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lib/App/Fasops/Command/links.pm  view on Meta::CPAN

package App::Fasops::Command::links;
use strict;
use warnings;
use autodie;

use App::Fasops -command;
use App::RL::Common;
use App::Fasops::Common;

sub abstract {
    return 'scan blocked fasta files and output bi/multi-lateral range links';
}

sub opt_spec {
    return (
        [ "outfile|o=s", "Output filename. [stdout] for screen." ],
        [ "pair|p",      "pairwise links" ],
        [ "best|b",      "best-to-best pairwise links" ],
        { show_defaults => 1, }
    );
}

sub usage_desc {
    return "fasops links [options] <infile> [more infiles]";
}

sub description {
    my $desc;
    $desc .= ucfirst(abstract) . ".\n";
    $desc .= <<'MARKDOWN';

* <infiles> are paths to axt files, .axt.gz is supported
* infile == stdin means reading from STDIN

MARKDOWN

    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 $_ eq "stdin";
        if ( !Path::Tiny::path($_)->is_file ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }
    }

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

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

    my @links;
    for my $infile ( @{$args} ) {
        my $in_fh;
        if ( lc $infile eq "stdin" ) {
            $in_fh = *STDIN{IO};
        }
        else {
            $in_fh = IO::Zlib->new( $infile, "rb" );