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1 package hmdb_api ;
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2
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3 use strict;
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4 use warnings ;
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5 use Exporter ;
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6 use Carp ;
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7
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8 use Data::Dumper ;
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9 use XML::Twig ;
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10
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11 use csv ;
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12
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13 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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14
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15 our $VERSION = "1.0";
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16 our @ISA = qw(Exporter);
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17 our @EXPORT = qw( getMetaboliteFeatures cowmetdb_handle cowmetdb_hash cowmetdb_hash_to_inhouse_format buildMetabolitesArray setMetaboliteAcurrateMzToModesMz);
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18 our %EXPORT_TAGS = ( ALL => [qw( getMetaboliteFeatures cowmetdb_handle cowmetdb_hash cowmetdb_hash_to_inhouse_format buildMetabolitesArray setMetaboliteAcurrateMzToModesMz)] );
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19
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20 =head1 NAME
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21
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22 My::Module - An example module
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23
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24 =head1 SYNOPSIS
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25
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26 use My::Module;
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27 my $object = My::Module->new();
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28 print $object->as_string;
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29
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30 =head1 DESCRIPTION
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31
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32 This module does not really exist, it
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33 was made for the sole purpose of
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34 demonstrating how POD works.
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35
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36 =head1 METHODS
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37
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38 Methods are :
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39
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40 =head2 METHOD new
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41
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42 ## Description : new
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43 ## Input : $self
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44 ## Ouput : bless $self ;
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45 ## Usage : new() ;
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46
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47 =cut
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48
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49 sub new {
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50 ## Variables
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51 my $self={};
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52 bless($self) ;
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53 return $self ;
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54 }
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55 ### END of SUB
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56
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57
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58 =head2 METHOD cowmetdb_handle
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59
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60 ## Description : open a flat file and push the contains in memory - compute entries number.
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61 ## Input : $flat
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62 ## Output : $handler, $entries
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63 ## Usage : my ( $handler ) = cowmetdb_handle( $flat ) ;
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64
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65 =cut
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66 ## START of SUB
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67 sub cowmetdb_handle {
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68 ## Retrieve Values
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69 my $self = shift ;
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70 my ( $flat ) = @_ ;
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71
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72 my @handle = () ;
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73 my $entries = 0 ;
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74 my ( $begin, $end ) = ( 0, 0 ) ;
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75
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76 if ( -e $flat ) {
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77 open(FILE, "<$flat") or die "Cant' read the file $flat\n" ;
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78 while (my $line = <FILE>){
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79 chomp $line ;
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80 push(@handle, $line) ;
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81 if ( $line =~ /^#BEGIN_METABOCARD/ ) { $begin = 1 ; }
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82 elsif ( ( $line =~ /^#END_METABOCARD/ ) and ( $begin == 1 ) ){ $end = 1 ; }
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83 ## count entries
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84 if ( ( $end == 1 ) and ( $begin == 1 ) ){ $entries++ ; ( $begin, $end ) = ( 0, 0 ) ; }
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85 }
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86 close(FILE) ;
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87 }
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88 else {
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89 croak "Can't find the source file $flat\n" ;
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90 }
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91
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92 return(\@handle, \$entries) ;
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93 }
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94 ## END of SUB
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95
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96 =head2 METHOD cowmetdb_hash
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97
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98 ## Description : work on a hmdb flat text handler and field data (selected fields), build a hash for each found entry
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99 ## Input : $handler
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100 ## Output : $entries
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101 ## Usage : my ( $entries ) = hmdb_hash( $handler ) ;
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102
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103 =cut
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104 ## START of SUB
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105 sub cowmetdb_hash {
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106 ## Retrieve Values
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107 my $self = shift ;
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108 my ( $handle ) = @_ ;
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109
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110 my @entries = () ;
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111 my %entry = () ;
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112 my $pos = 0 ;
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113
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114 if ( ( defined $handle ) ) {
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115 foreach my $data ( @$handle ) {
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116
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117 if( $data =~ /^#BEGIN_METABOCARD/ ) { %entry = () ; }
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118 elsif( $data =~ /^#END_METABOCARD/ ) { my %temp = %entry ; push (@entries, \%temp) ; }
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119 elsif( $data =~ /^# name:/ ) { $entry{'COMMON_NAME'} = $handle->[$pos+1] ; }
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120 elsif( $data =~ /^# iupac:/ ) { $entry{'IUPAC'} = $handle->[$pos+1] ; }
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121 elsif( $data =~ /^# kegg_compound_id:/ ) { $entry{'KEGG_ID'} = $handle->[$pos+1] ; }
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122 elsif( $data =~ /^# chemical_formula:/ ) { $entry{'FORMULA'} = $handle->[$pos+1] ; }
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123 elsif( $data =~ /^# taxonomy_super_class:/ ) { $entry{'TAXONOMY'} = $handle->[$pos+1] ; }
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124 elsif( $data =~ /^# cas_number:/ ) { $entry{'CAS'} = $handle->[$pos+1] ; }
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125 elsif( $data =~ /^# biofluid_location:/ ) { $entry{'LOCATION'} = $handle->[$pos+1] ; }
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126 elsif( $data =~ /^# inchi_identifier:/ ) { $entry{'INCHI'} = $handle->[$pos+1] ; }
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127 elsif( $data =~ /^# weight_average:/ ) { $entry{'MZ_AVERAGE'} = $handle->[$pos+1] ; }
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128 elsif( $data =~ /^# weight_mono:/ ) { $entry{'MZ_MONO'} = $handle->[$pos+1] ; }
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129 elsif( $data =~ /^# biocyc_id:/ ) { $entry{'BIOCYC_ID'} = $handle->[$pos+1] ; }
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130 elsif( $data =~ /^# hmdb_id:/ ) { $entry{'HMDB_ID'} = $handle->[$pos+1] ; }
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131
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132 $pos++ ;
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133 }
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134 }
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135 else {
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136 croak "Handle is not defined : parsing step impossible\n" ;
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137 }
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138
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139 return(\@entries) ;
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140 }
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141 ## END of SUB
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142
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143
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144
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145 =head2 METHOD getMetaboliteFeatures
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146
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147 ## Description : get metabolites features from a xml file
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148 ## Input : $xmlFile,
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149 ## Output : $metabolites
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150 ## Usage : $metabolites = getMetaboliteFeatures($xmlFile) ;
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151
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152 =cut
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153 sub getMetaboliteFeatures {
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154 ## Retrieve Values
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155 my $self = shift ;
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156 my ( $xmlFile ) = @_ ;
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157
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158 my %metabolites = () ;
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159 my $twig = undef ;
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160 my $id = undef ;
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161
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162 if (-e $xmlFile) {
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163
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164 $twig = XML::Twig->nparse_ppe(
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165
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166 twig_handlers => {
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167 'metabolite/accession' => sub {$id = $_ -> text_only ; $metabolites{$id} = undef ; } ,
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168 # metabolite name
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169 'metabolite/name' => sub { $metabolites{$id}{'metabolite_name'} = $_ -> text_only ; } ,
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170 # metabolite chemical_formula
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171 'metabolite/chemical_formula' => sub { $metabolites{$id}{'chemical_formula'} = $_ -> text_only ; } ,
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172 # metabolite monisotopic_molecular_weight
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173 'metabolite/monisotopic_molecular_weight' => sub { $metabolites{$id}{'monisotopic_molecular_weight'} = $_ -> text_only ; } , ## general case
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174 'metabolite/monisotopic_moleculate_weight' => sub { $metabolites{$id}{'monisotopic_molecular_weight'} = $_ -> text_only ; } , ##
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175 # metabolite inchikey
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176 'metabolite/inchikey' => sub { $metabolites{$id}{'inchikey'} = $_ -> text_only ; } ,
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177 },
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178 pretty_print => 'indented',
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179 error_context => 1, $xmlFile
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180 );
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181
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182 # $twig->print;
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183 $twig->purge ;
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184 }
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185
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186 ## get number of entries:
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187 my $X = keys %metabolites ;
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188
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189 return (\%metabolites, $X) ;
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190
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191
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192 }
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193 ### END of SUB
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194
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195 =head2 METHOD setMetaboliteAcurrateMzToModesMz
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196
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197 ## Description : set M+H and M-H masses from a metabolite (M) accurate mass
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198 ## Input : $metabolites, $proton_mass, $electron_mass
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199 ## Output : $mzsMetabolites
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200 ## Usage : my ( $mzsMetabolites ) = setMetaboliteAcurrateMzToModesMz ( $metabolites, $proton_mass, $electron_mass ) ;
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201
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202 =cut
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203 ## START of SUB
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204 sub setMetaboliteAcurrateMzToModesMz {
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205 ## Retrieve Values
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206 my $self = shift ;
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207 my ( $format, $metabolites, $proton_mass, $electron_mass, $charge ) = @_;
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208
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209 if ($format eq 'XML') {
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210 foreach my $id (sort keys %{$metabolites}) {
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211 if ( $metabolites->{$id}{'monisotopic_molecular_weight'} ) {
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212 my $tmp_mass = $metabolites->{$id}{'monisotopic_molecular_weight'} ;
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213 $metabolites->{$id}{'[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ;
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214 $metabolites->{$id}{'[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ;
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215 }
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216 else {
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217 warn "No monisotopic_molecular_weight field exists with metabolite $id\n " ;
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218 }
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219 }
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220 }
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221 elsif ( ($format eq 'CARD') ) {
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222 foreach my $entry (@$metabolites) {
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223 if ( $entry->{'MZ_MONO'} ) {
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224 my $tmp_mass = $entry->{'MZ_MONO'} ;
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225 $entry->{'MZ_[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ;
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226 $entry->{'MZ_[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ;
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227 }
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228 else {
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229 warn "No MZ_MONO field exists with metabolite $entry->{'HMDB_ID'}\n " ;
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230 }
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231 }
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232 }
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233
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234
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235 return ($metabolites) ;
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236 }
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237 ### END of SUB
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238
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239 =head2 METHOD buildMetabolitesArray
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240
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241 ## Description : build a metabolite list from xml extraction
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242 ## Input : $metabolites, $headers
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243 ## Output : $metabolitesSorted
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244 ## Usage : my ( $metabolitesSorted ) = buildMetabolitesArray ( $metabolites, $headers ) ;
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245
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246 =cut
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247 ## START of SUB
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248 sub buildMetabolitesArray {
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249 ## Retrieve Values
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250 my $self = shift ;
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251 my ( $metabolites, $headers ) = @_;
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252 my ( @metabolitesSorted ) = ( () ) ;
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253
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254 ## header format is ['HMDB_ID','MzBank', 'MetName', 'ChemFormula', 'INChIkey']
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255 if (defined $headers) {
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256 push ( @metabolitesSorted, $headers ) ;
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257 }
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258 else {
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259 push ( @metabolitesSorted, ['HMDB_ID','MzBank', '[M+H]+', '[M-H]-', 'MetName', 'ChemFormula', 'INChIkey'] ) ;
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260 }
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261
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262 foreach my $id (sort keys %{$metabolites}) {
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263 my @tmp = () ;
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264 push (@tmp, $id) ;
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265 push (@tmp, $metabolites->{$id}{'monisotopic_molecular_weight'}) ;
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266 push (@tmp, $metabolites->{$id}{'[M+H]+'}) ;
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267 push (@tmp, $metabolites->{$id}{'[M-H]-'}) ;
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268 push (@tmp, $metabolites->{$id}{'metabolite_name'}) ;
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269 push (@tmp, $metabolites->{$id}{'chemical_formula'}) ;
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270 push (@tmp, $metabolites->{$id}{'inchikey'}) ;
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271
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272 # merge
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273 push (@metabolitesSorted, \@tmp) ;
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274 }
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275
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276 return (\@metabolitesSorted) ;
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277 }
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278 ### END of SUB
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279
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280 =head2 METHOD cowmetdb_hash_to_inhouse_format
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281
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282 ## Description : adaptator from hash cowmetdb entry to inhouse format
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283 ## Input : $entries
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284 ## Output : $tsv_handler
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285 ## Usage : my ( $tsv_handler ) = cowmetdb_hash_to_inhouse_format( $entries ) ;
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286
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287 =cut
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288 ## START of SUB
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289 sub cowmetdb_hash_to_inhouse_format {
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290 ## Retrieve Values
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291 my $self = shift ;
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292 my ( $entries ) = @_ ;
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293
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294 my @fields_name = ('HMDB_ID', 'COMMON_NAME', 'CAS', 'FORMULA', 'MZ_MONO', 'MZ_AVERAGE', 'MZ_[M+H]+', 'MZ_[M-H]-', 'KEGG_ID', 'BIOCYC_ID', 'INCHI', 'LOCATION', 'TAXONOMY', 'IUPAC') ;
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295 my @tsv_handler = () ;
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296 push (@tsv_handler, \@fields_name) ; ## first line
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297
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298 foreach my $entry (@$entries) {
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299 my @tmp = ( $entry->{'HMDB_ID'}, $entry->{'COMMON_NAME'}, $entry->{'CAS'}, $entry->{'FORMULA'}, $entry->{'MZ_MONO'}, $entry->{'MZ_AVERAGE'}, $entry->{'MZ_[M+H]+'}, $entry->{'MZ_[M-H]-'}, $entry->{'KEGG_ID'}, $entry->{'BIOCYC_ID'},
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300 $entry->{'INCHI'}, $entry->{'LOCATION'}, $entry->{'TAXONOMY'}, $entry->{'IUPAC'} ) ;
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301 push (@tsv_handler, \@tmp) ; ## one entry by one line
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302 }
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303
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304 return(\@tsv_handler) ;
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305 }
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306 ## END of SUB
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307
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308
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309 1 ;
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310
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311
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312 __END__
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313
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314 =head1 SUPPORT
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315
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316 You can find documentation for this module with the perldoc command.
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317
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318 perldoc XXX.pm
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319
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320 =head1 Exports
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321
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322 =over 4
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323
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324 =item :ALL is ...
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325
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326 =back
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327
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328 =head1 AUTHOR
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329
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330 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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331
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332 =head1 LICENSE
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333
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334 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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335
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336 =head1 VERSION
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337
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338 version 1 : xx / xx / 201x
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339
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340 version 2 : ??
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341
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342 =cut |
