validate results from the CPAN

validate

App-Anchr

view release on metacpan or search on metacpan

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

    return "anchr anchors [options] <k_unitigs.fasta> <pe.cor.fa>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tFasta files can be gzipped\n";
    return $desc;
}

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

    if ( !( @{$args} == 2 ) ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr break [options] <dazz DB> <ovlp file>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tThis command relies on an existing dazz db.\n";
    return $desc;
}

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

    if ( @{$args} != 2 ) {
        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 ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr contained [options] <infile> [more infiles]";
}

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 or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr 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 ) {

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

    return "anchr dazzname [options] <infile>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tinfile == stdin means reading from STDIN\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} ) {
        next if lc $_ eq "stdin";

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

sub usage_desc {
    return "anchr dep [options]";
}

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

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

    if ( @{$args} != 0 ) {
        my $message = "This command need no input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
}

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

    return "anchr group [options] <dazz DB> <ovlp file>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tThis command relies on an existing dazz db.\n";
    return $desc;
}

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

    if ( @{$args} != 2 ) {
        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 ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr kunitigs [options] <pe.cor.fa> <environment.json>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tFasta files can be gzipped\n";
    return $desc;
}

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

    if ( !( @{$args} == 2 ) ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

sub usage_desc {
    return "anchr layout [options] <.ovlp.tsv> <.relation.tsv> <strand.fasta>";
}

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

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

    if ( @{$args} != 3 ) {
        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 ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr localcor [options] <dazz DB> <ovlp file>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tThis command relies on an existing dazz db.\n";
    return $desc;
}

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

    if ( @{$args} != 2 ) {
        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 ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

    return "anchr merge [options] <infile>";
}

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 ) {

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

}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tThis command is for small files.\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 or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tThis command is for small files.\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 or more input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

lib/App/Anchr/Command/overlap2.pm view on Meta::CPAN

}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tAll intermediate files (.fasta, .replace.tsv, .db, .las, .show.txt, .ovlp.tsv)";
    $desc .= " are keept in the working directory.\n";
    return $desc;
}

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

    if ( @{$args} != 2 ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

lib/App/Anchr/Command/paf2ovlp.pm view on Meta::CPAN

sub usage_desc {
    return "anchr paf2ovlp [options] <minimap outputs>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\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} ) {
        next if lc $_ eq "stdin";

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

    return "anchr quorum [options] <PE file1> <PE file2> [SE file]";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tFastq files can be gzipped\n";
    return $desc;
}

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

    if ( !( @{$args} == 2 or @{$args} == 3 ) ) {
        my $message = "This command need two or three input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

sub usage_desc {
    return "anchr replace [options] <.ovlp.tsv> <.replace.tsv>";
}

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

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

    if ( @{$args} != 2 ) {
        my $message = "This command need two 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/Anchr/Command/restrict.pm view on Meta::CPAN

sub usage_desc {
    return "anchr restrict [options] <.ovlp.tsv> <.restrict.tsv>";
}

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

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

    if ( @{$args} != 2 ) {
        my $message = "This command need two 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/Anchr/Command/scaffold.pm view on Meta::CPAN

sub usage_desc {
    return "anchr scaffold [options] <anchor.fasta> <pe.fa>";
}

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

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

    if ( !( @{$args} == 2 ) ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

lib/App/Anchr/Command/show2ovlp.pm view on Meta::CPAN

sub usage_desc {
    return "anchr show2ovlp [options] <fasta file> <LAshow outputs>";
}

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

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

    if ( @{$args} != 2 ) {
        my $message = "This command need two 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/Anchr/Command/trim.pm view on Meta::CPAN

    return "anchr trim [options] <PE file1> <PE file2>";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tFastq files can be gzipped\n";
    return $desc;
}

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

    if ( @{$args} != 2 ) {
        my $message = "This command need two input files.\n\tIt found";
        $message .= sprintf " [%s]", $_ for @{$args};
        $message .= ".\n";
        $self->usage_error($message);
    }
    for ( @{$args} ) {
        if ( !Path::Tiny::path($_)->is_file ) {

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

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= "\tAll operations are running in a tempdir and no intermediate files are kept.\n";
    $desc
        .= "\tThe inaccuracy of overlap boundary identified by mininap may loose some parts of reads, ";
    $desc .= "\tbut also prevent adaptor or chimeric sequences joining with good parts of reads.\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 ) {

( run in 1.023 second using v1.01-cache-2.11-cpan-a5abf4f5562 )