MNSMAR / CLIPSeqTools-0.1.0-TRIAL / lib / CLIPSeqTools / PreprocessApp / cut_adaptor.pm 

            

              
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=head1 NAME
CLIPSeqTools::PreprocessApp::cut_adaptor - Cut the adaptor sequence from the 3'end of reads.
=head1 SYNOPSIS
clipseqtools-preprocess cut_adaptor [options/parameters]
=head1 DESCRIPTION
Cut the adaptor sequence from the 3'end of reads.
Uses cutadapt to remove the adaptor which is usually ligated at the 3'end of reads.
=head1 OPTIONS
  Input.
    --fastq <Str>          FastQ file with the reads.
    --adaptor <Str>        adaptor sequence.
  Output
    --o_prefix <Str>       output path prefix. Script will create and add
                           extension to path. [Default: ./]
  Other options.
    --cutadapt_path <Str>  path to cutadapt executable. [Default: cutadapt].
    -v --verbose           print progress lines and extra information.
    -h -? --usage --help   print help message
=cut
package CLIPSeqTools::PreprocessApp::cut_adaptor;
$CLIPSeqTools::PreprocessApp::cut_adaptor::VERSION = '0.1.0'; # TRIAL
# Make it an app command
use MooseX::App::Command;
extends 'CLIPSeqTools::PreprocessApp';
#######################################################################
#######################   Load External modules   #####################
#######################################################################
use Modern::Perl;
use autodie;
use namespace::autoclean;
#######################################################################
#######################   Command line options   ######################
#######################################################################
option 'fastq' => (
        is            => 'rw',
        isa           => 'Str',
        required      => 1,
        documentation => 'FastQ file with the reads.',
);
option 'adaptor' => (
        is            => 'rw',
        isa           => 'Str',
        required      => 1,
        documentation => 'adaptor sequence.',
);
option 'cutadapt_path' => (
        is            => 'rw',
        isa           => 'Str',
        default       => 'cutadapt',
        documentation => 'path to cutadapt executable.',
);
#######################################################################
##########################   Consume Roles   ##########################
#######################################################################
with
        "CLIPSeqTools::Role::Option::OutputPrefix" => {
                -alias    => { validate_args => '_validate_args_for_output_prefix' },
                -excludes => 'validate_args',
        };
         
#######################################################################
########################   Interface Methods   ########################
#######################################################################
sub validate_args {
        my ($self) = @_;
         
        $self->_validate_args_for_output_prefix;
}
sub run {
        my ($self) = @_;
         
        warn "Starting job: cut_adaptor\n";
         
        warn "Validating arguments\n" if $self->verbose;
        $self->validate_args();
         
        warn "Preparing command\n" if $self->verbose;
        my $cmd = join(' ',
                $self->cutadapt_path,
                $self->fastq,
                '-n 3',
                '-m 15',
                '-e 0.25',
                '-a ' . $self->adaptor,
                '-o ' . $self->o_prefix . 'reads.adtrim.fastq'
        );
         
        warn "Creating output path\n" if $self->verbose;
        $self->make_path_for_output_prefix();
         
        warn "Running cutadapt\n" if $self->verbose;
        warn "Command: $cmd\n" if $self->verbose;
        system "$cmd";
}
1;