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

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

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

use constant abstract => "Run quorum to discard bad reads";

sub opt_spec {
    return (
        [ "outfile|o=s", "output filename, [stdout] for screen", { default => "quorum.sh" }, ],
        [ 'size|s=i',    'fragment size',                        { default => 300, }, ],
        [ 'std|d=i',     'fragment size standard deviation',     { default => 30, }, ],
        [ 'jf=i',        'jellyfish hash size',                  { default => 500_000_000, }, ],
        [ 'estsize=s',   'estimated genome size',                { default => "auto", }, ],
        [   "adapter|a=s", "adapter file",
            { default => File::ShareDir::dist_file( 'App-Anchr', 'adapter.jf' ) },
        ],
        [ 'parallel|p=i', 'number of threads', { default => 8, }, ],
        { show_defaults => 1, }
    );
}

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

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

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

    # A stream to 'stdout' or a standard file.
    my $out_fh;
    if ( lc $opt->{outfile} eq "stdout" ) {
        $out_fh = *STDOUT{IO};
    }
    else {
        open $out_fh, ">", $opt->{outfile};
    }

    my $tt   = Template->new;
    my $text = <<'EOF';
#!/usr/bin/env bash

#----------------------------#
# Colors in term
#----------------------------#
# http://stackoverflow.com/questions/5947742/how-to-change-the-output-color-of-echo-in-linux
GREEN=
RED=
NC=
if tty -s < /dev/fd/1 2> /dev/null; then
    GREEN='\033[0;32m'
    RED='\033[0;31m'
    NC='\033[0m' # No Color
fi

log_warn () {
    echo >&2 -e "${RED}==> $@ <==${NC}"
}

log_info () {
    echo >&2 -e "${GREEN}==> $@${NC}"
}

log_debug () {
    echo >&2 -e "  * $@"