view release on metacpan or  search on metacpan

t/blast.t  view on Meta::CPAN

    compare_filter_ok $report, file('test', 'ready_report.blastp.m6'),
        \&filter, 'wrote expected BLASTP report for pre-existing query file';
    $parser->remove;

    # 2. temporary query file (queries have to be degapped first)
    my $query = $qr_class->new( seqs => file('test', 'protquery.fasta') );
    $filename = $query->filename;
    explain $filename;

    # 2a. HTML format
    my $report_html = $db->blast($query, {
        -html   => undef,
        -evalue => 1e-50,
    } );
    ok $report_html =~ m/\.html\z/xms, "wrote HTML report: $report_html";

    # 2b. tabular format
    my $tab_parser = $db->blast($query, {
        -evalue => 1e-10,
    } );
    isa_ok($tab_parser, 'Bio::FastParsers::Blast::Table');

    $report_m6 = $tab_parser->filename;
    explain $report_m6;
    compare_filter_ok $report_m6, file('test', 'report.blastp.m6'),
        \&filter, 'wrote expected tabular BLASTP report';
    $tab_parser->remove;

    # 2c. XML format
    my $xml_parser = $db->blast($query, {
        -evalue => 1e-10,
        -outfmt => 5,
    } );
    isa_ok($xml_parser, 'Bio::FastParsers::Blast::Xml');

    cmp_ok $xml_parser->blast_output->count_iterations, '==', 7,
        'got expected number of iterations';

    $report_xml = $xml_parser->filename;
    explain $report_xml;
    compare_filter_ok $report_xml, file('test', 'report.blastp.xml'),
        \&filter, 'wrote expected XML BLASTP report';
    $xml_parser->remove;

    # blastdbcmd from temporary database
    my @ids = qw(seq2 seq4 seq6);
    my $seqs = $db->blastdbcmd( \@ids );
    cmp_ok $seqs->count_seqs, '==', 3,
        'fetched expected number of seqs from temporary database';
}
ok(!-e "$basename.$_", "deleted db file with expected suffix: $_")
    for qw(phr pin psq);
#   for qw(pdb phr pin pjs pog pos pot psq ptf pto);    # too stringent!
ok(!-e $filename,   'deleted query file');
ok(!-e $report_m6,  'deleted tabular report file');
ok(!-e $report_xml, 'deleted XML report file');

SKIP: {
    skip <<"EOT", 5 unless $ENV{$NET_VAR};
remote BLAST tests!
These tests are long to run and can hang if NCBI servers are too busy.
To enable them use:
\$ $NET_VAR=1 make test
EOT

    my $db = $db_class->new( file => 'core_nt', remote => 1 );
    cmp_ok $db->type, 'eq', 'nucl', 'got expected -db_type';
    $basename = $db->filename;
    explain $basename;

    my $query = $qr_class->new( seqs => file('test', 'nuclquery.fasta') );
    $filename = $query->filename;
    explain $filename;

    my $parser = $db->blast($query, {
        '-entrez_query'    => q{'Euglenozoa[ORGN]'},
        '-evalue'          => 1e-250,
        '-outfmt'          => 7,
    } );
    isa_ok($parser, 'Bio::FastParsers::Blast::Table');

    my $hsp_count = 0;
    while ($parser->next_hsp) {
        $hsp_count++;
    }

    cmp_ok $hsp_count, '>', 5, 'got expected number of remote HSPs';

    SKIP: {
        skip 'due to unstable remote BLASTN results', 2;
        cmp_ok $hsp_count, '==', 7, 'got expected number of remote HSPs';

        my $report = $parser->filename;
        explain $report;
        compare_filter_ok $report, file('test', 'report.blastn.m7'),
            \&filter, 'wrote expected tabular report after remote BLASTN';
        $parser->remove;
    }
}

{
    my $db = $db_class->new( file => file('test', 'prebuiltdb') );
    cmp_ok $db->type, 'eq', 'prot', 'got expected -db_type';
    $basename = $db->filename;
    ok(-e "$basename.$_", "found db file with expected suffix: $_")
        for qw(phr pin psq);
    #   for qw(pdb phr pin pjs pog pos pot psq ptf pto);    # too stringent!
    explain $basename;

    # blastdbcmd from prebuilt database
    my @ids = qw(gnl|Ca|29376464 gnl|Mg|16801896 gnl|Cu|29375460);
    my $seqs = $db->blastdbcmd( \@ids );
    cmp_ok $seqs->count_seqs, '==', 3,
        'fetched expected number of seqs from prebuilt database';
}

# TODO: test other BLAST variants and options?

sub filter {
    my $line = shift;
    $line =~ s{\t\ +}{\t}xmsg;      # normalize whitespace