App-Rangeops

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lib/App/Rangeops/Command/circos.pm  view on Meta::CPAN

    return "rangeops circos [options] <infiles>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tIt's assumed that all ranges in input files are valid.\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }

lib/App/Rangeops/Command/clean.pm  view on Meta::CPAN

}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc
        .= "\t<infiles> are bilateral links files, with or without hit strands\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        my $message = "This command need one or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";

lib/App/Rangeops/Command/connect.pm  view on Meta::CPAN

    return "rangeops connect [options] <infiles>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\t<infiles> are bilaterial links files without hit strands\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }

lib/App/Rangeops/Command/create.pm  view on Meta::CPAN

sub usage_desc {
    return "rangeops create [options] <infiles>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }

lib/App/Rangeops/Command/filter.pm  view on Meta::CPAN

    return "rangeops filter [options] <infiles>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tIt's assumed that all ranges in input files are valid.\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }

lib/App/Rangeops/Command/merge.pm  view on Meta::CPAN

}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tMerged ranges are always on positive strands.\n";

    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }

lib/App/Rangeops/Command/sort.pm  view on Meta::CPAN

sub usage_desc {
    return "rangeops sort [options] <infiles>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    return $desc;
}

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

    if ( !@{$args} ) {
        $self->usage_error("This command need one or more input files.");
    }
    for ( @{$args} ) {
        next if lc $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }