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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:56:18 +0000
parents 97ef96676b48
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1
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1 package CPT::Analysis::TerL;
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2
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3 # ABSTRACT: Guess phage packaging strategy based on homology to terminases (TerL) of phages with known packaging strategies
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4
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5 use strict;
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6 use warnings;
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7 use Data::Dumper;
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8 use autodie;
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9 use Moose;
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10 use Bio::SearchIO;
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11 use File::ShareDir;
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12 use File::Spec;
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13
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14 has 'hmmer_evalue_cutoff' => ( is => 'rw', isa => 'Int' );
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15 has 'blast_evalue_cutoff' => ( is => 'rw', isa => 'Int' );
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16 has 'blast_dice_cutoff' => ( is => 'rw', isa => 'Int' );
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17
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18 has 'search_hmmer' => ( is => 'rw', isa => 'Bool' );
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19 has 'search_blast' => ( is => 'rw', isa => 'Bool' );
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20
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21 has 'data_dir' => ( is => 'rw', isa => 'Any' );
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22
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23 has 'awk_string' => (
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24 is => 'ro',
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25 isa => 'Str',
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26 default =>
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27 '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);}'
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28 );
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29
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30 has 'input_file' => ( is => 'rw', isa => 'Str' );
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31
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32 my @column_max = ( 20, 10, 20, 10, 20, 60 );
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33 my %hits;
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34
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35 sub run {
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36 my ( $self, %data ) = @_;
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37
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38 #$self->prepare(%data);
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39 my $dir = '/galaxy/tool-data/' # File::ShareDir::dist_dir('CPT-Analysis-TerL');
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40 $self->data_dir($dir);
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41 $self->input_file( $data{input_file} );
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42
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43 if ( $self->search_hmmer() ) {
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44 $self->hmmer();
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45 }
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46 if ( $self->search_blast() ) {
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47 $self->blast($self);
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48 }
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49
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50 return $self->guess();
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51 }
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52
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53 sub hmmer {
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54 my ($self) = @_;
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55
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56 use Term::ProgressBar 2.00;
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57 my $progress = Term::ProgressBar->new(
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58 {
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59 name => 'HMMER',
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60 count => 100,
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61 ETA => 'linear',
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62 }
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63 );
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64 $progress->max_update_rate(1);
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65
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66 my $hmmer_db_dir =
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67 File::Spec->catdir( $self->data_dir(), 'db', 'hmmer' );
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68 my @hmmer_dbs = glob( File::Spec->catfile( $hmmer_db_dir, "*.hmm" ) );
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69
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70 my $i = 0;
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71 foreach (@hmmer_dbs) {
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72 $progress->update( 100 * ( $i++ ) / scalar @hmmer_dbs );
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73 my $db_name = substr( $_, rindex( $_, '/' ) + 1, -4 );
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74 my $output_filename = sprintf(
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75 '%s.%s.out',
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76 substr(
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77 $self->input_file(), 0,
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78 rindex( $self->input_file(), '.' )
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79 ),
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80 $db_name
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81 );
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82 my $query = sprintf( 'hmmsearch %s %s > %s',
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83 $_, $self->input_file(), $output_filename );
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84 system($query);
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85
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86 my $in = Bio::SearchIO->new(
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87 -format => 'hmmer',
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88 -file => $output_filename
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89 );
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90 while ( my $result = $in->next_result ) {
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91 while ( my $hit = $result->next_hit ) {
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92 while ( my $hsp = $hit->next_hsp ) {
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93 my ( $from, $to ) =
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94 ( $result->query_name, $hit->name );
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95 unless ( $hits{$to}{$from} ) {
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96 $hits{$to}{$from} = [];
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97 }
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98 push(
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99 $hits{$to}{$from},
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100 {
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101 'type' => 'hmmer',
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102 'data' => {
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103 'evalue' => (
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104 $hsp
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105 ->evalue
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106 eq '0'
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107 ? '0.0'
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108 : $hsp
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109 ->evalue
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110 ),
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111 }
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112 }
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113 );
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114 }
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115 }
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116 }
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117 unlink($output_filename);
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118 }
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119 $progress->update(100);
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120 }
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121
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122 sub blast {
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123 my ($self) = @_;
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124
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125 use Term::ProgressBar 2.00;
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126 my $progress = Term::ProgressBar->new(
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127 {
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128 name => 'Blast',
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129 count => 100,
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130 ETA => 'linear',
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131 }
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132 );
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133 $progress->max_update_rate(1);
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134
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135 my $blast_db_dir =
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136 File::Spec->catdir( $self->data_dir(), 'db', 'blast' );
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137 my @blast_dbs =
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138 map { substr( $_, 0, -4 ) }
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139 glob( File::Spec->catfile( $blast_db_dir, "*.phr" ) );
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140
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141 my $i = 0;
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142
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143 #my %hits;
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144
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145 foreach my $blast_db (@blast_dbs) {
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146 $progress->update( 100 * ( $i++ ) / scalar(@blast_dbs) );
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147 my $output_str =
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148 substr( $blast_db, rindex( $blast_db, '/' ) + 1 ) . '.csv';
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149 my $query = sprintf(
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150 'psiblast -query %s -db %s -evalue %s -outfmt "6 qseqid sseqid pident qlen slen evalue" | awk \'%s\' > %s',
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151 $self->input_file(), $blast_db, '1e-5',
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152 $self->awk_string(), $output_str );
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153 system($query);
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154 open( my $tmpfh, '<', $output_str );
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155 while (<$tmpfh>) {
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156 chomp $_;
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157 if ( $_ !~ /^#/ ) {
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158 my @line = split( /,/, $_ );
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159 unless ( $hits{ $line[1] }{ $line[2] } ) {
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160 $hits{ $line[1] }{ $line[2] } = [];
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161 }
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162 push(
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163 $hits{ $line[1] }{ $line[2] },
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164 {
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165 'type' => 'psiblast',
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166 'data' => {
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167 'evalue' => $line[4],
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168 'dice' => $line[3],
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169 }
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170 }
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171 );
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172 }
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173 }
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174 close($tmpfh);
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175 unlink($output_str);
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176
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177 }
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178 $progress->update(100);
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179 }
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180
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181 sub guess {
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182 my ($self) = @_;
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183
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184 open( my $groupings_fh,
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185 '<',
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186 File::Spec->catfile( $self->data_dir(), 'groupings.tsv' ) );
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187
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188 # Load groupings.tsv into memory
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189 my %data;
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190 while (<$groupings_fh>) {
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191 if ( $_ !~ /^#/ ) {
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192 chomp $_;
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193 my ( $major, $minor, $hit ) = split( /\t/, $_ );
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194 unless ( $data{$major}{$minor} ) {
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195 $data{$major}{$minor} = [];
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196 }
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197 push( $data{$major}{$minor}, $hit );
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198 }
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199 }
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200
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201 # Create a reverse lookup table
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202 my %rdata;
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203 foreach my $i ( keys %data ) {
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204 foreach my $j ( keys %{ $data{$i} } ) {
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205 foreach my $k ( @{ $data{$i}{$j} } ) {
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206 if ( defined($k) ) {
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207 $rdata{$k} = [ $i, $j ];
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208 }
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209 else {
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210 print "$i $j\n";
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211 }
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212 }
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213 }
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214 }
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215
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216 # Table printing stuff
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217 my @header = (
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218 'Major Category',
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219 'Major hits',
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220 'Minor Category',
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221 'Minor hits',
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222 'Analysis',
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223 'Evidence Type',
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224 'Evidence'
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225 );
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226 my %output;
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227
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228 # Loop across the input keys
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229 foreach my $input_key ( keys %hits ) {
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230 my %guesses;
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231 my %guess_evidence;
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232
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233 # And across all of the hits that the query hit to
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234 foreach my $against ( keys %{ $hits{$input_key} } ) {
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235
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236 # We look at the evidence
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237 my @evidence = @{ $hits{$input_key}{$against} };
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238
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239 my ( $type_major, $type_minor );
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240 if ( $rdata{$against} ) {
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241 ( $type_major, $type_minor ) =
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242 @{ $rdata{$against} };
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243 }
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244 else {
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245 ( $type_major, $type_minor ) = (
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246 substr(
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247 $against, 0,
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248 rindex( $against, '_' )
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249 ),
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250 substr(
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251 $against,
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252 rindex( $against, '_' ) + 1
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253 )
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254 );
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255 }
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256
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257 # Prepare hashes.
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258 unless ( $guesses{$type_major} ) {
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259 $guesses{$type_major} = ();
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260 }
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261 unless ( $guesses{$type_major}{$type_minor} ) {
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262 $guesses{$type_major}{$type_minor} = ();
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263 }
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264
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265 # Loop across the evidence
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266 foreach my $piece_of_evidence (@evidence) {
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267
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268 # Here is an example piece of evidence
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269 # 'GK_Gilmour_Gene43' => {
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270 # 'SP18' => [
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271 # {
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272 # 'data' => {
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273 # 'evalue' => '2e-08',
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274 # 'dice' => '23.8627'
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275 # },
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276 # 'type' => 'psiblast'
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277 # }
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278 # ],
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279 #
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280 if ( $type_major !~ /subject i/ ) {
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281 my %piece = %{$piece_of_evidence};
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282 if (
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283 $self->validate_evidence(
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284 $piece_of_evidence) > 0
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285 )
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286 {
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287 $guess_evidence{$type_major}++;
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288 $guess_evidence{
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289 "$type_major$type_minor"
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290 }++;
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291
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292 # If it's not defined, set up sub arrays.
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293 unless ( $guesses{$type_major}
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294 {$type_minor}
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295 { $piece{'type'} } )
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296 {
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297 if ( $piece{'type'}
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298 eq 'psiblast' )
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299 {
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300 $guesses{
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301 $type_major
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302 }{$type_minor}
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303 {
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304 $piece{
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305 'type'
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306 }
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307 }
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308 = {
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309 'evalue'
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310 => [],
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311 'dice'
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312 => []
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313 };
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314 }
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315 else {
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316 $guesses{
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317 $type_major
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318 }{$type_minor}
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319 {
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320 $piece{
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321 'type'
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322 }
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323 }
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324 = { 'evalue'
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325 => []
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326 };
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327 }
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parents:
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328 }
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parents:
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329
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330 # If it's zero, correct to zero.
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331 if ( $piece{'data'}{'evalue'}
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parents:
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332 eq '0.0' )
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333 {
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334 $piece{'data'}{'evalue'}
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parents:
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335 = '0.0';
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parents:
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336 }
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337
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338 # Add our evalue
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parents:
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339 push(
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parents:
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340 $guesses{$type_major}
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341 {$type_minor}
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342 { $piece{'type'} }
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343 {'evalue'},
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344 $piece{'data'}{'evalue'}
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parents:
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345 );
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346
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347 # And if psiblast, add dice
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348 if ( $piece{'type'} eq
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349 'psiblast' )
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parents:
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350 {
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351 push(
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parents:
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352 $guesses{
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353 $type_major
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parents:
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354 }{$type_minor}
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parents:
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355 {
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parents:
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356 $piece{
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parents:
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357 'type'
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parents:
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358 }
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359 }{'dice'},
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parents:
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360 $piece{'data'}
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361 {'dice'}
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parents:
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362 );
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parents:
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363 }
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parents:
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364 }
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parents:
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365 }
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parents:
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366 }
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parents:
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367 }
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368
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369 my @output_sheet;
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370
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371 foreach my $major ( keys %guesses ) {
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372 if ( $guess_evidence{$major} ) {
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373 foreach my $minor ( keys %{ $guesses{$major} } )
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374 {
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375 if ( $guess_evidence{"$major$minor"} ) {
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376 foreach my $evidence_category (
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parents:
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377 keys %{
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378 $guesses{$major}
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parents:
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379 {$minor}
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380 }
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381 )
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382 {
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parents:
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383 if ( $evidence_category
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384 ne 'evidence' )
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385 {
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386 # things like evalue, dice
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387 my %hits = %{
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388 $guesses{
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389 $major
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390 }{
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391 $minor
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392 }{
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393 $evidence_category
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394 }
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395 };
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396 foreach
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397 my $subtype (
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398 keys
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399 %hits )
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400 { # should be evalue, dice
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401 push(
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402 @output_sheet,
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403 [
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404 $major,
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405 $guess_evidence{
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406 $major
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407 }
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408 ,
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409 $minor,
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410 $guess_evidence{
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411 "$major$minor"
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412 }
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413 ,
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414 $evidence_category,
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415 $subtype,
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416 join
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417 (
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418 ',',
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419 @{
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420 $hits{
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421 $subtype
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422 }
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423 }
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424 )
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425 ]
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426 );
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427 }
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428 }
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429 }
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430 }
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431 }
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432 }
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433 }
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434
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435 if ( !scalar @output_sheet ) {
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436 @output_sheet = ( ['No evidence above threshold'], );
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437 }
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438 $output{$input_key} = {
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439 header => \@header,
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440 data => \@output_sheet,
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441 };
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442 }
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443 return \%output;
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444 }
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445
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446 sub validate_evidence {
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447 my ( $self, $piece_of_evidence ) = @_;
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448 my %piece = %{$piece_of_evidence};
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449
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450 #my ($self, $type, $subtype, $value) = @_;
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451 # {
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452 # 'data' => {
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453 # 'evalue' => '2e-08',
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454 # 'dice' => '23.8627'
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455 # },
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456 # 'type' => 'psiblast'
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457 # }
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458 if ( $piece{type} eq 'hmmer' ) {
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459 my $value = $piece{data}{evalue};
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460 if ( $value eq '0.0' || $value eq '0' ) {
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461 return 1;
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462 }
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463 elsif ( !defined($value) || $value eq '' ) {
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464 return 0;
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465 }
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466 else {
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467 return ( log($value) < $self->hmmer_evalue_cutoff() )
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468 ; # -64
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parents:
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469 }
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470 }
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471 elsif ( $piece{type} eq 'psiblast' ) {
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472 my $evalue = $piece{data}{evalue};
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parents:
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473 my $dice = $piece{data}{dice};
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parents:
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474
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475 my $evalue_return = 0;
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476 if ( $evalue eq '0.0' || $evalue eq '0' ) {
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parents:
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477 $evalue_return = 1;
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parents:
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478 }
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479 else {
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parents:
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480 $evalue_return =
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481 ( log($evalue) < $self->blast_evalue_cutoff() ); #-140
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482 }
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parents:
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483
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484 return $evalue_return
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parents:
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485 && ( $dice > $self->blast_dice_cutoff() ); # 30
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parents:
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486 }
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parents:
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487 }
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parents:
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488
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489 1;
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parents:
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490
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parents:
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491 __END__
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parents:
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492
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parents:
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493 =pod
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parents:
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494
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parents:
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495 =encoding UTF-8
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parents:
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496
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parents:
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497 =head1 NAME
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parents:
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498
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499 CPT::Analysis::TerL - Guess phage packaging strategy based on homology to terminases (TerL) of phages with known packaging strategies
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parents:
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500
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parents:
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501 =head1 VERSION
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parents:
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502
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parents:
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503 version 1.96
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parents:
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504
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parents:
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505 =head1 AUTHOR
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parents:
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506
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parents:
diff changeset
507 Eric Rasche <rasche.eric@yandex.ru>
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parents:
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508
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parents:
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509 =head1 COPYRIGHT AND LICENSE
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parents:
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510
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parents:
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511 This software is Copyright (c) 2014 by Eric Rasche.
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parents:
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512
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parents:
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513 This is free software, licensed under:
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parents:
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514
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515 The GNU General Public License, Version 3, June 2007
97ef96676b48 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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516
97ef96676b48 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
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517 =cut