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annotate wsdl_hmdb.pl @ 4:6091a80df951 draft

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author fgiacomoni
date Fri, 19 Jan 2018 09:38:17 -0500
parents 6d0a0f8f672a
children 97788e4bf3fc
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1 #!perl
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2
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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
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32
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33 #=============================================================================
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34 # Manage EXCEPTIONS
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35 #=============================================================================
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36
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37 &GetOptions ( "h" => \$help, # HELP
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38 "mass:s" => \$mass, ## option : one masse
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39 "masses:s" => \$masses_file, ## option : path to the input
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40 "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file
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41 "nblineheader:i" => \$nbline_header, ## numbre of header line present in file
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42 "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file
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43 "delta:f" => \$delta,
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44 "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral)
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45 "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 )
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46 "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results )
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47 "output_html|v:s" => \$out_html, ## option : path to the results view (output2)
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48 "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output
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49 ) ;
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50
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51 #=============================================================================
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52 # EXCEPTIONS
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53 #=============================================================================
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54 $help and &help ;
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55
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56 #=============================================================================
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57 # MAIN SCRIPT
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58 #=============================================================================
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59
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60
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61 ## -------------- Conf file ------------------------ :
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62 my ( $CONF ) = ( undef ) ;
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63 foreach my $conf ( <$binPath/*.cfg> ) {
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64 my $oConf = lib::conf::new() ;
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65 $CONF = $oConf->as_conf($conf) ;
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66 }
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67
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68 ## -------------- HTML template file ------------------------ :
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69 foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; }
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70
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71 if (!defined $max_query) {
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72 $max_query = $CONF->{'HMDB_MAX_QUERY'} ;
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73 }
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74
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75
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76 ## --------------- Global parameters ---------------- :
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77 my ( $ids, $masses, $results ) = ( undef, undef, undef ) ;
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78 my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ;
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79 my $metabocard_features = undef ;
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80 my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ;
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81
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82 ## --------------- retrieve input data -------------- :
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83
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84 ## manage only one mass
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85 if ( ( defined $mass ) and ( $mass ne '' ) ) {
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86 my @masses = split(" ", $mass);
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87 $masses = \@masses ;
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88 for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
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89 } ## END IF
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90 ## manage csv file containing list of masses
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91 elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) {
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92 ## parse all csv for later : output csv build
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93 my $ocsv_input = lib::csv->new() ;
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94 my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ;
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95 $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ;
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96
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97 ## parse masses and set ids
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98 my $ocsv = lib::csv->new() ;
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99 my $csv = $ocsv->get_csv_object( "\t" ) ;
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100 if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; }
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101 $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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102 my $nbmz = @$masses ;
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103 for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); }
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104 }
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105 else {
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106 warn "[warning] Input data are missing : none mass or file of masses\n" ;
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107 &help ;
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108 }
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109 #print Dumper $masses ;
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110 ## ---------------- launch queries -------------------- :
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111
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112 if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) {
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113 ## prepare masses list and execute query
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114 my $oHmdb = lib::hmdb::new() ;
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115 my $hmdb_pages = undef ;
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116 my $hmdb_ids = undef ;
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117
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118 $results = [] ; # prepare arrays ref
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119 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ;
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120
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121 ## get the hmdb server status by a test query - continuous queries or kill script.
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122 my $status = $oHmdb->test_matches_from_hmdb_ua() ;
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123 $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution
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124
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125 foreach my $mzs ( @{$submasses} ) {
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126
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127 my $result = undef ;
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128 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
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129 $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
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130 ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result
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131 ## This previous step return results with cutoff on the number of entries returned !
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132 $results = [ @$results, @$result ] ;
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133 }
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134
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135 ## foreach metabolite get its own metabocard
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136 $hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ;
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137 # $hmdb_ids->{'HMDB03125'} = 1 ,
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138 $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying
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139
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140 ## Map metabocards with results (add supplementary data)
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141
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142 # print Dumper $results ;
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143 # print Dumper $hmdb_ids ;
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144 # print Dumper $metabocard_features ;
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145
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146 if ( ( defined $results ) and ( defined $metabocard_features ) ) {
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147 $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ;
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148 }
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149
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150 ## Uses N mz and theirs entries per page (see config file).
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151 # how many pages you need with your input mz list?
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152 $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
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153
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154 # print Dumper $results ;
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155 }
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156 else {
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157 croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ;
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158 } ## end ELSE
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159
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160 ## -------------- Produce HTML/CSV output ------------------ :
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161
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162 if ( ( defined $out_html ) and ( defined $results ) ) {
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163 my $oHtml = lib::hmdb::new() ;
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164 my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ;
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165 ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ;
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166 ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ;
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167 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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168
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169 } ## END IF
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170 else {
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171 warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ;
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172 }
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173
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174 if ( ( defined $out_tab ) and ( defined $results ) ) {
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175 # produce a csv based on METLIN format
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176 my $ocsv = lib::hmdb::new() ;
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177 if (defined $masses_file) {
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178 my $lm_matrix = undef ;
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179 if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) {
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180 # $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ;
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181 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ;
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182 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ;
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183 }
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184 elsif ( ( $header_choice eq 'no' ) ) {
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185 # $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ;
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186 $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ;
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187 $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ;
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188 }
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189 $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ;
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190 }
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191 elsif (defined $mass) {
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192 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ;
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193 }
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194 } ## END IF
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195 else {
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196 warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ;
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197 }
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198
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199 ## Write XLS like format
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200 if ( ( defined $out_xls ) and ( defined $results ) ) {
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201 my $ocsv = lib::hmdb::new() ;
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202 $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ;
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203 }
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204
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205
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206 #====================================================================================
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207 # Help subroutine called with -h option
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208 # number of arguments : 0
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209 # Argument(s) :
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210 # Return : 1
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211 #====================================================================================
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212 sub help {
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213 print STDERR "
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214 help of wsdl_hmdb
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215
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216 # 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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217 # Input : accurate mz or list of accurate masses
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218 # Author : Franck Giacomoni and Marion Landi
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219 # Email : fgiacomoni\@inra.fr
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220 # Version : 1.5
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221 # Created : 08/07/2012
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222 # Updated : 19/01/2018
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223 USAGE :
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224 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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225
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226 or
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227 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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228 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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229
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230 or
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231 wsdl_hmdb.pl -h for help
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232
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233 ";
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234 exit(1);
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235 }
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236
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237 ## END of script - F Giacomoni
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238
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239 __END__
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240
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241 =head1 NAME
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242
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243 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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244
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245 =head1 USAGE
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246
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247 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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248
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249 or
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250 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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251 -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file]
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252
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253 =head1 SYNOPSIS
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254
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255 This script manages batch queries on HMDB server.
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256
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257 =head1 DESCRIPTION
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258
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259 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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260
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261 =over 4
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262
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263 =item B<function01>
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264
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265 =item B<function02>
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266
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267 =back
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268
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269 =head1 AUTHOR
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270
4
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271 Franck Giacomoni E<lt>franck.giacomoni@inra.frE<gt>
1
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272
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273 =head1 LICENSE
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274
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275 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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276
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277 =head1 VERSION
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278
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279 version 1.0 : 06 / 06 / 2013
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280
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281 version 1.2 : 27 / 01 / 2014
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282
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283 version 1.3 : 19 / 11 / 2014
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284
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285 version 1.4 : 21 / 01 / 2016 - a clean version for community
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286
4
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287 version 1.5 : 19 / 01 / 2018 - modifiy parser to match HMDB V4.0 formats
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288
1
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289 =cut