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

        $meta_of->{TRUSTED}->subtract( $meta_of->{NON_OVERLAPPED} );
        $meta_of->{TRUSTED}->subtract( $meta_of->{REPEAT_LIKE} );
    }

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

        if ( !$tempdir->child("$basename.covered.txt")->is_file ) {
            Carp::croak "Failed: create $basename.covered.txt\n";
        }
    }

    # anchor_id => covered ragion
    my $covered_of = {};
    $meta_of->{PARTIAL_COVERED} = AlignDB::IntSpan->new;
    for my $line ( App::RL::Common::read_lines("$basename.covered.txt") ) {
        my @parts = split ":", $line;
        next unless @parts == 2;

        my $seq_id = $parts[0];
        next unless $first_range->contains($seq_id);

        my $covered = AlignDB::IntSpan->new()->add_runlist( $parts[1] );

        if ( $covered->size < $len_of->{$seq_id} ) {
            $meta_of->{TRUSTED}->remove($seq_id);
            $meta_of->{PARTIAL_COVERED}->add($seq_id);
            $covered_of->{$seq_id} = $covered->runlist;
        }
    }

    #    {
    #        # Create covered.fasta
    #        $tempdir->child("covered.fasta")->remove;
    #        for my $serial ( sort { $a <=> $b } keys %{$covered_of} ) {
    #            if ( $trusted->contains($serial) ) {
    #                my $cmd;
    #                $cmd .= "DBshow -U $basename $serial";
    #                $cmd .= " | faops replace -l 0 stdin first.replace.tsv stdout";
    #                $cmd .= " >> covered.fasta";
    #                App::Anchr::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );
    #            }
    #            else {
    #
    #                #@type AlignDB::IntSpan
    #                my $region = $covered_of->{$serial}{ $opt->{coverage} };
    #
    #                for my $set ( $region->sets ) {
    #                    next if $set->size < $opt->{len};
    #
    #                    my $cmd;
    #                    $cmd .= "DBshow -U $basename $serial";
    #                    $cmd .= " | faops replace -l 0 stdin first.replace.tsv stdout";
    #                    $cmd .= " | faops frag -l 0 stdin @{[$set->min]} @{[$set->max]} stdout";
    #                    $cmd .= " >> covered.fasta";
    #                    App::Anchr::Common::exec_cmd( $cmd, { verbose => $opt->{verbose}, } );
    #                }
    #            }
    #        }
    #
    #        if ( !$tempdir->child("covered.fasta")->is_file ) {
    #            Carp::croak "Failed: create covered.fasta\n";
    #        }
    #    }

    {
        $meta_of->{TRUSTED}         = $meta_of->{TRUSTED}->runlist;
        $meta_of->{NON_OVERLAPPED}  = $meta_of->{NON_OVERLAPPED}->runlist;
        $meta_of->{REPEAT_LIKE}     = $meta_of->{REPEAT_LIKE}->runlist;
        $meta_of->{PARTIAL_COVERED} = $meta_of->{PARTIAL_COVERED}->runlist;
        $meta_of->{TOTAL_RANGE}     = $first_range->runlist;

        $tempdir->child("meta.cover.json")
            ->spew( JSON::to_json( $meta_of, { pretty => 1, canonical => 1, } ) );
        $tempdir->child("meta.cover.json")->copy( $opt->{outfile} );

        $tempdir->child("partial.txt")
            ->spew( map { sprintf "%s:%s\n", $_, $covered_of->{$_} } keys %{$covered_of} );
        $tempdir->child("partial.txt")->copy("$opt->{outfile}.partial.txt");

        YAML::Syck::DumpFile( "coverage.yml", $coverage_of );
        $tempdir->child("coverage.yml")->copy("$opt->{outfile}.coverage.yml");
    }

    chdir $cwd;
}

1;