annotate lib/CPT/Analysis/TerL.pm @ 1:d724f34e671d draft default tip

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

package CPT::Analysis::TerL;

# ABSTRACT: Guess phage packaging strategy based on homology to terminases (TerL) of phages with known packaging strategies

use strict;
use warnings;
use Data::Dumper;
use autodie;
use Moose;
use Bio::SearchIO;
use File::ShareDir;
use File::Spec;

has 'hmmer_evalue_cutoff' => ( is => 'rw', isa => 'Int' );
has 'blast_evalue_cutoff' => ( is => 'rw', isa => 'Int' );
has 'blast_dice_cutoff'   => ( is => 'rw', isa => 'Int' );

has 'search_hmmer' => ( is => 'rw', isa => 'Bool' );
has 'search_blast' => ( is => 'rw', isa => 'Bool' );

has 'data_dir' => ( is => 'rw', isa => 'Any' );

has 'awk_string' => (
	is  => 'ro',
	isa => 'Str',
	default =>
'BEGIN{print "#row,query id,subject id,evalue,dice" } {qid=$1;sid=$2;percent_identical=$3;query_length=$4;subject_length=$5;evalue=$6;dice=(2*percent_identical*subject_length/ ( subject_length + query_length ) );printf("%d,%s,%s,%s,%s\n",FNR, qid, sid, dice, evalue);}'
);

has 'input_file' => ( is => 'rw', isa => 'Str' );

my @column_max = ( 20, 10, 20, 10, 20, 60 );
my %hits;

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

	#$self->prepare(%data);
	my $dir = '/galaxy/tool-data/' # File::ShareDir::dist_dir('CPT-Analysis-TerL');
	$self->data_dir($dir);
	$self->input_file( $data{input_file} );

	if ( $self->search_hmmer() ) {
		$self->hmmer();
	}
	if ( $self->search_blast() ) {
		$self->blast($self);
	}

	return $self->guess();
}

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

	use Term::ProgressBar 2.00;
	my $progress = Term::ProgressBar->new(
		{
			name  => 'HMMER',
			count => 100,
			ETA   => 'linear',
		}
	);
	$progress->max_update_rate(1);

	my $hmmer_db_dir =
	  File::Spec->catdir( $self->data_dir(), 'db', 'hmmer' );
	my @hmmer_dbs = glob( File::Spec->catfile( $hmmer_db_dir, "*.hmm" ) );

	my $i = 0;
	foreach (@hmmer_dbs) {
		$progress->update( 100 * ( $i++ ) / scalar @hmmer_dbs );
		my $db_name = substr( $_, rindex( $_, '/' ) + 1, -4 );
		my $output_filename = sprintf(
			'%s.%s.out',
			substr(
				$self->input_file(), 0,
				rindex( $self->input_file(), '.' )
			),
			$db_name
		);
		my $query = sprintf( 'hmmsearch %s %s > %s',
			$_, $self->input_file(), $output_filename );
		system($query);

		my $in = Bio::SearchIO->new(
			-format => 'hmmer',
			-file   => $output_filename
		);
		while ( my $result = $in->next_result ) {
			while ( my $hit = $result->next_hit ) {
				while ( my $hsp = $hit->next_hsp ) {
					my ( $from, $to ) =
					  ( $result->query_name, $hit->name );
					unless ( $hits{$to}{$from} ) {
						$hits{$to}{$from} = [];
					}
					push(
						$hits{$to}{$from},
						{
							'type' => 'hmmer',
							'data' => {
								'evalue' => (
									$hsp
									  ->evalue
									  eq '0'
									? '0.0'
									: $hsp
									  ->evalue
								),
							}
						}
					);
				}
			}
		}
		unlink($output_filename);
	}
	$progress->update(100);
}

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

	use Term::ProgressBar 2.00;
	my $progress = Term::ProgressBar->new(
		{
			name  => 'Blast',
			count => 100,
			ETA   => 'linear',
		}
	);
	$progress->max_update_rate(1);

	my $blast_db_dir =
	  File::Spec->catdir( $self->data_dir(), 'db', 'blast' );
	my @blast_dbs =
	  map { substr( $_, 0, -4 ) }
	  glob( File::Spec->catfile( $blast_db_dir, "*.phr" ) );

	my $i = 0;

	#my %hits;

	foreach my $blast_db (@blast_dbs) {
		$progress->update( 100 * ( $i++ ) / scalar(@blast_dbs) );
		my $output_str =
		  substr( $blast_db, rindex( $blast_db, '/' ) + 1 ) . '.csv';
		my $query = sprintf(
'psiblast -query %s -db %s -evalue %s -outfmt "6 qseqid sseqid pident qlen slen evalue" | awk \'%s\' > %s',
			$self->input_file(), $blast_db, '1e-5',
			$self->awk_string(), $output_str );
		system($query);
		open( my $tmpfh, '<', $output_str );
		while (<$tmpfh>) {
			chomp $_;
			if ( $_ !~ /^#/ ) {
				my @line = split( /,/, $_ );
				unless ( $hits{ $line[1] }{ $line[2] } ) {
					$hits{ $line[1] }{ $line[2] } = [];
				}
				push(
					$hits{ $line[1] }{ $line[2] },
					{
						'type' => 'psiblast',
						'data' => {
							'evalue' => $line[4],
							'dice'   => $line[3],
						}
					}
				);
			}
		}
		close($tmpfh);
		unlink($output_str);

	}
	$progress->update(100);
}

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

	open( my $groupings_fh,
		'<',
		File::Spec->catfile( $self->data_dir(), 'groupings.tsv' ) );

	# Load groupings.tsv into memory
	my %data;
	while (<$groupings_fh>) {
		if ( $_ !~ /^#/ ) {
			chomp $_;
			my ( $major, $minor, $hit ) = split( /\t/, $_ );
			unless ( $data{$major}{$minor} ) {
				$data{$major}{$minor} = [];
			}
			push( $data{$major}{$minor}, $hit );
		}
	}

	# Create a reverse lookup table
	my %rdata;
	foreach my $i ( keys %data ) {
		foreach my $j ( keys %{ $data{$i} } ) {
			foreach my $k ( @{ $data{$i}{$j} } ) {
				if ( defined($k) ) {
					$rdata{$k} = [ $i, $j ];
				}
				else {
					print "$i $j\n";
				}
			}
		}
	}

	# Table printing stuff
	my @header = (
		'Major Category',
		'Major hits',
		'Minor Category',
		'Minor hits',
		'Analysis',
		'Evidence Type',
		'Evidence'
	);
	my %output;

	# Loop across the input keys
	foreach my $input_key ( keys %hits ) {
		my %guesses;
		my %guess_evidence;

		# And across all of the hits that the query hit to
		foreach my $against ( keys %{ $hits{$input_key} } ) {

			# We look at the evidence
			my @evidence = @{ $hits{$input_key}{$against} };

			my ( $type_major, $type_minor );
			if ( $rdata{$against} ) {
				( $type_major, $type_minor ) =
				  @{ $rdata{$against} };
			}
			else {
				( $type_major, $type_minor ) = (
					substr(
						$against, 0,
						rindex( $against, '_' )
					),
					substr(
						$against,
						rindex( $against, '_' ) + 1
					)
				);
			}

			# Prepare hashes.
			unless ( $guesses{$type_major} ) {
				$guesses{$type_major} = ();
			}
			unless ( $guesses{$type_major}{$type_minor} ) {
				$guesses{$type_major}{$type_minor} = ();
			}

			# Loop across the evidence
			foreach my $piece_of_evidence (@evidence) {

				# Here is an example piece of evidence
				#    'GK_Gilmour_Gene43' => {
				#        'SP18' => [
				#             {
				#               'data' => {
				#                           'evalue' => '2e-08',
				#                           'dice' => '23.8627'
				#                         },
				#               'type' => 'psiblast'
				#             }
				#           ],
				#
				if ( $type_major !~ /subject i/ ) {
					my %piece = %{$piece_of_evidence};
					if (
						$self->validate_evidence(
							$piece_of_evidence) > 0
					  )
					{
						$guess_evidence{$type_major}++;
						$guess_evidence{
							"$type_major$type_minor"
						}++;

				       # If it's not defined, set up sub arrays.
						unless ( $guesses{$type_major}
							{$type_minor}
							{ $piece{'type'} } )
						{
							if ( $piece{'type'}
								eq 'psiblast' )
							{
								$guesses{
									$type_major
								  }{$type_minor}
								  {
									$piece{
'type'
									}
								  }
								  = {
									'evalue'
									  => [],
									'dice'
									  => []
								  };
							}
							else {
								$guesses{
									$type_major
								  }{$type_minor}
								  {
									$piece{
'type'
									}
								  }
								  = { 'evalue'
									  => []
								  };
							}
						}

						# If it's zero, correct to zero.
						if ( $piece{'data'}{'evalue'}
							eq '0.0' )
						{
							$piece{'data'}{'evalue'}
							  = '0.0';
						}

						# Add our evalue
						push(
							$guesses{$type_major}
							  {$type_minor}
							  { $piece{'type'} }
							  {'evalue'},
							$piece{'data'}{'evalue'}
						);

						# And if psiblast, add dice
						if ( $piece{'type'} eq
							'psiblast' )
						{
							push(
								$guesses{
									$type_major
								  }{$type_minor}
								  {
									$piece{
'type'
									}
								  }{'dice'},
								$piece{'data'}
								  {'dice'}
							);
						}
					}
				}
			}
		}

		my @output_sheet;

		foreach my $major ( keys %guesses ) {
			if ( $guess_evidence{$major} ) {
				foreach my $minor ( keys %{ $guesses{$major} } )
				{
					if ( $guess_evidence{"$major$minor"} ) {
						foreach my $evidence_category (
							keys %{
								$guesses{$major}
								  {$minor}
							}
						  )
						{
							if ( $evidence_category
								ne 'evidence' )
							{
						      # things like evalue, dice
								my %hits = %{
									$guesses{
										$major
									  }{
										$minor
									  }{
										$evidence_category
									  }
								};
								foreach
								  my $subtype (
									keys
									%hits )
								{ # should be evalue, dice
									push(
										@output_sheet,
										[
											$major,
											$guess_evidence{
												$major
											  }
											,
											$minor,
											$guess_evidence{
"$major$minor"
											  }
											,
											$evidence_category,
											$subtype,
											join
											  (
',',
												@{
													$hits{
														$subtype
													}
												}
											  )
										]
									);
								}
							}
						}
					}
				}
			}
		}

		if ( !scalar @output_sheet ) {
			@output_sheet = ( ['No evidence above threshold'], );
		}
		$output{$input_key} = {
			header => \@header,
			data   => \@output_sheet,
		};
	}
	return \%output;
}

sub validate_evidence {
	my ( $self, $piece_of_evidence ) = @_;
	my %piece = %{$piece_of_evidence};

	#my ($self, $type, $subtype, $value) = @_;
	#             {
	#               'data' => {
	#                           'evalue' => '2e-08',
	#                           'dice' => '23.8627'
	#                         },
	#               'type' => 'psiblast'
	#             }
	if ( $piece{type} eq 'hmmer' ) {
		my $value = $piece{data}{evalue};
		if ( $value eq '0.0' || $value eq '0' ) {
			return 1;
		}
		elsif ( !defined($value) || $value eq '' ) {
			return 0;
		}
		else {
			return ( log($value) < $self->hmmer_evalue_cutoff() )
			  ;    # -64
		}
	}
	elsif ( $piece{type} eq 'psiblast' ) {
		my $evalue = $piece{data}{evalue};
		my $dice   = $piece{data}{dice};

		my $evalue_return = 0;
		if ( $evalue eq '0.0' || $evalue eq '0' ) {
			$evalue_return = 1;
		}
		else {
			$evalue_return =
			  ( log($evalue) < $self->blast_evalue_cutoff() ); #-140
		}

		return $evalue_return
		  && ( $dice > $self->blast_dice_cutoff() );               # 30
	}
}

1;

__END__

=pod

=encoding UTF-8

=head1 NAME

CPT::Analysis::TerL - Guess phage packaging strategy based on homology to terminases (TerL) of phages with known packaging strategies

=head1 VERSION

version 1.96

=head1 AUTHOR

Eric Rasche <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2014 by Eric Rasche.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut