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lib/Bio/MUST/Apps/HmmCleaner.pm  view on Meta::CPAN

    my $ali = $self->ali;
    my $ali_model = $self->ali_model;
    my $lookup = $ali->new_lookup;

    # Cleaners container
    my @cleaners;

    # arguments for Hmmer driver
    my $model_args = {
        '--plaplace'    => undef,
        '--fragthresh'  => "0.0",
        '--symfrac'     => $self->symfrac,
        #~ '--wnone'     => undef,
    };

    # arguments for Temporary fasta files
    my $alitemp_args = {
            degap       => 0,
            persistent  => ($self->debug_mode) ? 1 : 0,
            gapify      => ($self->consider_X) ? 'X' : '*', # if consider_X changing MISS Char to X ...
            clean       => 1,

t/process.t  view on Meta::CPAN

say 'Note: tests designed for: HMMER 3.3.2 (Nov 2020); http://hmmer.org/';

my $class = 'Bio::MUST::Apps::HmmCleaner::Process';

# Creation of the 3 elements needed to build a process
my $ali = Bio::MUST::Core::Ali->load('test/GNTPAN12210.ali');

my $model_args = {
    '--plaplace'    => undef,
    '--fragthresh'  => "0.0",
    '--symfrac'     => 0.5,
};

my $alitemp_args = {
    degap       => 0,
    gapify      => 'X',
    clean       => 1,
};

# Creation of global profile