File Coverage

lib/Bio/Tradis/CommandLine/TradisAnalysis.pm

Criterion	Covered	Total	%
statement	80	122	65.5
branch	21	54	38.8
condition	4	12	33.3
subroutine	13	17	76.4
pod	0	4	0.0
total	118	209	56.4

package Bio::Tradis::CommandLine::TradisAnalysis;
$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.3.3';
# ABSTRACT: Perform full tradis analysis


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd qw(abs_path cwd);
use Bio::Tradis::RunTradis;
use TryCatch;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'tag'         => ( is => 'rw', isa => 'Str',      required => 0 );
has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
has 'tagdirection' =>
  ( is => 'rw', isa => 'Str', required => 0, default => '3' );
has 'reference' => ( is => 'rw', isa => 'Str',  required => 0 );
has 'help'      => ( is => 'rw', isa => 'Bool', required => 0 );
has 'mapping_score' =>
  ( is => 'rw', isa => 'Int', required => 0, default => 30 );
has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 );
has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 );
has 'essentiality' => ( is => 'rw', isa => 'Bool',  required => 0, default => 0);

has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );

has '_output_directory' => (
    is       => 'rw',
    isa      => 'Str',
    required => 0,
    lazy     => 1,
    builder  => '_build__output_directory'
);

has '_stats_handle' => (
    is       => 'ro',
    isa      => 'FileHandle',
    required => 0,
    lazy     => 1,
    builder  => '_build__stats_handle'
);

sub BUILD {
    my ($self) = @_;

    my (
        $fastqfile, $tag,     $td,      $mismatch, $ref,$smalt_n, $essentiality,
        $map_score, $smalt_k, $smalt_s, $smalt_y, $smalt_r, $help, $verbose,$samtools_exec
    );

    GetOptionsFromArray(
        $self->args,
        'f|fastqfile=s'     => \$fastqfile,
        't|tag=s'           => \$tag,
        'td|tagdirection=i' => \$td,
        'mm|mismatch=i'     => \$mismatch,
        'r|reference=s'     => \$ref,
        'm|mapping_score=i' => \$map_score,
        'sk|smalt_k=i'      => \$smalt_k,
        'ss|smalt_s=i'      => \$smalt_s,
        'sy|smalt_y=f'      => \$smalt_y,
				'n|smalt_n=i'       => \$smalt_n,
	      'sr|smalt_r=i'      => \$smalt_r,
        'v|verbose'         => \$verbose,
        'samtools_exec=s'   => \$samtools_exec,
				'e|essentiality'    => \$essentiality,
        'h|help'            => \$help
    );

    #Essentiality analysis requires different defaults.
    if(!defined($smalt_r) && !defined($map_score) && defined($essentiality))
		{
       $self->essentiality($essentiality)   if ( defined($essentiality));
			 $smalt_r = 0;
			 $map_score = 0;
    }

    $self->fastqfile( abs_path($fastqfile) ) if ( defined($fastqfile) );
    $self->tag( uc($tag) )                   if ( defined($tag) );
    $self->tagdirection($td)                 if ( defined($td) );
    $self->mismatch($mismatch)               if ( defined($mismatch) );
    $self->reference( abs_path($ref) )       if ( defined($ref) );
    $self->mapping_score($map_score)         if ( defined($map_score) );
    $self->smalt_k($smalt_k)                 if ( defined($smalt_k) );
    $self->smalt_s($smalt_s)                 if ( defined($smalt_s) );
    $self->smalt_y($smalt_y)                 if ( defined($smalt_y) );
    $self->smalt_r($smalt_r)		         if ( defined($smalt_r) );
	$self->smalt_n($smalt_n)		         if ( defined($smalt_n) );
    $self->help($help)                       if ( defined($help) );
    $self->verbose($verbose)                 if ( defined($verbose));
    $self->samtools_exec($samtools_exec)     if ( defined($samtools_exec) );

    # print usage text if required parameters are not present
    ( $fastqfile && $tag && $ref ) or die $self->usage_text;
}

sub run {
    my ($self) = @_;

    if ( defined( $self->help ) ) {

        #if ( scalar( @{ $self->args } ) == 0 ) {
        $self->usage_text;
    }

    #parse list of files and run pipeline for each one if they all exist
    my $fq = $self->fastqfile;
    open( FILES, "<", $fq ) or die "Cannot find $fq";
    my @filelist = <FILES>;
    my $file_dir = $self->get_file_dir;

    #check files exist before running
    my $line_no = 0;
    my $full_path;
    foreach my $f1 (@filelist) {
        chomp($f1);
        $line_no++;
        if   ( $f1 =~ /^\// ) { $full_path = $f1; }
        else                  { $full_path = "$file_dir/$f1"; }
        unless ( -e $full_path ) {
            die "File $full_path does not exist ($fq, line $line_no)\n";
        }
    }

    #if all files exist, continue with analysis
    my $at_least_one_good_fastq = 0;
    foreach my $f2 (@filelist) {
        chomp($f2);
        if   ( $f2 =~ /^\// ) { $full_path = $f2; }
        else                  { $full_path = "$file_dir/$f2"; }
        my $analysis = Bio::Tradis::RunTradis->new(
            fastqfile        => $full_path,
            tag              => $self->tag,
            tagdirection     => $self->tagdirection,
            mismatch         => $self->mismatch,
            reference        => $self->reference,
            mapping_score    => $self->mapping_score,
            output_directory => $self->_output_directory,
            _stats_handle    => $self->_stats_handle,
            smalt_k          => $self->smalt_k,
            smalt_s          => $self->smalt_s,
            smalt_y          => $self->smalt_y,
            smalt_r          => $self->smalt_r,
			smalt_n          => $self->smalt_n,
            verbose          => $self->verbose,
            samtools_exec    => $self->samtools_exec
        );
	try {
            $analysis->run_tradis;
            $at_least_one_good_fastq = 1;
        }
	catch (Bio::Tradis::Exception::TagFilterError $e) {
		my $tag = $self->tag;
		warn "There was a problem filtering '$full_path' by '$tag'; it looks like the tag was not found in any read\n";
	}
    }
    if ( ! $at_least_one_good_fastq ) {
        Bio::Tradis::Exception::TagFilterError->throw( error => "None of the input files contained the specified tag.  Please check that your inputs are valid fastq files and that at least one read in one of them starts with the specified tag\n" );
    }

    $self->_tidy_stats;
    close(FILES);

    #$self->_combine_plots;
}

sub _build__output_directory {
    return cwd();
}

sub _stats_filename {
    my ($self)           = @_;
    my $dir              = $self->get_file_dir;
    my $output_directory = $self->_output_directory;
    my $stats_filename   = $self->fastqfile;
    $stats_filename =~ s/$dir\///;
    $stats_filename =~ s/[^\.]+$/stats/;
    return "$output_directory/$stats_filename";
}

sub _build__stats_handle {
    my ($self)         = @_;
    my $stats_filename = $self->_stats_filename();
    open( my $stats, ">", $stats_filename );
    return $stats;
}

sub _tidy_stats {
    my ($self)           = @_;
    my $output_directory = $self->_output_directory;
    my $stats_filename   = $self->_stats_filename();
    open( STATS, '<', $stats_filename );
    open( TMP,   '>', "$output_directory/tmp.stats" );

    my $header = 0;
    while ( my $line = <STATS> ) {
        if ( $line =~ /^File/ ) {
            if ( $header == 0 ) {
                print TMP "$line";
                $header = 1;
            }
        }
        else {
            print TMP "$line";
        }
    }
    close(TMP);
    close(STATS);
    system("mv $output_directory/tmp.stats $stats_filename");
}

sub _combine_plots {
    my ($self) = @_;
    my $filelist = $self->fastqfile;

    return 1;
}

sub get_file_dir {
    my ($self) = @_;
    my $fq = $self->fastqfile;

    my @dirs = split( '/', $fq );
    pop(@dirs);
    return join( '/', @dirs );
}

sub usage_text {
    print <<USAGE;
Run a TraDIS analysis. This involves:
1: filtering the data with tags matching that passed via -t option
2: removing the tags from the sequences
3: mapping
4: creating an insertion site plot
5: creating a stats summary

Usage: bacteria_tradis [options]

Options:
-f        : text file listing fastq files with tradis tags attached
-t        : tag to search for
-r        : reference genome in fasta format (.fa)
-td       : tag direction - 3 or 5 (optional. default = 3)
-mm       : number of mismatches allowed when matching tag (optional. default = 0)
-m        : mapping quality cutoff score (optional. default = 30)
--smalt_k : custom k-mer value for SMALT mapping (optional)
--smalt_s : custom step size for SMALT mapping (optional)
--smalt_y : custom y parameter for SMALT (optional. default = 0.96)
--smalt_r : custom r parameter for SMALT (optional. default = -1)
-n        : number of threads to use for SMALT and samtools sort (optional. default = 1)
-e        : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
-v        : verbose debugging output
USAGE
    exit;
}

__PACKAGE__->meta->make_immutable;
no Moose;
1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Tradis::CommandLine::TradisAnalysis - Perform full tradis analysis

=head1 VERSION

version 1.3.3

=head1 SYNOPSIS

Takes a fastq, reference and a tag and generates insertion
site plots for use in Artemis

=head1 AUTHOR

Carla Cummins <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut