annotate wsdl_hmdb.pl @ 20:b5a1d5e43685 draft

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date Wed, 23 Jan 2019 07:49:34 -0500
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1 #!perl
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3 ## script : wsdl_hmdb.pl
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4 #=============================================================================
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5 # Included modules and versions
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6 #=============================================================================
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7 ## Perl modules
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8 use strict ;
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9 use warnings ;
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10 use Carp qw (cluck croak carp) ;
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11
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12 use Data::Dumper ;
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13 use Getopt::Long ;
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14 use POSIX ;
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15 use FindBin ; ## Permet de localisez le repertoire du script perl d'origine
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16
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17 ## Specific Modules (Home made...)
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18 use lib $FindBin::Bin ;
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19 my $binPath = $FindBin::Bin ;
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20 use lib::hmdb qw( :ALL ) ;
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21 ## PFEM Perl Modules
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22 use lib::conf qw( :ALL ) ;
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23 use lib::csv qw( :ALL ) ;
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24
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25 ## Initialized values
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26 my ( $help ) = undef ;
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27 my ( $mass ) = undef ;
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28 my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ;
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29 my $max_query = undef ;
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30 my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ;
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31 my $advancedFeatures = 0 ;
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32 my $VERBOSE = ( 3 ) ;
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34
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35 #=============================================================================
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36 # Manage EXCEPTIONS
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37 #=============================================================================
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38
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39 &GetOptions ( "h" => \$help, # HELP
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40 "mass:s" => \$mass, ## option : one masse
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41 "masses:s" => \$masses_file, ## option : path to the input
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42 "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file
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43 "nblineheader:i" => \$nbline_header, ## numbre of header line present in file
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44 "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file
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45 "delta:f" => \$delta,
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46 "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral)
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47 "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 )
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48 "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
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49 "output_html|v:s" => \$out_html, ## option : path to the results view (output2)
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50 "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
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51 "advancedFeatures:s"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only.
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52 "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool
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53 ) ;
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54
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55 #=============================================================================
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56 # EXCEPTIONS
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57 #=============================================================================
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58 $help and &help ;
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59
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60 #=============================================================================
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61 # MAIN SCRIPT
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62 #=============================================================================
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63
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64 print "* * * The hmdb client program is launched: * * *\n" if ($VERBOSE>1) ;
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65
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66 ## -------------- Conf file ------------------------ :
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67 my ( $CONF ) = ( undef ) ;
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68 foreach my $conf ( <$binPath/*.cfg> ) {
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69 my $oConf = lib::conf::new() ;
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70 $CONF = $oConf->as_conf($conf) ;
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71 }
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72
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73 ## -------------- HTML template file ------------------------ :
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74 foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; }
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75
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76 if (!defined $max_query) {
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77 $max_query = $CONF->{'HMDB_MAX_QUERY'} ;
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78 }
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79
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80
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81 ## --------------- Global parameters ---------------- :
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82 my ( $ids, $masses, $results ) = ( undef, undef, undef ) ;
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83 my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
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84 my $metabocard_features = undef ;
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85 my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ;
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86
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87 print "\t with $search_condition\n" if ($VERBOSE>1) ;
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88
1
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89 ## --------------- retrieve input data -------------- :
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90
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91 ## manage only one mass
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92 if ( ( defined $mass ) and ( $mass ne '' ) ) {
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93 my @masses = split(" ", $mass);
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94 $masses = \@masses ;
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95 for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
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96 } ## END IF
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97 ## manage csv file containing list of masses
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98 elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
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99 ## parse all csv for later : output csv build
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100 my $ocsv_input = lib::csv->new() ;
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101 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
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102 $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
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103
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104 ## parse masses and set ids
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105 my $ocsv = lib::csv->new() ;
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106 my $csv = $ocsv->get_csv_object( "\t" ) ;
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107 if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; }
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108 $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv
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109 my $nbmz = @$masses ;
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110 for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
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111 }
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112 else {
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113 warn "[warning] Input data are missing : none mass or file of masses\n" ;
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114 &help ;
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115 }
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116 #print Dumper $masses ;
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117
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118 ## ---------------- launch queries -------------------- :
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119
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120 if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) {
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121 ## prepare masses list and execute query
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122 my $oHmdb = lib::hmdb::new() ;
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123 my $hmdb_pages = undef ;
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124 my $status = undef ;
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125 my $hmdb_ids = undef ;
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126
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127 $results = [] ; # prepare arrays ref
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128 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
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129
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130 print "\t and ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ;
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131
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132 ## get the hmdb server status by a test query - continuous queries or kill script.
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133 $status = $oHmdb->testMatchesFromHmdbWithUA() ;
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134 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
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135
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136 my $cluster = 1 ;
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137 foreach my $mzs ( @{$submasses} ) {
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138 # print Dumper $mzs ;
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139 my $result = undef ;
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140
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141 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
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142
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143 print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ;
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144
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145 ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species) ;
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146 print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ;
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147
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148 # print Dumper $hmdb_pages ;
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149
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150 sleep(1) ;
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151
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152 ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result
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153 ## This previous step return results with cutoff on the number of entries returned !
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154 $results = [ @$results, @$result ] ;
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155
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156 # sleep(1) ;
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157 $cluster ++ ;
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158 }
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159
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160 ## Add more information of each found metabolite (1 for extra or 0 by default)
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161 if ($advancedFeatures > 0) {
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162
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163 ## foreach metabolite get its own metabocard
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164 $hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ;
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165
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166 print "\tComplementary annotation: asking for ".scalar(@$results)." metabocards\n" if ($VERBOSE>1) ;
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167
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168 # $hmdb_ids->{'HMDB03125'} = 1 ,
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169 $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
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170 # print Dumper $results ;
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171 # print Dumper $hmdb_ids ;
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172 # print Dumper $metabocard_features ;
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173 ## Map metabocards with results (add supplementary data)
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174 if ( ( defined $results ) and ( defined $metabocard_features ) ) {
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175 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
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176 }
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177 }
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178 else {
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179 print "\tNo complementary annotation asked\n" if ($VERBOSE>1) ;
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180 ## Fill with msg not asked advanced annotation
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181 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, undef) ;
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182 }
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183
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184
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185
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186 ## Uses N mz and theirs entries per page (see config file).
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187 # how many pages you need with your input mz list?
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188 $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
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189
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190 # print Dumper $results ;
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191 }
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192 else {
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193 croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ;
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194 } ## end ELSE
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195
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196 ## -------------- Produce HTML/CSV output ------------------ :
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197 print "\n\tProducing html and tabular outputs\n" if ($VERBOSE>1) ;
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198
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199 if ( ( defined $out_html ) and ( defined $results ) ) {
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200 my $oHtml = lib::hmdb::new() ;
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201 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
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202 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
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203 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
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204 my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ;
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205
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206 } ## END IF
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207 else {
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208 warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;
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209 }
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210
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211 if ( ( defined $out_tab ) and ( defined $results ) ) {
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212 # produce a csv based on METLIN format
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213 my $ocsv = lib::hmdb::new() ;
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214 if (defined $masses_file) {
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215 my $lm_matrix = undef ;
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216 if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) {
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217 # $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ;
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218 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ;
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219 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
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220 }
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221 elsif ( ( $header_choice eq 'no' ) ) {
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222 # $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ;
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223 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ;
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224 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
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225 }
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226 $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
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227 }
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228 elsif (defined $mass) {
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229 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ;
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230 }
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231 } ## END IF
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232 else {
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233 warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ;
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234 }
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235
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236 ## Write XLS like format
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237 if ( ( defined $out_xls ) and ( defined $results ) ) {
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238 my $ocsv = lib::hmdb::new() ;
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239 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ;
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240 }
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241
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242 print "\n* * * The hmdb client program ended * * *\n" if ($VERBOSE>1) ;
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243
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244 #====================================================================================
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245 # Help subroutine called with -h option
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246 # number of arguments : 0
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247 # Argument(s) :
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248 # Return : 1
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249 #====================================================================================
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250 sub help {
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251 print STDERR "
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252 help of wsdl_hmdb
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253
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254 # wsdl_hmdb is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
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255 # Input : accurate mz or list of accurate masses
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256 # Author : Franck Giacomoni and Marion Landi
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257 # Email : fgiacomoni\@inra.fr
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258 # Version : 1.6
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259 # Created : 08/07/2012
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260 # Updated : 23/01/2019 - 1.6
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261 USAGE :
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262 wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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263
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264 or
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265 wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n]
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266 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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267 -advancedFeatures [Default 0, set to 1 for advanced features as logp, inchi, ...]
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268
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269 or
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270 wsdl_hmdb.pl -h for help
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271
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272 ";
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273 exit(1);
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274 }
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275
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276 ## END of script - F Giacomoni
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277
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278 __END__
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279
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280 =head1 NAME
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281
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282 wsdl_hmdb.pl -- script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
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283
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284 =head1 USAGE
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285
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286 wsdl_hmdb.pl -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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287
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288 or
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289 wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n]
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290 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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291
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292 =head1 SYNOPSIS
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293
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294 This script manages batch queries on HMDB server.
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295
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296 =head1 DESCRIPTION
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297
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298 This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
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299
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300 =over 4
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301
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302 =item B<function01>
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303
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304 =item B<function02>
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305
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306 =back
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307
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308 =head1 AUTHOR
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309
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310 Franck Giacomoni E<lt>franck.giacomoni@inra.frE<gt>
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311
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312 =head1 LICENSE
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313
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314 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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315
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316 =head1 VERSION
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317
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318 version 1.0 : 06 / 06 / 2013
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319
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320 version 1.2 : 27 / 01 / 2014
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321
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322 version 1.3 : 19 / 11 / 2014
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323
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324 version 1.4 : 21 / 01 / 2016 - a clean version for community
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325
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326 version 1.5 : 19 / 01 / 2018 - modify parser to match HMDB V4.0 formats
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327
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328 version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb.
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329
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330 =cut