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#-*-perl-*-
#$Id$
use strict;
use warnings;
no warnings qw(once);
our $home;
BEGIN {
$home = '.'; # set to '.' for Build use,
# '..' for debugging from .t file
unshift @INC, $home;
use Bio::Root::Test;
test_begin(-tests => 41,
-requires_modules => [qw(IPC::Run Bio::Tools::Run::Samtools)]);
}
use File::Copy;
use Bio::Tools::Run::WrapperBase;
my $DEBUG = test_debug();
ok my $samt = Bio::Tools::Run::Samtools->new(
-command => 'pileup',
-refseq => 'my.fas',
-theta => 0.05,
-verbose => $DEBUG
), "make a factory using command 'pileup'";
# ParameterBaseI compliance : really AssemblerBase tests...
ok $samt->parameters_changed, "parameters changed on construction";
ok $samt->refseq, "access parameter";
ok !$samt->parameters_changed, "parameters_changed cleared on read";
ok $samt->set_parameters( -n_haplos => 4 ), "set a param not set in constructor";
ok $samt->parameters_changed, "parameters_changed set";
is ($samt->n_haplos, 4, "parameter really set");
is ($samt->refseq, 'my.fas', "original parameter unchanged");
ok !$samt->parameters_changed, "parameters_changed cleared on read";
ok $samt->set_parameters( -refseq => 'their.fas' ), "change an original parameter";
is ($samt->refseq, 'their.fas', "parameter really changed");
ok $samt->reset_parameters( -refseq => 'our.fas' ), "reset parameters with arg";
ok !$samt->theta, "original parameters undefined";
is ($samt->refseq, 'our.fas', "parameter really reset via arg");
#back to beginning
$samt->set_parameters(
-command => 'pileup',
-refseq => 'my.fas',
-theta => 0.05,
-verbose => $DEBUG
);
ok $samt->parameters_changed, "parameters changed";
is( scalar $samt->available_parameters, 14, "all available options");
is( scalar $samt->available_parameters('params'), 9, "available parameters" );
is( scalar $samt->available_parameters('switches'), 5, "available switches" );
my %pms = $samt->get_parameters;
is_deeply( \%pms,
{ command => 'pileup',
refseq => 'my.fas',
theta => 0.05 }, "get_parameters correct");
is( $samt->command, 'pileup', "command attribute set");
is_deeply( $samt->{_options}->{_commands},
[@Bio::Tools::Run::Samtools::program_commands],
"internal command array set" );
is_deeply( $samt->{_options}->{_prefixes},
{%Bio::Tools::Run::Samtools::command_prefixes},
"internal prefix hash set");
is_deeply( $samt->{_options}->{_params},
[qw( command refseq map_qcap ref_list site_list theta n_haplos exp_hap_diff indel_prob )],
"commands filtered by prefix");
my @a = @{$samt->_translate_params};
is shift @a, 'pileup', 'translate_params: command correct';
my ($k, %h);
for (@a) {
(/^-/) ? ( $h{$k = $_} = undef ) : ( $h{$k} = $_ );
}
is_deeply( \%h, { '-T' => 0.05, '-f' => 'my.fas' }, 'translate_params: options correct');
SKIP : {
test_skip( -requires_executable => $samt,
-tests => 16 );
my $new_bam = Bio::Tools::Run::Samtools->new(
-verbose => $DEBUG,
-command => 'merge',
)->run(
-obm => 'output_file.bam',
-ibm => ['t/data/Ft.bam', 't/data/Ft.bam']
);
# test run
ok($new_bam, 'merge bam factory instantiated');
ok(-f 'output_file.bam', 'merged bam file created');
unlink('output_file.bam');
my %tmpfiles;
for (qw(refseq bamfile samfile rtbamfile sorted_bamfile fai bai)) {
$tmpfiles{$_} = test_output_file();
}
copy(test_input_file('Ft.bam'), $tmpfiles{bamfile}) or die "copy failed (1)";
copy(test_input_file('Ft.frag.fas'), $tmpfiles{refseq}) or die "copy failed (2)";
ok $samt = Bio::Tools::Run::Samtools->new( -command => 'faidx' ), "fasta index factory";
ok $samt->run( -fas => $tmpfiles{refseq}, -out => $tmpfiles{fai}), "make fasta index";
ok -e $tmpfiles{fai}, "fai file present";
ok $samt = Bio::Tools::Run::Samtools->new( -command => 'view' ), "bam -> sam cvt factory";
ok $samt->run( -bam => $tmpfiles{bamfile}, -out => $tmpfiles{samfile} ), "convert bam -> sam";
ok -T $tmpfiles{samfile}, "sam file present and text";
ok $samt->set_parameters( -sam_input => 1, -bam_output => 1, -refseq => $tmpfiles{refseq} ), "sam -> bam cvt factory";
ok $samt->run( -bam => $tmpfiles{samfile}, -out => $tmpfiles{rtbamfile} ), "convert sam -> bam";
ok -B $tmpfiles{rtbamfile}, "bam file present and binary";
ok $samt = Bio::Tools::Run::Samtools->new( -command => 'sort' ), 'bam sort factory';
ok $samt->run( -bam => $tmpfiles{rtbamfile}, -pfx => 'sorted_bam'), 'sort bam file';
ok $samt = Bio::Tools::Run::Samtools->new( -command => 'index' ), 'bam index factory';
ok $samt->run( -bam => 'sorted_bam', -out => $tmpfiles{bai}), 'make bam index';
ok -B $tmpfiles{bai}, 'bai file present and binary';
unlink('sorted_bam');
unlink('sorted_bam.bai');
}