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1 #!/usr/bin/env perl
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2
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3 use strict;
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4 use FindBin;
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5 use Bio::SeqIO;
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6 use Bio::Seq;
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7 use Path::Tiny;
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8 use File::Basename;
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9 use File::Spec;
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10 use File::Path qw(make_path remove_tree);
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11 use List::Util qw(first);
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12 use Cwd qw(abs_path);
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13 use Data::Dumper;
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14 use LWP::Simple;
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15 use JSON;
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16
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17 #..............................................................................
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18 # Globals
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19
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20 my $EXE = basename($0);
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21 my $ABX_SEP = ';';
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22
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23 my %DATABASE = (
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24 'resfinder' => \&get_resfinder,
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25 'plasmidfinder' => \&get_plasmidfinder,
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26 'megares' => \&get_megares,
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27 'argannot' => \&get_argannot,
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28 'card' => \&get_card,
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29
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30 # 'ncbibetalactamase' => \&get_ncbibetalactamase,
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31 'ncbi' => \&get_ncbi,
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32 'vfdb' => \&get_vfdb,
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33 'ecoli_vf' => \&get_ecoli_vf, # https://github.com/phac-nml/ecoli_vf
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34 'ecoh' => \&get_ecoh,
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35 'bacmet2' => \&get_bacmet2,
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36 'victors' => \&get_victors,
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37
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38 # 'serotypefinder' => \&get_serotypefinder,
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39 );
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40 my $DATABASES = join( ' ', sort keys %DATABASE );
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41
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42 #..............................................................................
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43 # Command line options
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44
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45 my ( @Options, $debug, $outdir, $db, $force );
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46 setOptions();
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47
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48 $db or err("Please choose a --db from: $DATABASES");
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49 exists $DATABASE{$db} or err("Unknown --db '$db', choose from: $DATABASES ");
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50 -d $outdir or err("--outdir '$outdir' does not exist");
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51
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52 my $dir = abs_path( File::Spec->catdir( $outdir, $db ) );
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53 make_path($dir);
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54 msg("Setting up '$db' in '$dir'");
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55
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56 #my $tmpdir = tempdir("$db-XXXXXXXX", DIR=>$dir, CLEANUP=>0);
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57 #my $tmpdir = "/home/tseemann/git/abricate/db/resfinder/resfinder-6Kuphtvv";
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58 my $tmpdir = "$dir/src";
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59 make_path($tmpdir);
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60
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61 # run the specific function from --db
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62 chdir $tmpdir;
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63 my $seq = $DATABASE{$db}->();
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64 map { is_full_gene($_) } @$seq; # doesn't do anything?
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65 $seq = dedupe_seq($seq);
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66
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67 #print Dumper($seq);
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68 msg("Sorting sequences by ID");
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69 $seq = [ sort { $a->{ID} cmp $b->{ID} } @$seq ];
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70 save_fasta( "$dir/sequences", $seq );
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71
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72 msg("Formatting BLASTN database: $dir/sequences");
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73 my $logfile = "$tmpdir/makeblastdb.log";
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74 my $ncbi_title = $db;
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75 if ( "$db" eq "ncbi" ) {
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76 $ncbi_title = "ncbiamrplus";
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77 }
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78 my $ec = system(
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79 "makeblastdb -in '$dir/sequences' -title '$ncbi_title' -dbtype nucl -hash_index -logfile $logfile"
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80 );
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81 if ( $ec != 0 ) {
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82 system("tail '$logfile'");
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83 err("Error with makign BLAST database. See $logfile");
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84 }
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85
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86 #msg("Run 'abricate --setupdb' to format the database");
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87
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88 msg("Done.");
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89
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90 #..............................................................................
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91
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92 sub download {
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93 my ( $url, $dest ) = @_;
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94 if ( -r $dest and not $force ) {
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95 msg("Won't re-download existing $dest (use --force)");
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96
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97 #exit(1);
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98 }
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99 else {
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100 msg("Downloading: $url");
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101 my $ec = mirror( $url, $dest );
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102 msg("HTTP Result: $ec");
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103 ( $ec == 200 or $ec = 304 )
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104 or err("HTTP $ec | failed to download $url"); # is HTTP OK ?
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105 }
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106 msg("Destination: $dest");
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107 msg( "Filesize:", ( -s $dest ), "bytes" );
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108 }
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109
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110 #..............................................................................
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111 sub trim_spaces {
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112 my ($s) = @_;
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113 $s =~ s/^\s+//;
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114 $s =~ s/\s+$//;
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115 return $s;
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116 }
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117
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118 #..............................................................................
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119 sub get_resfinder {
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120 my $name = "resfinder_db";
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121
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122 # FIXME - can we just get HEAD.zip like in plasmidfinder?
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123 my $url = "https://bitbucket.org/genomicepidemiology/$name.git";
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124
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125 if (-r $name and not $force) {
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126 msg("Won't overwrite existing $name (use --force)");
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127 exit(1);
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128 }
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129 else {
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130 msg("Nuking existing folder: $name");
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131 remove_tree("./$name");
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132 msg("Cloning $url to $name");
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133 system("git clone --quiet $url $name");
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134 }
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135
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136 #<*.fsa>
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137 #>aac(6')-Ib_2_M23634
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138 #>blaNDM-19_1_MF370080
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139 #>mcr-1.1_1_KP347127
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140 #>fosB1_1_CP001903
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141 #>fusB_1_AY373761
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142 #>VanHAX_1_FJ866609
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143 #>ere(A)_6_DQ157752
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144 #>nimA_1_X71444
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145 #>cfr_1_AM408573
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146 #>catB3_2_U13880
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147 #>qnrA1_1_AY070235
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148 #>ARR-2_1_HQ141279
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149 #>sul1_2_U12338
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150 #>tet_1_M74049
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151 #>dfrA19_1_EU855687
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152
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153 #<notes.txt>
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154 #aac(6')-Iv:Aminoglycoside resistance:
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155 #aac(6')-Iw:Aminoglycoside resistance:Alternate name; aac(6')-Ix
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156 #sul3:Sulphonamide resistance:
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157 ##Tetracycline:
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158 #ort(B):Tetracycline resistance:
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159 #blaCMY-59:Beta-lactam resistance:
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160
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161 #<phenotypes.txt>
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162 #Gene_accession no. Class Phenotype PMID Mechanism of resistance Notes Required_gene
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163 #ant(2'')-Ia_1_X04555 Aminoglycoside Gentamicin, Tobramycin 3024112 Enzymatic modification Alternative name aadB
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164 #ant(2'')-Ia_2_JF826500 Aminoglycoside Gentamicin, Tobramycin 22271862 Enzymat
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165
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166 # $name = "~/apps/bettercallsal/assets/abricate_dbs/$name";
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167 my $metafn = "$name/phenotypes.txt";
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168 my @meta = path($metafn)->lines( { chomp => 1 } );
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169 my %anno;
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170 foreach (@meta) {
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171 next if m/^#/;
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172 my @x = split m/\t/;
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173
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174 #msg("$metafn: @x");
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175 my ($gene) = ( $x[0] =~ m/^(.*?)_\w+$/ );
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176 $anno{$gene}{ABX} = [
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177 map { trim_spaces($_) }
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178 grep { !m/(unknown|notes|^none)/i }
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179 split m/,\s*/,
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180 $x[2]
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181 ];
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182
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183 #msg("$metafn: $gene |", $anno{$gene}{ABX}->@*);
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184 }
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185 msg( "get_resfinder: $metafn", scalar( keys %anno ), "genes" );
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186
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187 #print Dumper(\%anno);
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188
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189 my @seq;
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190 for my $fasta (<$name/*.fsa>) {
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191
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192 # Issue #62 - repair broken fasta files like this:
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193 # GCTTTAAATTGGAAAAAAGATAGTCAAACTCTTTAA>cmr_1_U43535
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194 # inline replacement
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195 system( 'sed', '-i.bak', 's/\([A-Z]\)>/\1\n>/gi', $fasta );
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196 my $args = load_fasta($fasta);
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197
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198 # use name of fasta file as antibiotic name
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199 #my $abx = basename($fasta, '.fsa');
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200 #msg("$fasta: Assigning '$abx' to all genes");
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201 #push @{$_->{ABX}}, $abx for (@$args);
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202 push @seq, @$args;
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203 }
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204
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205 # https://github.com/tseemann/abricate/issues/92
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206 # mcr-9_1_NZ_NAAN01000063.1
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207 #>mcr-9_1_NZ_NAAN01000063.1
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208 # mcr-9.1:Colistin resistance:
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209
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210 for my $seq (@seq) {
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211 my ( $id, $copy, $acc ) = $seq->{ID} =~ m/^(.*?)_(\d+)_(\S+)$/;
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212
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213 #msg("resfinder: $1 $2 $3", $anno{$1});
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214 $seq->{ID} = "${id}_${copy}";
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215 $seq->{ACC} = $acc;
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216 $seq->{DESC} = $anno{$id}{DESC} || $id;
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217 push @{ $seq->{ABX} }, @{ $anno{$id}{ABX} } if $anno{$id}{ABX};
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218 }
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219
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220 return \@seq;
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221 }
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222
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223 #..............................................................................
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224 sub get_serotypefinder {
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225 my $name = "serotypefinder_db";
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226 my $url = "https://bitbucket.org/genomicepidemiology/$name.git";
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227
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228 if ( -r $name and not $force ) {
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229 msg("Won't overwrite existing $name (use --force)");
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230
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231 # exit(1);
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232 }
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233 else {
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234 msg("Nuking existing folder: $name");
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235 remove_tree("./$name");
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236 msg("Cloning $url to $name");
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237 system("git clone --quiet $url $name");
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238 }
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239
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240 my @seq;
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241 for my $fasta (<$name/*.fsa>) {
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242 push @seq, @{ load_fasta($fasta) };
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243 }
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244
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245 # >fliC_44444_AY250028_H52
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246 # FIXME - this is already in EcOH database!
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247 for my $seq (@seq) {
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248 my ( $id, $copy, $acc ) = $seq->{ID} =~ m/^(.*)_(\d+)_(\w+)$/;
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249
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250 #msg("serotypefinder: $1 $2 $3", $anno{$1});
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251 $seq->{ID} = "${id}_${copy}";
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252 $seq->{ACC} = $acc;
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253
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254 #$seq->{DESC} = $anno{$id} || '';
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255 }
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256
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257 return \@seq;
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258 }
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259
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260 #..............................................................................
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261 sub get_tag {
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262 my ( $f, $tag ) = @_;
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263 if ( $f->has_tag($tag) ) {
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264 my ($val) = $f->get_tag_values($tag);
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265 return $val;
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266 }
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267 return '';
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268 }
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269
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270 #..............................................................................
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271 sub get_ncbi {
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272 my $AFP =
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273 "https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest";
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274
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275 #my $src = "https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/data/latest/AMR_CDS";
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276 my $src = "$AFP/AMR_CDS.fa";
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277 my $name = "amr_cds.ffn";
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278
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279 #my $src2 = "https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/data/latest/ReferenceGeneCatalog.txt";
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280 my $src2 = "$AFP/ReferenceGeneCatalog.txt";
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281 my $name2 = "amr_cds.tsv";
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282
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283 if ( -r $name and -r $name2 and not $force ) {
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284 msg("Won't overwrite existing $name/$name2 (use --force)");
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285
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286 # exit(1);
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287 }
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288 else {
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289 download( $src, $name );
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290 download( $src2, $name2 );
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291 }
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292
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293 #1 allele
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294 #2 gene_family ble
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295 #3 whitelisted_taxa
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296 #4 product_name BLMA family bleomycin binding protein
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297 #5 scope core
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298 #6 type AMR
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299 #7 subtype AMR
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300 #8 class BLEOMYCIN
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301 #9 subclass BLEOMYCIN
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302 #10 refseq_protein_accession WP_063842967.1
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303 #11 refseq_nucleotide_accession NG_047554.1
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304 #12 curated_refseq_start No
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305 #13 genbank_protein_accession CAA02068.1
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306 #14 genbank_nucleotide_accession A31900.1
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307 #15 genbank_strand_orientation +
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308 #16 genbank_cds_start 6
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309 #17 genbank_cds_stop 374
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310 #18 pubmed_reference
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311 #19 blacklisted_taxa
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312 #20 db_version 2019-08-27.1
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313
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314 my $tsv = load_tabular( $name2, 10 ); # refseq_nucleotide_accession
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315 msg( "[$name2] Loaded", scalar keys %$tsv, "records" );
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316
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317 # https://github.com/ncbi/amr/wiki/AMRFinderPlus-database#amrprot
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318 # 0 1 2 3 4 5 6 7
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319 # >1000909371|WP_061158039.1|NG_050200|1|1|blaTEM-156|blaTEM|class_A_beta-lactamase_TEM-156 NG_050200:101-961
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320 my @seq;
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321 my $in = Bio::SeqIO->new( -file => $name, -format => "fasta" );
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322 while ( my $rec = $in->next_seq ) {
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323
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324 # parse ID
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325 my ( $gi, $pi, $acc, $fp, $fn, $gene, $fam, $prod ) = split m/\|/,
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326 $rec->id;
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327
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328 # skip fusion genes
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329 next unless $fp == 1 and $fn == 1;
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330
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331 # only keep true ARGs
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332 $acc .= ".1" unless $acc =~ m/\.\d+$/;
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333 my $t = $tsv->{$acc} or next;
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334 next unless ( $t->{scope} eq 'plus' || $t->{scope} eq 'core' );
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335
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336 # next unless $t->{type} eq 'VIRULENCE';
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337 # next unless $t->{subtype} eq 'VIRULENCE';
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338 # construct sequence record
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339 $prod =~ s/_/ /g;
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340 err("$pi: gene is empty") unless $gene;
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341 err("$pi: product is empty") unless $prod;
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342 my $s = {
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343 ID => $gene,
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344 ACC => $acc,
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345 DESC => $prod,
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346 SEQ => $rec->seq,
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347 ABX => [ split m'/', $t->{subclass} ]
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348 };
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349 push @seq, $s;
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350 msg( "[$name]", 0 + @seq, "|", $s->{ID}, "|", $s->{ACC}, "|",
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351 $s->{DESC} );
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352
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353 #msg(Dumper($s));
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354 msg( $s->{ID}, " is fusion $fp/$fn" ) if "$fp$fn" ne '11';
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355 }
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356 return \@seq;
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357 }
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358
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359 #..............................................................................
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360 sub get_plasmidfinder {
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361 my $name = "plasmidfinder";
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362 my $zip = "$name.zip";
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363
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364 # download("https://cge.cbs.dtu.dk/cge/download_data.php?folder=$name&filename=$zip&submit=$zip", $zip);
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365 download(
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366 "https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/HEAD.zip",
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367 $zip
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368 );
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369 system("unzip -j -u $zip");
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370
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371 my @seq;
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372 for my $fasta (<*.fsa>) {
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373 push @seq, @{ load_fasta($fasta) };
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374 }
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375
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376 for my $seq (@seq) {
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377 $seq->{DESC} = $seq->{ID}; # no desc, so use ORIGINAL ID as desc
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378 my ( $id, $acc ) =
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379 ( $seq->{ID} =~ m/^(.*)_(([A-Z]+|NC_)\d+(\.\d+)?)$/ );
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380 $id =~ s/_+$//g;
|
|
|
381 $seq->{ID} = $id || $seq->{ID};
|
|
|
382 $seq->{ACC} = $acc || '';
|
|
|
383 wrn( "Parsed empty ID:",
|
|
|
384 $seq->{DESC},
|
|
|
385 "=> id='$id' acc='$acc' seq=" . substr( $seq->{SEQ}, 0, 10 ) )
|
|
|
386 if not $id;
|
|
|
387 }
|
|
|
388
|
|
|
389 return \@seq;
|
|
|
390 }
|
|
|
391
|
|
|
392 #..............................................................................
|
|
|
393 sub get_megares {
|
|
|
394 my $zip = "megares.zip";
|
|
|
395 download( 'https://www.meglab.org/downloads/megares_v3.00.zip', $zip );
|
|
|
396 system("unzip -j -u $zip");
|
|
|
397 my $seqs = load_fasta( glob("megares_drugs_*.fasta") );
|
|
|
398 my @okseq;
|
|
|
399
|
|
|
400 # >MEG_372|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_MATE_efflux_pumps|ABEM
|
|
|
401 # >MEG_411|Multi-compound|Drug_and_biocide_resistance|Drug_and_biocide_RND_efflux_regulator|ACRR|RequiresSNPConfirmation
|
|
|
402 # >MEG_7860|Drugs|betalactams|Class_B_betalactamases|ZOG
|
|
|
403 # >MEG_7439|Drugs|Glycopeptides|VanI-type_resistance_protein|VANI
|
|
|
404 # >MEG_7245|Drugs|Tetracyclines|Tetracycline_resistance_MFS_efflux_pumps|TETY
|
|
|
405 # >MEG_9|Drugs|Aminoglycosides|Aminoglycoside-resistant_16S_ribosomal_subunit_protein|A16S|RequiresSNPConfirmation
|
|
|
406
|
|
|
407 for my $s (@$seqs) {
|
|
|
408 my ( $id, $type, $class, $mech, $group, $note ) = split m/\|/, $s->{ID};
|
|
|
409 if ($note) {
|
|
|
410
|
|
|
411 # "RequiresSNPConfirmation" is the common one; we can't do that
|
|
|
412 msg("Skipping $id due to: $note");
|
|
|
413 next;
|
|
|
414 }
|
|
|
415 $s->{ID} = $group;
|
|
|
416 $s->{ACC} = $id;
|
|
|
417 $s->{DESC} = join( ':', $type, $class, $mech, $group );
|
|
|
418 push @okseq, $s;
|
|
|
419 }
|
|
|
420 return [@okseq];
|
|
|
421
|
|
|
422 #return $seqs;
|
|
|
423 }
|
|
|
424
|
|
|
425 #..............................................................................
|
|
|
426 sub get_argannot {
|
|
|
427 my $fasta = 'arg-annot.fa';
|
|
|
428 download(
|
|
|
429 # 'http://www.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/1425/argannot-aa-v3-march2017_doc.fasta',
|
|
|
430 # 'http://www.mediterranee-infection.com/arkotheque/client/ihumed/_depot_arko/articles/691/argannot-nt_doc.fasta',
|
|
|
431 'https://www.mediterranee-infection.com/wp-content/uploads/2019/09/ARG-ANNOT_NT_V6_July2019.txt',
|
|
|
432 $fasta
|
|
|
433 );
|
|
|
434
|
|
|
435 # fix syntax errors in the FASTA file...
|
|
|
436 path($fasta)->edit( sub { s/\\//g; $_ } );
|
|
|
437
|
|
|
438 my $seqs = load_fasta($fasta);
|
|
|
439
|
|
|
440 # 0 1 2 3
|
|
|
441 # >(AGly)Aac2-Ie:NC_011896:3039059-3039607:549
|
|
|
442 for my $s (@$seqs) {
|
|
|
443 my @x = split m/:/, $s->{ID};
|
|
|
444 $s->{ID} = $x[0];
|
|
|
445 $s->{ACC} = $x[1] . ':' . $x[2];
|
|
|
446 $s->{DESC} = '';
|
|
|
447 }
|
|
|
448
|
|
|
449 return $seqs;
|
|
|
450 }
|
|
|
451
|
|
|
452 #..............................................................................
|
|
|
453 sub get_bacmet2 {
|
|
|
454 my $fasta = 'bacmet2.fa';
|
|
|
455 download(
|
|
|
456 'http://bacmet.biomedicine.gu.se/download/BacMet2_EXP_database.fasta',
|
|
|
457 $fasta );
|
|
|
458
|
|
|
459 # This is a PROTEIN file
|
|
|
460 my $seqs = load_fasta($fasta);
|
|
|
461
|
|
|
462 # 0 1 2 3 4 ^
|
|
|
463 # >BAC0098|ctpC|sp|P0A502|CTPC_MYCTU Probable manganese/zinc-exporting
|
|
|
464 for my $s (@$seqs) {
|
|
|
465 my @x = split m/\|/, $s->{ID};
|
|
|
466 $s->{ID} = $x[1] . '-' . $x[0];
|
|
|
467 $s->{ACC} = $x[2] . ':' . $x[3];
|
|
|
468 }
|
|
|
469
|
|
|
470 return $seqs;
|
|
|
471 }
|
|
|
472
|
|
|
473 #..............................................................................
|
|
|
474 sub get_card {
|
|
|
475
|
|
|
476 # https://github.com/tseemann/abricate/issues/25
|
|
|
477 my $tarball = 'card.tar.bz2';
|
|
|
478 download(
|
|
|
479 #'https://card.mcmaster.ca/download/0/broadstreet-v2.0.2.tar.gz',
|
|
|
480 'https://card.mcmaster.ca/latest/data',
|
|
|
481
|
|
|
482 #'https://card.mcmaster.ca/latest/data/card-data.tar.bz2',
|
|
|
483 $tarball # yes, it's really BZ2 not GZ ...
|
|
|
484 );
|
|
|
485
|
|
|
486 # my $fasta = "./nucleotide_fasta_protein_homolog_model.fasta";
|
|
|
487 my $jsonfile = "./card.json";
|
|
|
488 system( "tar", "xf", $tarball, $jsonfile ) == 0
|
|
|
489 or err("Problem with tar xf $tarball $jsonfile");
|
|
|
490 -r $jsonfile or err("Could not extract $jsonfile from $tarball");
|
|
|
491
|
|
|
492 # JSON
|
|
|
493 my $json = path($jsonfile)->slurp_utf8;
|
|
|
494 my $card = from_json( $json, { latin1 => 1 } );
|
|
|
495 my @seq;
|
|
|
496 for my $g ( values %$card ) {
|
|
|
497 next unless ref($g) eq 'HASH';
|
|
|
498
|
|
|
499 # msg(Dumper($g));
|
|
|
500 next
|
|
|
501 unless $g->{model_type} eq
|
|
|
502 "protein homolog model"; # only 'acquired' genes
|
|
|
503 my $id = $g->{model_name};
|
|
|
504 err("$id has {model_param}{snp}") if exists $g->{model_param}{snp};
|
|
|
505
|
|
|
506 # msg("CARD: $id");
|
|
|
507 # print STDERR Dumper($g);
|
|
|
508 my $dna = $g->{model_sequences}{sequence}
|
|
|
509 or err("$id: no {model_sequences}{sequence} found");
|
|
|
510 my ($key) = sort keys %$dna; # first key
|
|
|
511 $dna = $dna->{$key} or err("$id: invalid key '$key'");
|
|
|
512 $dna = $dna->{dna_sequence} or err("$id: no dna_sequence");
|
|
|
513
|
|
|
514 # msg(Dumper($dna)) if $id eq 'OXA-25';
|
|
|
515
|
|
|
516 # ARO_category => {
|
|
|
517 # 'category_aro_name' => 'cephalosporin',
|
|
|
518 # 'category_aro_class_name' => 'Drug Class',
|
|
|
519 my $is_amr_gene = 0;
|
|
|
520 my @abx;
|
|
|
521 for my $key ( keys $g->{ARO_category}->%* ) {
|
|
|
522 my $c = $g->{ARO_category}{$key};
|
|
|
523 if ( $c->{category_aro_class_name} eq 'Drug Class' ) {
|
|
|
524 my $abx = $c->{category_aro_name};
|
|
|
525 $abx =~ s/ antibiotic//;
|
|
|
526 $abx =~ s/\s/_/g;
|
|
|
527 push @abx, $abx;
|
|
|
528 }
|
|
|
529 if ( $c->{category_aro_class_name} eq 'AMR Gene Family' ) {
|
|
|
530 $is_amr_gene++;
|
|
|
531 }
|
|
|
532 }
|
|
|
533
|
|
|
534 #err("CARD | $id | ", Dumper($g->{ARO_category}) ) unless $is_amr_gene;
|
|
|
535 #msg("ABX=$_") for @abx;
|
|
|
536
|
|
|
537 # put coordinates into normal form
|
|
|
538 my ( $start, $stop ) =
|
|
|
539 $dna->{strand} eq '-'
|
|
|
540 ? ( $dna->{fmax}, $dna->{fmin} )
|
|
|
541 : ( $dna->{fmin}, $dna->{fmax} );
|
|
|
542
|
|
|
543 $id =~ s/\s+/_/g;
|
|
|
544 push @seq,
|
|
|
545 {
|
|
|
546 ID => $id,
|
|
|
547 ACC => $dna->{accession} . ":$start-$stop",
|
|
|
548 DESC => ( $g->{ARO_description} || $g->{ARO_accession} ),
|
|
|
549 SEQ => $dna->{sequence},
|
|
|
550 ABX => [@abx],
|
|
|
551 };
|
|
|
552
|
|
|
553 # msg(Dumper($seq[-1]));
|
|
|
554 }
|
|
|
555
|
|
|
556 return \@seq;
|
|
|
557 }
|
|
|
558
|
|
|
559 #..............................................................................
|
|
|
560 sub get_victors {
|
|
|
561
|
|
|
562 # the CDS data is in .ffn and has source GI and coords
|
|
|
563 # the PROT data is in .faa and has the protein ref and /product
|
|
|
564
|
|
|
565 #>gi|115534241:2616-3152 Campylobacter jejuni plasmid pCJ01, complete sequence
|
|
|
566 download( 'http://www.phidias.us/victors/downloads/gen_downloads.php',
|
|
|
567 'victors.ffn' );
|
|
|
568
|
|
|
569 #>gi|115534244|ref|YP_783826.1| hypothetical protein pCJ01p4 [Campylobacter jejuni]
|
|
|
570 download(
|
|
|
571 'http://www.phidias.us/victors/downloads/gen_downloads_protein.php',
|
|
|
572 'victors.faa' );
|
|
|
573
|
|
|
574 my %gi;
|
|
|
575 open my $FAA, '<', 'victors.faa';
|
|
|
576 while (<$FAA>) {
|
|
|
577
|
|
|
578 #>gi|115534244|ref|YP_783826.1| hypothetical protein pCJ01p4 [Campylobacter jejuni]
|
|
|
579 next unless m"^>gi.(\d+).ref.([^|]+). ([^[]+)";
|
|
|
580 $gi{$1}{ACC} = $2;
|
|
|
581 $gi{$1}{DESC} = $3;
|
|
|
582 }
|
|
|
583
|
|
|
584 my $seqs = load_fasta("victors.ffn");
|
|
|
585
|
|
|
586 for my $s (@$seqs) {
|
|
|
587
|
|
|
588 #>gi|115534241:2616-3152 Campylobacter jejuni plasmid pCJ01, complete sequence
|
|
|
589 $s->{ID} =~ m/gi.(\d+):(\d+)-(\d+)/;
|
|
|
590 $s->{ACC} = $gi{$1}{ACC} || "gi|$1:$2-$3";
|
|
|
591 $s->{DESC} =~ $gi{$1}{DESC} || 'hypothetical protein';
|
|
|
592 }
|
|
|
593
|
|
|
594 # print Dumper($seqs); exit;
|
|
|
595
|
|
|
596 return $seqs;
|
|
|
597 }
|
|
|
598
|
|
|
599 #..............................................................................
|
|
|
600 sub get_vfdb {
|
|
|
601 download( 'http://www.mgc.ac.cn/VFs/Down/VFDB_setA_nt.fas.gz',
|
|
|
602 'vfdb.fa.gz' );
|
|
|
603 system("gzip -f -d -c vfdb.fa.gz > vfdb.fa");
|
|
|
604 my $seqs = load_fasta("vfdb.fa");
|
|
|
605
|
|
|
606 # >VFG000676(gb|AAD32411) (lef) anthrax toxin lethal factor precursor [Anthrax toxin (VF0142)] [Bacillus anthracis str. Sterne]
|
|
|
607 for my $s (@$seqs) {
|
|
|
608
|
|
|
609 # https://github.com/tseemann/abricate/issues/64#issuecomment-421895159 by @VGalata
|
|
|
610 $s->{ID} =~ m/^(\w+)\(\w+\|(\w+)(\.\d+)?\)$/; #
|
|
|
611 #$s->{ID} =~ m/^(\w+)\(\w+\|(\w+)\)$/;
|
|
|
612 $s->{ACC} = $2 if $2;
|
|
|
613 $s->{DESC} =~ m/^\((.*?)\)/;
|
|
|
614 $s->{ID} = $1 if $1;
|
|
|
615
|
|
|
616 # print STDERR Dumper($s); exit;
|
|
|
617 }
|
|
|
618
|
|
|
619 return $seqs;
|
|
|
620 }
|
|
|
621
|
|
|
622 #..............................................................................
|
|
|
623 sub get_ncbibetalactamase {
|
|
|
624 my $fasta = "ncbi.fa";
|
|
|
625 download(
|
|
|
626 'ftp://ftp.ncbi.nlm.nih.gov/pathogen/betalactamases/Allele-dna.fa',
|
|
|
627 $fasta );
|
|
|
628 my $tab = "ncbi.tab";
|
|
|
629 download( 'ftp://ftp.ncbi.nlm.nih.gov/pathogen/betalactamases/Allele.tab',
|
|
|
630 $tab );
|
|
|
631
|
|
|
632 # >ACD12694.1 EU650653.1:1-1173
|
|
|
633 my $seqs = load_fasta($fasta);
|
|
|
634
|
|
|
635 # ACC-1 ACD12694.1 EU650653.1 blaACC-1 1 1173 + cephalosporin-hydrolyzing class C beta-lactamase ACC-1
|
|
|
636 my %anno;
|
|
|
637 my @anno = grep { !m/^#/ } path($tab)->lines( { chomp => 1 } );
|
|
|
638 msg( "Read", 0 + @anno, "annotations" );
|
|
|
639 foreach (@anno) {
|
|
|
640 my ( $name, $id, $acc, $gene, $begin, $end, undef, $product ) =
|
|
|
641 split m/\t/;
|
|
|
642 $anno{$id} = {
|
|
|
643 ID => $gene,
|
|
|
644 DESC => $product,
|
|
|
645 ACC => "$acc:$begin-$end",
|
|
|
646 };
|
|
|
647 }
|
|
|
648
|
|
|
649 # print Dumper(\%anno);
|
|
|
650
|
|
|
651 for my $s (@$seqs) {
|
|
|
652 my $id = $s->{ID};
|
|
|
653 next unless exists $anno{$id};
|
|
|
654 $s->{ID} = $anno{$id}{ID};
|
|
|
655 $s->{ACC} = $anno{$id}{ACC};
|
|
|
656 $s->{DESC} = $anno{$id}{DESC};
|
|
|
657 }
|
|
|
658
|
|
|
659 # print Dumper($seqs);
|
|
|
660
|
|
|
661 return $seqs;
|
|
|
662 }
|
|
|
663
|
|
|
664 #..............................................................................
|
|
|
665 sub get_ecoh {
|
|
|
666 my $fasta = "EcOH.fa";
|
|
|
667 download(
|
|
|
668 'https://raw.githubusercontent.com/katholt/srst2/master/data/EcOH.fasta',
|
|
|
669 $fasta
|
|
|
670 );
|
|
|
671
|
|
|
672 # https://github.com/katholt/srst2#generating-srst2-compatible-clustered-database-from-raw-sequences
|
|
|
673 # [clusterID]__[gene]__[allele]__[seqID] [other stuff]
|
|
|
674 # >1__fliC__fliC-H1__1 AB028471.1;flagellin;H1
|
|
|
675 # >8__wzx__wzx-O41__246 AB811617.1;O antigen flippase;O41
|
|
|
676 # >9__wzy__wzy-OgN31__597 LC125932.1;O antigen polyermase;OgN31
|
|
|
677 my $seqs = load_fasta($fasta);
|
|
|
678
|
|
|
679 for my $s (@$seqs) {
|
|
|
680 my @id = split m/__/, $s->{ID};
|
|
|
681 my @desc = split m';', $s->{DESC};
|
|
|
682 $s->{ID} = $id[2];
|
|
|
683 $s->{ACC} = shift(@desc);
|
|
|
684 $s->{DESC} = join( ' ', @desc );
|
|
|
685 }
|
|
|
686
|
|
|
687 # print Dumper($seqs);
|
|
|
688 return $seqs;
|
|
|
689 }
|
|
|
690
|
|
|
691 #..............................................................................
|
|
|
692 sub get_ecoli_vf {
|
|
|
693 my $fasta = "ecoli_vf.ffn";
|
|
|
694 download(
|
|
|
695 'https://github.com/phac-nml/ecoli_vf/raw/master/data/repaired_ecoli_vfs_shortnames.ffn',
|
|
|
696 $fasta
|
|
|
697 );
|
|
|
698 my $seqs = load_fasta($fasta);
|
|
|
699
|
|
|
700 # >VFG000748(gi:2865308) (espF) EspF [EspF (VF0182)] [Escherichia coli O127:H6 str. E2348/69]
|
|
|
701 # >VFG000749(gi:6009379) (bfpA) Bundlin [BFP (VF0174)] [Escherichia coli B171]
|
|
|
702 # >SPG000142 (cvac) Escherichia coli cvi cvaC operon. [X57525 434-745]
|
|
|
703 # >SPG000143 (iss2) Escherichia coli Iss (iss) gene, complete cds. [AF042279 292-600]
|
|
|
704
|
|
|
705 for my $s (@$seqs) {
|
|
|
706
|
|
|
707 #print STDERR Dumper("IN", $s);
|
|
|
708 $s->{ID} =~ m/ ^ (\w+) (?: \( (.*?) \) )? $ /x
|
|
|
709 or die "Can't parse $fasta at " . Dumper($s);
|
|
|
710 $s->{ID} = $1 if $1;
|
|
|
711 $s->{ACC} = $2 || $1;
|
|
|
712 $s->{DESC} =~ s/\s\[.*?\]$//g; # remove strain name
|
|
|
713 $s->{DESC} =~ m/^(?:\((.*?)\)\s+)?(.*?)$/;
|
|
|
714 $s->{ID} = $1 if $1;
|
|
|
715 $s->{DESC} = $2;
|
|
|
716
|
|
|
717 #print STDERR Dumper("OUT", $s);
|
|
|
718 #print STDERR "="x60, "\n";
|
|
|
719 }
|
|
|
720
|
|
|
721 # print Dumper($seqs);
|
|
|
722 return $seqs;
|
|
|
723 }
|
|
|
724
|
|
|
725 #..............................................................................
|
|
|
726 sub is_full_gene {
|
|
|
727 my ($s) = @_;
|
|
|
728 my $has_ambig = 0;
|
|
|
729
|
|
|
730 my $id = $s->{ID};
|
|
|
731 my $L = length( $s->{SEQ} );
|
|
|
732 if ( $L % 3 != 0 ) {
|
|
|
733 wrn("$id - length $L bp is not multiple of 3");
|
|
|
734 return;
|
|
|
735 }
|
|
|
736 if ( $s->{SEQ} !~ m/^[AGCT]+$/ ) {
|
|
|
737 wrn("$id - has non-AGTC bases");
|
|
|
738 return;
|
|
|
739 }
|
|
|
740
|
|
|
741 my $seq = Bio::Seq->new( -id => $s->{ID}, -seq => $s->{SEQ} );
|
|
|
742
|
|
|
743 my $aa = $seq->translate->seq;
|
|
|
744
|
|
|
745 if ( $aa =~ m/\*./ ) {
|
|
|
746 wrn("$id - has internal stop codons, trying revcom");
|
|
|
747 $aa = $seq->revcom->translate->seq;
|
|
|
748 if ( $aa =~ m/\*./ ) {
|
|
|
749 wrn("$id - revcom has internal stop codons too");
|
|
|
750 return;
|
|
|
751 }
|
|
|
752 else {
|
|
|
753 msg("$id - revcom resolves problem, hooray!");
|
|
|
754 $s->{SEQ} = $seq->revcom->seq;
|
|
|
755 }
|
|
|
756 }
|
|
|
757
|
|
|
758 return $L;
|
|
|
759 }
|
|
|
760
|
|
|
761 #..............................................................................
|
|
|
762 sub dedupe_seq {
|
|
|
763 my ($seq) = @_;
|
|
|
764 my %seen;
|
|
|
765 my $good = [];
|
|
|
766 for my $s (@$seq) {
|
|
|
767 if ( $seen{ $s->{SEQ} } ) {
|
|
|
768 wrn( "duplicate", length( $s->{SEQ} ),
|
|
|
769 "bp sequence:", $s->{ID}, '~', $seen{ $s->{SEQ} } );
|
|
|
770 }
|
|
|
771 else {
|
|
|
772 push @$good, $s;
|
|
|
773 }
|
|
|
774 $seen{ $s->{SEQ} } .= ' ' . $s->{ID};
|
|
|
775 }
|
|
|
776 msg( "dedupe_seq: read", scalar(@$seq), "/ kept", scalar(@$good) );
|
|
|
777 return $good;
|
|
|
778 }
|
|
|
779
|
|
|
780 #..............................................................................
|
|
|
781 sub load_tabular {
|
|
|
782 my ( $fname, $keycol, $sep ) = @_;
|
|
|
783 $keycol //= 0;
|
|
|
784 $sep //= "\t";
|
|
|
785 my $hash = {};
|
|
|
786 my @hdr;
|
|
|
787 my $row = 0;
|
|
|
788 open my $TSV, '<', $fname or err("Can't read TSV file: $fname");
|
|
|
789 while (<$TSV>) {
|
|
|
790 chomp;
|
|
|
791 my @col = split m/$sep/;
|
|
|
792 $row++;
|
|
|
793 if (@hdr) {
|
|
|
794 @hdr == @col or err("Header and row $row differ in column count");
|
|
|
795
|
|
|
796 #my $key = $col[$keycol] or wrn("Empty key column $keycol: $_");
|
|
|
797 #exists{$hash->{$col[$key}} and wrn("WARNING: dupe key $key at row: $_");
|
|
|
798 my $key = $col[$keycol];
|
|
|
799 $hash->{$key} ||=
|
|
|
800 { map { ( $hdr[$_] => $col[$_] ) } ( 0 .. $#hdr ) };
|
|
|
801 }
|
|
|
802 else {
|
|
|
803 @hdr = @col;
|
|
|
804 }
|
|
|
805 }
|
|
|
806 close $TSV;
|
|
|
807 return $hash;
|
|
|
808 }
|
|
|
809
|
|
|
810 #..............................................................................
|
|
|
811 sub load_fasta {
|
|
|
812 my ($fasta) = @_;
|
|
|
813 my %seen;
|
|
|
814 my $list;
|
|
|
815 my $dbtype = 'unknown';
|
|
|
816 msg("load_fasta: $fasta");
|
|
|
817 my $in = Bio::SeqIO->new( -file => $fasta, -format => 'fasta' );
|
|
|
818 while ( my $seq = $in->next_seq ) {
|
|
|
819 my $id = $seq->id or err("Empty ID in $fasta");
|
|
|
820 if ( $seen{$id} ) {
|
|
|
821 wrn("Duplicate ID '$id' in $fasta");
|
|
|
822 $id = $id . '_dupe';
|
|
|
823 }
|
|
|
824 $seen{$id}++;
|
|
|
825 my $s = uc( $seq->seq );
|
|
|
826 $dbtype = $seq->alphabet eq 'dna' ? 'nucl' : 'prot';
|
|
|
827 $dbtype eq 'nucl' ? $s =~ s/[^AGTC]/N/g : $s =~ s/[^A-Z]/X/g;
|
|
|
828 push @$list,
|
|
|
829 {
|
|
|
830 ID => $id,
|
|
|
831 ACC => '',
|
|
|
832 DESC => $seq->desc,
|
|
|
833 SEQ => $s,
|
|
|
834 TYPE => $dbtype,
|
|
|
835 };
|
|
|
836 }
|
|
|
837 msg( "load_fasta: read", scalar(@$list), "$dbtype sequences" );
|
|
|
838 return $list;
|
|
|
839 }
|
|
|
840
|
|
|
841 #..............................................................................
|
|
|
842 sub save_fasta {
|
|
|
843 my ( $fasta, $seq ) = @_;
|
|
|
844 msg("save_fasta: $fasta");
|
|
|
845 my %seen;
|
|
|
846 my $out = Bio::SeqIO->new( -file => ">$fasta", -format => 'fasta' );
|
|
|
847 for my $s (@$seq) {
|
|
|
848 $seen{ $s->{ID} }++;
|
|
|
849 my $freq = $seen{ $s->{ID} };
|
|
|
850
|
|
|
851 #wrn("seen $s->{ID} now $freq times") if $freq > 1;
|
|
|
852 # print Dumper($s);
|
|
|
853 my $ABX =
|
|
|
854 defined( $s->{ABX} ) ? join( $ABX_SEP, sort @{ $s->{ABX} } ) : '';
|
|
|
855 $ABX =~ s/\s+/_/g; # remove spaces!
|
|
|
856 my $obj = Bio::Seq->new(
|
|
|
857 -id => join( '~~~', $db, $s->{ID}, $s->{ACC}, $ABX ),
|
|
|
858 -desc => ( $s->{DESC} || $s->{ID} ),
|
|
|
859 -seq => $s->{SEQ},
|
|
|
860 );
|
|
|
861
|
|
|
862 # $obj->desc( hash_encode($s) );
|
|
|
863 $out->write_seq($obj);
|
|
|
864
|
|
|
865 # $seen{ $s->{ID} }++;
|
|
|
866 }
|
|
|
867 msg( "save_fasta: wrote", scalar(@$seq), "sequences" );
|
|
|
868 }
|
|
|
869
|
|
|
870 #----------------------------------------------------------------------
|
|
|
871 sub msg {
|
|
|
872 print STDERR "@_\n";
|
|
|
873 }
|
|
|
874
|
|
|
875 #----------------------------------------------------------------------
|
|
|
876 sub wrn {
|
|
|
877 msg( "WARNING:", @_ ) if $debug;
|
|
|
878 }
|
|
|
879
|
|
|
880 #----------------------------------------------------------------------
|
|
|
881 sub err {
|
|
|
882 msg( "ERROR:", @_ );
|
|
|
883 exit(1);
|
|
|
884 }
|
|
|
885
|
|
|
886 #----------------------------------------------------------------------
|
|
|
887 # Option setting routines
|
|
|
888
|
|
|
889 sub setOptions {
|
|
|
890 use Getopt::Long;
|
|
|
891
|
|
|
892 @Options = (
|
|
|
893 { OPT => "help", VAR => \&usage, DESC => "This help" },
|
|
|
894 {
|
|
|
895 OPT => "debug!",
|
|
|
896 VAR => \$debug,
|
|
|
897 DEFAULT => 0,
|
|
|
898 DESC => "Verbose debug output"
|
|
|
899 },
|
|
|
900 {
|
|
|
901 OPT => "dbdir=s",
|
|
|
902 VAR => \$outdir,
|
|
|
903 DEFAULT => abs_path("$FindBin::RealBin/../db"),
|
|
|
904 DESC => "Parent folder"
|
|
|
905 },
|
|
|
906 {
|
|
|
907 OPT => "db=s",
|
|
|
908 VAR => \$db,
|
|
|
909 DEFAULT => "",
|
|
|
910 DESC => "Choices: $DATABASES"
|
|
|
911 },
|
|
|
912 {
|
|
|
913 OPT => "force!",
|
|
|
914 VAR => \$force,
|
|
|
915 DEFAULT => 0,
|
|
|
916 DESC => "Force download even if exists"
|
|
|
917 },
|
|
|
918 );
|
|
|
919
|
|
|
920 &GetOptions( map { $_->{OPT}, $_->{VAR} } @Options ) || usage(1);
|
|
|
921
|
|
|
922 # Now setup default values.
|
|
|
923 foreach (@Options) {
|
|
|
924 if ( defined( $_->{DEFAULT} ) && !defined( ${ $_->{VAR} } ) ) {
|
|
|
925 ${ $_->{VAR} } = $_->{DEFAULT};
|
|
|
926 }
|
|
|
927 }
|
|
|
928 }
|
|
|
929
|
|
|
930 sub usage {
|
|
|
931 my ($exitcode) = @_;
|
|
|
932 $exitcode = 0 if $exitcode eq 'help'; # what gets passed by getopt func ref
|
|
|
933 $exitcode ||= 0;
|
|
|
934 select STDERR if $exitcode; # write to STDERR if exitcode is error
|
|
|
935
|
|
|
936 print "SYNOPIS\n Download databases for abricate to use\n";
|
|
|
937 print "USAGE\n $EXE [options] --db DATABASE\n";
|
|
|
938 print "OPTIONS\n";
|
|
|
939 foreach (@Options) {
|
|
|
940 printf " --%-13s %s%s.\n", $_->{OPT}, $_->{DESC},
|
|
|
941 defined( $_->{DEFAULT} ) ? " (default '$_->{DEFAULT}')" : "";
|
|
|
942 }
|
|
|
943 exit($exitcode);
|
|
|
944 }
|
|
|
945
|
|
|
946 #----------------------------------------------------------------------
|
|
|
947
|
