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#-*-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;
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