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lib/App/Dazz/Command/cover.pm  view on Meta::CPAN

package App::Dazz::Command::cover;
use strict;
use warnings;
use autodie;

use App::Dazz -command;
use App::Dazz::Common;

use constant abstract => "trusted regions in the first file covered by the second";

sub opt_spec {
    return (
        [ "outfile|o=s", "output filename, [stdout] for screen", ],
        [ "range|r=s",    "ranges of first sequences",    { required => 1 }, ],
        [ 'coverage|c=i', 'minimal coverage',             { default  => 2 }, ],
        [ 'max|m=i',      'maximal coverage',             { default  => 200 }, ],
        [ "len|l=i",      "minimal length of overlaps",   { default  => 1000 }, ],
        [ "idt|i=f",      "minimal identity of overlaps", { default  => 0.85 }, ],
        [ "tmp=s",        "user defined tempdir", ],
        [ "verbose|v",    "verbose mode", ],
        { show_defaults => 1, }
    );
}

sub usage_desc {
    return "dazz cover [options] <.ovlp.tsv>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tAll operations are running in a tempdir and no intermediate files are kept.\n";
    return $desc;
}

sub validate_args {
    my ( $self, $opt, $args ) = @_;

    if ( @{$args} != 1 ) {
        my $message = "This command need one input file.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }
    }

    if ( !exists $opt->{outfile} ) {
        $opt->{outfile} = Path::Tiny::path( $args->[0] )->absolute . ".cover.json";
    }
}

sub execute {
    my ( $self, $opt, $args ) = @_;

    # make paths absolute before we chdir
    my $infile = Path::Tiny::path( $args->[0] )->absolute->stringify;

    if ( lc $opt->{outfile} ne "stdout" ) {
        $opt->{outfile} = Path::Tiny::path( $opt->{outfile} )->absolute->stringify;
    }

    # record cwd, we'll return there
    my $cwd = Path::Tiny->cwd;
    my $tempdir;
    if ( $opt->{tmp} ) {
        $tempdir = Path::Tiny->tempdir(
            TEMPLATE => "dazz_cover_XXXXXXXX",
            DIR      => $opt->{tmp},
        );
    }
    else {
        $tempdir = Path::Tiny->tempdir("dazz_cover_XXXXXXXX");
    }
    chdir $tempdir;

    my $basename = $tempdir->basename();
    $basename =~ s/\W+/_/g;

    #@type AlignDB::IntSpan
    my $first_range = AlignDB::IntSpan->new->add_runlist( $opt->{range} );

    {
        # paf to meancov
        my $cmd;
        $cmd .= "ovlpr covered";
        $cmd .= " $infile";
        $cmd .= " --coverage $opt->{max}";
        $cmd .= " --mean";
        $cmd .= " --len $opt->{len} --idt $opt->{idt}";
        $cmd .= " -o $basename.meancov.txt";
        App::Dazz::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );