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

package App::Anchr::Command::orient;
use strict;
use warnings;
use autodie;

use App::Anchr -command;
use App::Anchr::Common;

use constant abstract => "orient overlapped sequences to the same strand";

sub opt_spec {
    return (
        [ "outfile|o=s",  "output filename, [stdout] for screen", ],
        [ "restrict|r=s", "limit to known pairs", ],
        [ "len|l=i",      "minimal length of overlaps",   { default => 1000 }, ],
        [ "idt|i=f",      "minimal identity of overlaps", { default => 0.85 }, ],
        [ "parallel|p=i", "number of threads",            { default => 4 }, ],
        [ "verbose|v",    "verbose mode", ],
        { show_defaults => 1, }
    );
}

sub usage_desc {
    return "anchr orient [options] <infiles>";
}

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 ) {
            $self->usage_error("The input file [$_] doesn't exist.");
        }
    }

    if ( exists $opt->{restrict} ) {
        if ( !Path::Tiny::path( $opt->{restrict} )->is_file ) {
            $self->usage_error("The restrict file [$opt->{restrict}] doesn't exist.\n");
        }
    }

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

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

    # absolute pathes as we will chdir to tempdir later
    my @infiles;
    for my $infile ( @{$args} ) {
        push @infiles, Path::Tiny::path($infile)->absolute->stringify;
    }

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

    if ( $opt->{restrict} ) {
        $opt->{restrict} = Path::Tiny::path( $opt->{restrict} )->absolute->stringify;
    }