lookup{$command}) {
m/^(?:bed|bedpe|tab)$/ && do {
is( $guesser->guess, 'tab', "file format of '$file' consistent with claim for '$command'" );
last;
};
m/^fasta$/ && do {
is( $guesser->guess, 'fasta', "file format consistent with claim for '$command'" );
}
}
}
$v && diag(" check can get and set wanted result type");
is( $bedtoolsfac->want('Bio::Root::IO'), 'Bio::Root::IO',
"can set want to IO object for command '$command'" );
$v && diag(" check can get a Bio::Root::IO object");
ok( my $objres = $bedtoolsfac->result, "can get the basic object result for command '$command'" );
$v && diag(" - check can it is actually a Bio::Root::IO object");
isa_ok( $objres, 'Bio::Root::IO', "returned object is correct for command '$command'" );
for ($format_lookup{$command}) {
$v && diag(" check can can get format-specific result object if supported");
m/(?:bed|bedpe)/ && do {
$v && diag(" - Bio::SeqFeature::Collection");
ok( my $objres = $bedtoolsfac->result( -want => 'Bio::SeqFeature::Collection' ),
"can get the specific object result for command '$command'" );
isa_ok( $objres, 'Bio::SeqFeature::Collection',
"returned object is correct for command '$command'" );
$v && diag(" - correct number of features");
is( scalar $objres->get_all_features, $result_lookup{$command},
"correct number of features for command '$command'" );
last;
};
m/^fasta$/ && do {
$v && diag(" - Bio::SeqIO");
ok( my $objres = $bedtoolsfac->result( -want => 'Bio::SeqIO' ),
"can get the specific object result for command '$command'" );
isa_ok( $objres, 'Bio::SeqIO',
"returned object is correct for command '$command'" );
my $seq_count = 0;
while( my $seq = $objres->next_seq ) {
$seq_count++;
}
$v && diag(" - correct number of sequences");
is( $seq_count, $result_lookup{$command}, "correct number of sequences for command '$command'" );
}
}
}
}
1;