annotate lib/hmdb.pm @ 4:6091a80df951 draft

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date Fri, 19 Jan 2018 09:38:17 -0500
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1 package lib::hmdb ;
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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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8 use LWP::Simple;
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9 use LWP::UserAgent;
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10 use URI::URL;
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11 use SOAP::Lite;
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12 use Encode;
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13 use HTML::Template ;
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14 use XML::Twig ;
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15 use Text::CSV ;
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16
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17 use Data::Dumper ;
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19 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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21 our $VERSION = "1.0";
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22 our @ISA = qw(Exporter);
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23 our @EXPORT = qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass );
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24 our %EXPORT_TAGS = ( ALL => [qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] );
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26 =head1 NAME
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28 My::Module - An example module
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29
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30 =head1 SYNOPSIS
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31
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32 use My::Module;
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33 my $object = My::Module->new();
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34 print $object->as_string;
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35
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36 =head1 DESCRIPTION
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37
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38 This module does not really exist, it
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39 was made for the sole purpose of
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40 demonstrating how POD works.
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41
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42 =head1 METHODS
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43
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44 Methods are :
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45
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46 =head2 METHOD new
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47
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48 ## Description : new
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49 ## Input : $self
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50 ## Ouput : bless $self ;
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51 ## Usage : new() ;
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52
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53 =cut
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54
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55 sub new {
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56 ## Variables
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57 my $self={};
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58 bless($self) ;
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59 return $self ;
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60 }
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61 ### END of SUB
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62
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63
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64 =head2 METHOD extract_sub_mz_lists
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65
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66 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
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67 ## Input : $HMDB_LIMITS, $masses
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68 ## Output : $sublists
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69 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
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70
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71 =cut
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72 ## START of SUB
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73 sub extract_sub_mz_lists {
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74 ## Retrieve Values
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75 my $self = shift ;
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76 my ( $masses, $HMDB_LIMITS ) = @_ ;
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77
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78 my ( @sublists, @sublist ) = ( (), () ) ;
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79 my $nb_mz = 0 ;
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80 my $nb_total_mzs = scalar(@{$masses}) ;
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81
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82 if ($nb_total_mzs == 0) {
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83 die "The provided mzs list is empty" ;
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84 }
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85
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86 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
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87
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88 if ( $nb_mz < $HMDB_LIMITS ) {
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89 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
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90 }
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91 elsif ( $nb_mz == $HMDB_LIMITS ) {
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92 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
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93 $current_pos-- ;
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94 }
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95 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
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96 }
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97 return(\@sublists) ;
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98 }
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99 ## END of SUB
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100
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101 =head2 METHOD prepare_multi_masses_query
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102
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103 ## Description : Generate the adapted format of the mz list for HMDB
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104 ## Input : $masses
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105 ## Output : $hmdb_masses
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106 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
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107
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108 =cut
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109 ## START of SUB
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110 sub prepare_multi_masses_query {
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111 ## Retrieve Values
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112 my $self = shift ;
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113 my ( $masses ) = @_ ;
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114
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115 my $hmdb_masses = undef ;
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116 my $sep = '%0D%0A' ; ## retour chariot encode
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117 my ($nb_masses, $i) = (0, 0) ;
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118
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119 if ( defined $masses ) {
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120 my @masses = @{$masses} ;
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121 my $nb_masses = scalar ( @masses ) ;
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122 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
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123 elsif ( $nb_masses >= 150 ) { croak "Your mass list is too long : HMDB allows maximum 150 query masses per request \n" ; } ## Del it --- temporary patch
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124
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125 foreach my $mass (@masses) {
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126
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127 if ($i < $nb_masses) {
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128 $hmdb_masses .= $mass.$sep ;
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129 }
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130 elsif ( $i == $nb_masses ) {
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131 $hmdb_masses .= $mass ;
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132 }
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133 else {
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134 last ;
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135 }
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136 $i ++ ;
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137 }
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138 }
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139 else {
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140 croak "No mass list found \n" ;
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141 }
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142 return($hmdb_masses, $nb_masses) ;
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143 }
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144 ## END of SUB
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145
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146 =head2 METHOD test_matches_from_hmdb_ua
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147
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148 ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
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149 ## Input : none
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150 ## Output : $status_line
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151 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
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152
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153 =cut
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154 ## START of SUB
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155 sub test_matches_from_hmdb_ua {
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156 ## Retrieve Values
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157 my $self = shift ;
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158
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159 my @page = () ;
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160
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161 my $ua = new LWP::UserAgent;
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162 $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36");
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163
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164 my $req = HTTP::Request->new(
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165 POST => 'http://specdb.wishartlab.com/ms/search.csv');
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166
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167 $req->content_type('application/x-www-form-urlencoded');
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168 $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV');
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169
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170 my $res = $ua->request($req);
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171 # print $res->as_string;
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172 my $status_line = $res->status_line ;
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173 ($status_line) = ($status_line =~ /(\d+)/);
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174
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175
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176 return (\$status_line) ;
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177 }
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178 ## END of SUB
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179
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180 =head2 METHOD check_state_from_hmdb_ua
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181
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182 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
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183 ## Input : $status
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184 ## Output : none
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185 ## Usage : check_state_from_hmdb_ua($status) ;
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186
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187 =cut
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188 ## START of SUB
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189 sub check_state_from_hmdb_ua {
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190 ## Retrieve Values
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191 my $self = shift ;
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192 my ($status) = @_ ;
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193
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194 if (!defined $$status) {
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195 croak "No http status is defined for the distant server" ;
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196 }
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197 else {
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198 unless ( $$status == 200 ) {
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199 if ( $$status == 504 ) { croak "Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server" ; }
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200 else {
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201 ## None supported http code error ##
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202 }
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203 }
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204 }
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205
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206 return (1) ;
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207 }
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208 ## END of SUB
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209
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210 =head2 METHOD get_matches_from_hmdb_ua
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211
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212 ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
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213 ## Input : $mass, $delta, $mode
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214 ## Output : $results
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215 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
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216
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217 =cut
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218 ## START of SUB
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219 sub get_matches_from_hmdb_ua {
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220 ## Retrieve Values
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221 my $self = shift ;
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222 my ( $masses, $delta, $mode ) = @_ ;
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223
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224 my @page = () ;
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225
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226 my $ua = new LWP::UserAgent;
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227 $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36");
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228 $ua->timeout(500);
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229
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230 my $req = HTTP::Request->new(
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231 POST => 'http://specdb.wishartlab.com/ms/search.csv');
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232
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233 $req->content_type('application/x-www-form-urlencoded');
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234 $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
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235
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236 my $res = $ua->request($req);
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237 # print $res->as_string;
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238 if ($res->is_success) {
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239 @page = split ( /\n/, $res->decoded_content ) ;
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240 } else {
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241 my $status_line = $res->status_line ;
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242 ($status_line) = ($status_line =~ /(\d+)/);
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243 croak "HMDB service none available !! Status of the HMDB server is : $status_line\n" ;
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244 }
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245
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246
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247 return (\@page) ;
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248 }
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249 ## END of SUB
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250
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251 =head2 METHOD parse_hmdb_csv_results
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252
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253 ## Description : parse the csv results and get data
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254 ## Input : $csv
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255 ## Output : $results
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256 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
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257
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258 =cut
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259 ## START of SUB
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260 sub parse_hmdb_csv_results {
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261 ## Retrieve Values
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262 my $self = shift ;
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263 my ( $csv, $masses, $max_query ) = @_ ;
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264
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265 my $test = 0 ;
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266 my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ;
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267
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268 my %result_by_entry = () ;
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269 my %features = () ;
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270
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271 # print Dumper $csv ;
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272
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273 foreach my $line (@{$csv}) {
4
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274 ## HMDB csv output - [DEPRECATED]...
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275 # if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
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276 # my @entry = split(/,/, $line) ;
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277 #
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278 # if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
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279 #
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280 # $features{ENTRY_ENTRY_ID} = $entry[1] ;
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281 # $features{ENTRY_FORMULA} = $entry[2] ;
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282 # $features{ENTRY_CPD_MZ} = $entry[3] ;
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283 # $features{ENTRY_ADDUCT} = $entry[4] ;
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284 # $features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
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285 # $features{ENTRY_ADDUCT_MZ} = $entry[6] ;
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286 # $features{ENTRY_DELTA} = $entry[7] ;
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287 #
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288 # my %temp = %features ;
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289 #
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290 # push (@{$result_by_entry{$entry[0]} }, \%temp) ;
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291 # }
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292 ## NEW HMDB format V4.0 - dec2017
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293 if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) {
1
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294
4
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295 if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) {
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296 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
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297
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298 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
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299
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300 $features{ENTRY_ENTRY_ID} = $entry[1] ;
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301 $features{ENTRY_FORMULA} = $entry[4] ;
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302 $features{ENTRY_CPD_MZ} = $entry[5] ;
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303 $features{ENTRY_ADDUCT} = $entry[6] ;
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304 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
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305 $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
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306 $features{ENTRY_DELTA} = $entry[9] ;
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307
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308 my %temp = %features ;
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309 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
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310 }
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311 else {
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312 warn "The parsed line ($line) does not match your pattern\n " ;
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313 }
1
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314 }
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315 else {
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316 next ;
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317 }
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318 } ## end foreach
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319
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320 ## manage per query_mzs (keep query masses order by array)
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321 my @results = () ;
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322 foreach (@{$masses}) {
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323 if ($result_by_entry{$_}) {
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324
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325 ## cut all entries > $max_query
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326 my @temp_entries = @{$result_by_entry{$_}} ;
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327 my @temp_cut = () ;
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328 my $current_query = 0 ;
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329 foreach (@temp_entries) {
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330 $current_query ++ ;
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331 if ($current_query > $max_query) {
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332 last ;
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333 }
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334 else {
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335 push (@temp_cut, $_) ;
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336 }
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337 }
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338 push (@results, \@temp_cut) ;
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339 # push (@results, $result_by_entry{$_}) ;
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340 }
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341 else {push (@results, [] ) ;} ;
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342
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343 }
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344 return(\@results) ;
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345 }
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346 ## END of SUB
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347
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348 =head2 METHOD parse_hmdb_page_results
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349
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350 ## Description : [DEPRECATED] old HMDB html page parser
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351 ## Input : $page
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352 ## Output : $results
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353 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
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354
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355 =cut
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356 ## START of SUB
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357 sub parse_hmdb_page_results {
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358 ## Retrieve Values
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359 my $self = shift ;
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360 my ( $page ) = @_ ;
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361
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362 my @results = () ;
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363 my ($catch_table, $catch_name) = (0, 0) ;
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364 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
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365
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366 if ( defined $page ) {
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367
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368 my @page = @{$page} ;
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369 my $ID = undef ;
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370 my @result_by_mz = () ;
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371 my %result_by_entry = () ;
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fgiacomoni
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372
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373 foreach my $line (@page) {
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374
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375 #Section de la page contenant les resultat
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376 if( $line =~/<table>/ ) { $catch_table = 1 ; }
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377
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fgiacomoni
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378 ## Si il existe un resultat :
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379 if($catch_table == 1) {
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380
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381 #Id de la molecule, et creation du lien
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382 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
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383 $ID = $1 ;
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384 $catch_name = 0 ;
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385 next ;
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386 }
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fgiacomoni
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387 #Nom de la molecule ONLY!!
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388 if ( $catch_name == 0 ) {
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389
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390 if( $line =~ /<td>(.+)<\/td>/ ) {
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391
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392 if ( !defined $name ) {
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393 $name = $1 ;
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394 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
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395 $result_by_entry{'ENTRY_NAME'} = $name ;
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396 next ;
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397 }
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398 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
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399 if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; }
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400 if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; }
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401 if ( !defined $delta ) {
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402 $delta = $1 ;
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403 $result_by_entry{'ENTRY_DELTA'} = $delta ;
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404 $catch_name = 1 ;
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405 my %tmp = %result_by_entry ;
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406 push (@result_by_mz, \%tmp) ;
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407 %result_by_entry = () ;
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408 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
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409 next ;
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410 }
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411 }
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412 }
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413 }
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fgiacomoni
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414 #Fin de la section contenant les resultats
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415 if( $line =~ /<\/table>/ ) {
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416 $catch_table = 0 ;
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417 my @Tmp = @result_by_mz ;
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418 push(@results, \@Tmp) ;
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419 @result_by_mz = () ;
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420 }
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421 }
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422 }
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423 return(\@results) ;
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424 }
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fgiacomoni
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425 ## END of SUB
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fgiacomoni
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426
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427
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fgiacomoni
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428 =head2 METHOD get_unik_ids_from_results
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fgiacomoni
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429
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fgiacomoni
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430 ## Description : get all unik ids from the hmdb result object
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431 ## Input : $results
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432 ## Output : $ids
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433 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
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fgiacomoni
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434
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fgiacomoni
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435 =cut
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fgiacomoni
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436 ## START of SUB
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fgiacomoni
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437 sub get_unik_ids_from_results {
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fgiacomoni
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438 ## Retrieve Values
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439 my $self = shift ;
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440 my ( $results ) = @_;
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441 my ( %ids ) = ( () ) ;
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442
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443 foreach my $result (@{$results}) {
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444
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445 foreach my $entries (@{$result}) {
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446
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447 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
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448 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
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449 }
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450 }
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451 }
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fgiacomoni
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452
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453 return (\%ids) ;
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454 }
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fgiacomoni
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455 ### END of SUB
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456
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fgiacomoni
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457
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fgiacomoni
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458
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fgiacomoni
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459 =head2 METHOD get_hmdb_metabocard_from_id
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fgiacomoni
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460
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fgiacomoni
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461 ## Description : get a metabocard (xml format from an ID on HMDB)
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fgiacomoni
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462 ## Input : $ids
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fgiacomoni
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463 ## Output : $metabocard_features
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fgiacomoni
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464 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
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fgiacomoni
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465
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fgiacomoni
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466 =cut
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fgiacomoni
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467 ## START of SUB
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fgiacomoni
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468 sub get_hmdb_metabocard_from_id {
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fgiacomoni
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469 ## Retrieve Values
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fgiacomoni
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470 my $self = shift ;
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471 my ( $ids, $hmdb_url ) = @_;
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472 my ( %metabocard_features ) = ( () ) ;
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473 my $query = undef ;
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fgiacomoni
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474
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fgiacomoni
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475 ## structure %metabocard_features
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parents:
diff changeset
476 # metabolite_id = (
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fgiacomoni
parents:
diff changeset
477 # 'metabolite_name' => '__name__',
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fgiacomoni
parents:
diff changeset
478 # 'metabolite_inchi' => '__inchi__',
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fgiacomoni
parents:
diff changeset
479 # 'metabolite_logp' => '__logp-ALOGPS__',
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fgiacomoni
parents:
diff changeset
480 #
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fgiacomoni
parents:
diff changeset
481 # )
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fgiacomoni
parents:
diff changeset
482
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fgiacomoni
parents:
diff changeset
483
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fgiacomoni
parents:
diff changeset
484 if( (defined $ids) and ($ids > 0 ) ) {
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fgiacomoni
parents:
diff changeset
485
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fgiacomoni
parents:
diff changeset
486 foreach my $id (keys %{$ids}) {
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fgiacomoni
parents:
diff changeset
487
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fgiacomoni
parents:
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488 # print "\n============== > $id **********************\n " ;
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fgiacomoni
parents:
diff changeset
489 my $twig = undef ;
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fgiacomoni
parents:
diff changeset
490
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fgiacomoni
parents:
diff changeset
491 if (defined $hmdb_url) {
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fgiacomoni
parents:
diff changeset
492 $query = $hmdb_url.$id.'.xml' ;
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fgiacomoni
parents:
diff changeset
493
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fgiacomoni
parents:
diff changeset
494 ## test the header if exists
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fgiacomoni
parents:
diff changeset
495 my $response = head($query) ;
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fgiacomoni
parents:
diff changeset
496
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fgiacomoni
parents:
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497 if (!defined $response) {
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fgiacomoni
parents:
diff changeset
498 $metabocard_features{$id}{'metabolite_name'} = undef ;
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fgiacomoni
parents:
diff changeset
499 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
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fgiacomoni
parents:
diff changeset
500 $metabocard_features{$id}{'metabolite_logp'} = undef ;
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fgiacomoni
parents:
diff changeset
501 ## Need to be improve to manage http 404 or other response diff than 200
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fgiacomoni
parents:
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502 }
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fgiacomoni
parents:
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503 elsif ($response->is_success) {
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fgiacomoni
parents:
diff changeset
504
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fgiacomoni
parents:
diff changeset
505 $twig = XML::Twig->nparse_ppe(
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fgiacomoni
parents:
diff changeset
506
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fgiacomoni
parents:
diff changeset
507 twig_handlers => {
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fgiacomoni
parents:
diff changeset
508 # metabolite name
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fgiacomoni
parents:
diff changeset
509 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; } ,
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fgiacomoni
parents:
diff changeset
510 # metabolite inchi
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fgiacomoni
parents:
diff changeset
511 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; } ,
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fgiacomoni
parents:
diff changeset
512 ## metabolite logP
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fgiacomoni
parents:
diff changeset
513 'metabolite/predicted_properties/property' => sub {
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fgiacomoni
parents:
diff changeset
514
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fgiacomoni
parents:
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515 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
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fgiacomoni
parents:
diff changeset
516
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fgiacomoni
parents:
diff changeset
517 if (defined $_->children ) {
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fgiacomoni
parents:
diff changeset
518 foreach my $field ($_->children) {
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fgiacomoni
parents:
diff changeset
519 if ( $field->name eq 'kind') { $kind = $field->text ; }
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fgiacomoni
parents:
diff changeset
520 elsif ( $field->name eq 'source') { $source = $field->text ; }
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fgiacomoni
parents:
diff changeset
521 elsif ( $field->name eq 'value') { $value = $field->text ; }
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fgiacomoni
parents:
diff changeset
522
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fgiacomoni
parents:
diff changeset
523 if (defined $source ) {
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fgiacomoni
parents:
diff changeset
524 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
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fgiacomoni
parents:
diff changeset
525 $metabocard_features{$id}{'metabolite_logp'} = $value ;
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fgiacomoni
parents:
diff changeset
526 }
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fgiacomoni
parents:
diff changeset
527 ($kind, $source, $value ) = ( undef, undef, undef ) ;
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fgiacomoni
parents:
diff changeset
528 }
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fgiacomoni
parents:
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529 }
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fgiacomoni
parents:
diff changeset
530 }
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fgiacomoni
parents:
diff changeset
531 }
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fgiacomoni
parents:
diff changeset
532 },
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fgiacomoni
parents:
diff changeset
533 pretty_print => 'indented',
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fgiacomoni
parents:
diff changeset
534 error_context => 1, $query
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fgiacomoni
parents:
diff changeset
535 );
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fgiacomoni
parents:
diff changeset
536
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fgiacomoni
parents:
diff changeset
537 # $twig->print;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
538 $twig->purge ;
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fgiacomoni
parents:
diff changeset
539
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fgiacomoni
parents:
diff changeset
540 if (!$@) {
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fgiacomoni
parents:
diff changeset
541
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fgiacomoni
parents:
diff changeset
542 }
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fgiacomoni
parents:
diff changeset
543 else {
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fgiacomoni
parents:
diff changeset
544 warn $@ ;
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fgiacomoni
parents:
diff changeset
545 }
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fgiacomoni
parents:
diff changeset
546 }
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fgiacomoni
parents:
diff changeset
547 }
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fgiacomoni
parents:
diff changeset
548 else {
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fgiacomoni
parents:
diff changeset
549 warn "The hmdb metabocard url is not defined\n" ;
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fgiacomoni
parents:
diff changeset
550 last;
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fgiacomoni
parents:
diff changeset
551 }
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fgiacomoni
parents:
diff changeset
552 }
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fgiacomoni
parents:
diff changeset
553 }
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fgiacomoni
parents:
diff changeset
554 else {
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fgiacomoni
parents:
diff changeset
555 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
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fgiacomoni
parents:
diff changeset
556 }
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fgiacomoni
parents:
diff changeset
557
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fgiacomoni
parents:
diff changeset
558 # print Dumper %metabocard_features ;
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fgiacomoni
parents:
diff changeset
559 return (\%metabocard_features) ;
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fgiacomoni
parents:
diff changeset
560 }
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fgiacomoni
parents:
diff changeset
561 ### END of SUB
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fgiacomoni
parents:
diff changeset
562
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
563
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
564 =head2 METHOD map_suppl_data_on_hmdb_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
565
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
566 ## Description : map supplementary data with already collected results with hmdb search
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
567 ## Input : $results, $features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
568 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
569 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
570
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
571 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
572 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
573 sub map_suppl_data_on_hmdb_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
574 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
575 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
576 my ( $results, $features ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
577 my ( @more_results ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
578
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
579 @more_results = @{$results} ; ## Dump array ref to map
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
580
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
581 foreach my $result (@more_results) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
582
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
583 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
584
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
585 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
586 ## check that we have a ID for mapping
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
587 my $current_id = $entries->{'ENTRY_ENTRY_ID'} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
588 if ($features->{"$current_id"}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
589 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
590 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
591 $entries->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
592 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
593 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
594 $entries->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
595 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
596 ## Metabolite INCHI
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
597 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
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598 $entries->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
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599 }
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600 else {
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601 $entries->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
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602 }
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603 ## Metabolite LOGP
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604 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
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605 $entries->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
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606 }
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607 else {
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608 $entries->{'ENTRY_ENTRY_LOGP'} = 'NA' ;
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609 }
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610 }
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611 else {
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612 warn "This HMDB id doesn't match any collected ids\n" ;
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613 }
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614 }
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615 }
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616 }
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617
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618 return (\@more_results) ;
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619 }
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620 ### END of SUB
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621
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622
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623 =head2 METHOD set_html_tbody_object
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624
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625 ## Description : initializes and build the tbody object (perl array) needed to html template
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626 ## Input : $nb_pages, $nb_items_per_page
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627 ## Output : $tbody_object
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628 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
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629
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fgiacomoni
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630 =cut
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fgiacomoni
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631 ## START of SUB
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632 sub set_html_tbody_object {
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633 my $self = shift ;
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634 my ( $nb_pages, $nb_items_per_page ) = @_ ;
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635
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636 my ( @tbody_object ) = ( ) ;
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637
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638 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
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fgiacomoni
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639
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640 my %pages = (
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fgiacomoni
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641 # tbody feature
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642 PAGE_NB => $i,
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643 MASSES => [], ## end MASSES
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644 ) ; ## end TBODY N
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645 push (@tbody_object, \%pages) ;
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646 }
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647 return(\@tbody_object) ;
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fgiacomoni
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648 }
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fgiacomoni
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649 ## END of SUB
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650
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651 =head2 METHOD add_mz_to_tbody_object
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652
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653 ## Description : initializes and build the mz object (perl array) needed to html template
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fgiacomoni
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654 ## Input : $tbody_object, $nb_items_per_page, $mz_list
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655 ## Output : $tbody_object
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656 ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
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657
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fgiacomoni
parents:
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658 =cut
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fgiacomoni
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659 ## START of SUB
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660 sub add_mz_to_tbody_object {
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661 my $self = shift ;
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662 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
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663
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664 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
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665
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666 foreach my $page ( @{$tbody_object} ) {
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667
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668 my @colors = ('white', 'green') ;
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669 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
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fgiacomoni
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670
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671 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
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fgiacomoni
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672 #
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673 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
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674 $current_index = 0 ;
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fgiacomoni
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675 last ; ##
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676 }
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677 else {
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678 $current_index++ ;
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679 if ( $icolor > 1 ) { $icolor = 0 ; }
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680
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681 if ( exists $mz_list->[$mz_index] ) {
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fgiacomoni
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682
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fgiacomoni
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683 my %mz = (
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fgiacomoni
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684 # mass feature
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fgiacomoni
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685 MASSES_ID_QUERY => $ids_list->[$mz_index],
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686 MASSES_MZ_QUERY => $mz_list->[$mz_index],
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687 MZ_COLOR => $colors[$icolor],
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688 MASSES_NB => $mz_index+1,
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689 ENTRIES => [] ,
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690 ) ;
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691 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
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fgiacomoni
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692 # Html attr for mass
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693 $icolor++ ;
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694 }
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695 }
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696 $mz_index++ ;
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697 } ## foreach mz
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698
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699 $current_page++ ;
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700 }
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701 return($tbody_object) ;
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fgiacomoni
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702 }
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fgiacomoni
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703 ## END of SUB
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fgiacomoni
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704
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fgiacomoni
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705 =head2 METHOD add_entries_to_tbody_object
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fgiacomoni
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706
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fgiacomoni
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707 ## Description : initializes and build the entries object (perl array) needed to html template
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fgiacomoni
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708 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
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fgiacomoni
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709 ## Output : $tbody_object
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fgiacomoni
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710 ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
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fgiacomoni
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711
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fgiacomoni
parents:
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712 =cut
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fgiacomoni
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713 ## START of SUB
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fgiacomoni
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714 sub add_entries_to_tbody_object {
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fgiacomoni
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715 ## Retrieve Values
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fgiacomoni
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716 my $self = shift ;
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717 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
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diff changeset
718
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
719 my $index_page = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
720 my $index_mz_continous = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
721
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
722 foreach my $page (@{$tbody_object}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
723
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
724 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
725
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
726 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
727
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
728 my $index_entry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
729
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
730 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
731 my $check_rebond = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
732 my $check_noentry = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
733
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
734 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
735 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
736 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
737 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
738 if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
739 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
740
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
741 if ( $check_rebond == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
742
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
743 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
744
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
745 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
746 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
747 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
748 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
749 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
750 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
751 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
752 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
753 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
754 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
755 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
756 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
757 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
758 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
759
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
760 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
761 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
762 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
763 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
764 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
765 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
766 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
767 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
768 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
769 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
770 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
771 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
772 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
773 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
774 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
775 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
776 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
777 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
778 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
779 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
780 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
781 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
782 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
783 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
784 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
785 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
786 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
787 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
788 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
789 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
790
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
791 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
792
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
793 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
794 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
795 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
796 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
797
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
798 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
799 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
800 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
801 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
802 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
803 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
804
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
805 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
806
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
807 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
808 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
809
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
810 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
811 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
812 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
813 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
814 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
815 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
816 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
817 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
818 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
819 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
820 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
821
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
822 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
823 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
824 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
825 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
826 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
827 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
828 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
829 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
830
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
831 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
832
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
833 ## Description : build the hmdb_row under its ref form
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834 ## Input : $header, $init_mzs, $entries
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835 ## Output : $hmdb_matrix
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836 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
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fgiacomoni
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diff changeset
837
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fgiacomoni
parents:
diff changeset
838 =cut
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fgiacomoni
parents:
diff changeset
839 ## START of SUB
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fgiacomoni
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840 sub set_lm_matrix_object {
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fgiacomoni
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841 ## Retrieve Values
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842 my $self = shift ;
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843 my ( $header, $init_mzs, $entries ) = @_ ;
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diff changeset
844
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845 my @hmdb_matrix = () ;
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fgiacomoni
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846
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fgiacomoni
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847 if ( defined $header ) {
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fgiacomoni
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848 my @headers = () ;
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fgiacomoni
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849 push @headers, $header ;
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fgiacomoni
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850 push @hmdb_matrix, \@headers ;
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851 }
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852
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853 my $index_mz = 0 ;
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fgiacomoni
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854
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855 foreach my $mz ( @{$init_mzs} ) {
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fgiacomoni
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856
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857 my $index_entries = 0 ;
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858 my @clusters = () ;
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859 my $cluster_col = undef ;
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860
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861 my @anti_redondant = ('N/A') ;
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862 my $check_rebond = 0 ;
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863
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864 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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865
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866 foreach my $entry (@{ $entries->[$index_mz] }) {
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867
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868 ## dispo anti doublons des entries
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fgiacomoni
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869 foreach my $rebond (@anti_redondant) {
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870 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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871 }
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872
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parents:
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873 if ( $check_rebond == 0 ) {
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874
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875 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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876
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877 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
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fgiacomoni
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878 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
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879 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
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fgiacomoni
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880
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fgiacomoni
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881 ## METLIN data display model
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fgiacomoni
parents:
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882 ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
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883 # manage final pipe
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884 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; }
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885 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
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886
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887 }
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888 $check_rebond = 0 ; ## reinit double control
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889 $index_entries++ ;
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fgiacomoni
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890 } ## end foreach
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891 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
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892 push (@clusters, $cluster_col) ;
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893 push (@hmdb_matrix, \@clusters) ;
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894 $index_mz++ ;
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895 }
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896 return(\@hmdb_matrix) ;
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897 }
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fgiacomoni
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898 ## END of SUB
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899
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fgiacomoni
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diff changeset
900 =head2 METHOD set_hmdb_matrix_object_with_ids
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fgiacomoni
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901
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fgiacomoni
parents:
diff changeset
902 ## Description : build the hmdb_row under its ref form (IDS only)
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fgiacomoni
parents:
diff changeset
903 ## Input : $header, $init_mzs, $entries
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fgiacomoni
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904 ## Output : $hmdb_matrix
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fgiacomoni
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diff changeset
905 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
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fgiacomoni
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906
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fgiacomoni
parents:
diff changeset
907 =cut
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fgiacomoni
parents:
diff changeset
908 ## START of SUB
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fgiacomoni
parents:
diff changeset
909 sub set_hmdb_matrix_object_with_ids {
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fgiacomoni
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910 ## Retrieve Values
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fgiacomoni
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diff changeset
911 my $self = shift ;
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fgiacomoni
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diff changeset
912 my ( $header, $init_mzs, $entries ) = @_ ;
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fgiacomoni
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913
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fgiacomoni
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914 my @hmdb_matrix = () ;
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915
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diff changeset
916 if ( defined $header ) {
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fgiacomoni
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diff changeset
917 my @headers = () ;
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fgiacomoni
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918
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fgiacomoni
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919 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
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fgiacomoni
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920 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
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fgiacomoni
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diff changeset
921 push @headers, $header ;
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fgiacomoni
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922 push @hmdb_matrix, \@headers ;
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fgiacomoni
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923 }
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fgiacomoni
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diff changeset
924
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fgiacomoni
parents:
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925 my $index_mz = 0 ;
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fgiacomoni
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diff changeset
926
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fgiacomoni
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diff changeset
927 foreach my $mz ( @{$init_mzs} ) {
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928
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929 my $index_entries = 0 ;
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930 my @clusters = () ;
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931 my $cluster_col = undef ;
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diff changeset
932
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933 my @anti_redondant = ('N/A') ;
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fgiacomoni
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934 my $check_rebond = 0 ;
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fgiacomoni
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diff changeset
935
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936 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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fgiacomoni
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937
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fgiacomoni
parents:
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938 foreach my $entry (@{ $entries->[$index_mz] }) {
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fgiacomoni
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diff changeset
939
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fgiacomoni
parents:
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940 ## dispo anti doublons des entries
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fgiacomoni
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941 foreach my $rebond (@anti_redondant) {
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fgiacomoni
parents:
diff changeset
942 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
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943 }
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diff changeset
944
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fgiacomoni
parents:
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945 if ( $check_rebond == 0 ) {
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fgiacomoni
parents:
diff changeset
946
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fgiacomoni
parents:
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947 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
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948 ##
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fgiacomoni
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949 my $hmdb_name = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ;
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fgiacomoni
parents:
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950 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
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fgiacomoni
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diff changeset
951 my $hmdb_formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
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952 my $hmdb_cpd_mz = $entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ;
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diff changeset
953 my $hmdb_adduct = $entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ;
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954 my $hmdb_delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
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955
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fgiacomoni
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956 ## METLIN data display model
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fgiacomoni
parents:
diff changeset
957 ## entry1= ENTRY_DELTA::ENTRY_ENTRY_NAME::ENTRY_CPD_MZ::ENTRY_FORMULA::ENTRY_ADDUCT::ENTRY_ENTRY_ID | entry2=VAR1::VAR2::VAR3::VAR4|...
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diff changeset
958 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
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959
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fgiacomoni
parents:
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960 # manage final pipe
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fgiacomoni
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diff changeset
961 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' | ' ; }
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962 else { $cluster_col .= $entry ; }
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963
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964 }
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965 $check_rebond = 0 ; ## reinit double control
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966 $index_entries++ ;
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967 } ## end foreach
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968 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
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969 push (@clusters, $cluster_col) ;
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970 push (@hmdb_matrix, \@clusters) ;
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fgiacomoni
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971 $index_mz++ ;
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972 }
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973 return(\@hmdb_matrix) ;
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974 }
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fgiacomoni
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975 ## END of SUB
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976
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977 =head2 METHOD add_lm_matrix_to_input_matrix
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fgiacomoni
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978
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979 ## Description : build a full matrix (input + lm column)
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980 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
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981 ## Output : $output_matrix_object
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982 ## Usage : my ( $output_matrix_object ) = add_lm_matrix_to_input_matrix( $input_matrix_object, $lm_matrix_object, $nb_header ) ;
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fgiacomoni
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983
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fgiacomoni
parents:
diff changeset
984 =cut
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fgiacomoni
parents:
diff changeset
985 ## START of SUB
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fgiacomoni
parents:
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986 sub add_lm_matrix_to_input_matrix {
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fgiacomoni
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987 ## Retrieve Values
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988 my $self = shift ;
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989 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
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fgiacomoni
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990
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991 my @output_matrix_object = () ;
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992 my $index_row = 0 ;
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fgiacomoni
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993 my $line = 0 ;
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994
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fgiacomoni
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995 foreach my $row ( @{$input_matrix_object} ) {
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996 my @init_row = @{$row} ;
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997 $line++;
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fgiacomoni
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998
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999 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
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fgiacomoni
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1000 push (@output_matrix_object, \@init_row) ;
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1001 next ;
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1002 }
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fgiacomoni
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1003
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1004 if ( $lm_matrix_object->[$index_row] ) {
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fgiacomoni
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1005 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
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fgiacomoni
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1006
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fgiacomoni
parents:
diff changeset
1007 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
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1008 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
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fgiacomoni
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diff changeset
1009
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fgiacomoni
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1010 push (@init_row, $lm_col) ;
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fgiacomoni
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1011 $index_row++ ;
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1012 }
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1013 push (@output_matrix_object, \@init_row) ;
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1014 }
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1015 return(\@output_matrix_object) ;
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1016 }
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fgiacomoni
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1017 ## END of SUB
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fgiacomoni
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diff changeset
1018
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fgiacomoni
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1019 =head2 METHOD write_csv_skel
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fgiacomoni
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diff changeset
1020
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fgiacomoni
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1021 ## Description : prepare and write csv output file
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fgiacomoni
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1022 ## Input : $csv_file, $rows
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fgiacomoni
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1023 ## Output : $csv_file
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fgiacomoni
parents:
diff changeset
1024 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
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fgiacomoni
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diff changeset
1025
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fgiacomoni
parents:
diff changeset
1026 =cut
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fgiacomoni
parents:
diff changeset
1027 ## START of SUB
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fgiacomoni
parents:
diff changeset
1028 sub write_csv_skel {
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fgiacomoni
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diff changeset
1029 ## Retrieve Values
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fgiacomoni
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diff changeset
1030 my $self = shift ;
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fgiacomoni
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1031 my ( $csv_file, $rows ) = @_ ;
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fgiacomoni
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diff changeset
1032
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fgiacomoni
parents:
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1033 my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
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fgiacomoni
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1034 my $csv = $ocsv->get_csv_object("\t") ;
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fgiacomoni
parents:
diff changeset
1035 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
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fgiacomoni
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diff changeset
1036
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fgiacomoni
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1037 return($csv_file) ;
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fgiacomoni
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diff changeset
1038 }
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fgiacomoni
parents:
diff changeset
1039 ## END of SUB
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fgiacomoni
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diff changeset
1040
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fgiacomoni
parents:
diff changeset
1041 =head2 METHOD write_csv_one_mass
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fgiacomoni
parents:
diff changeset
1042
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fgiacomoni
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diff changeset
1043 ## Description : print a cvs file
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fgiacomoni
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diff changeset
1044 ## Input : $masses, $ids, $results, $file
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fgiacomoni
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1045 ## Output : N/A
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fgiacomoni
parents:
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1046 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
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fgiacomoni
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diff changeset
1047
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fgiacomoni
parents:
diff changeset
1048 =cut
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fgiacomoni
parents:
diff changeset
1049 ## START of SUB
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fgiacomoni
parents:
diff changeset
1050 sub write_csv_one_mass {
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fgiacomoni
parents:
diff changeset
1051 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
1052 my $self = shift ;
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fgiacomoni
parents:
diff changeset
1053 my ( $masses, $ids, $results, $file, ) = @_ ;
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fgiacomoni
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diff changeset
1054
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fgiacomoni
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1055 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
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fgiacomoni
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1056 print CSV "ID\tQuery(Da)\tDelta\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
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fgiacomoni
parents:
diff changeset
1057
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fgiacomoni
parents:
diff changeset
1058 my $i = 0 ;
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fgiacomoni
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diff changeset
1059
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fgiacomoni
parents:
diff changeset
1060 foreach my $id (@{$ids}) {
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fgiacomoni
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1061 my $mass = undef ;
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fgiacomoni
parents:
diff changeset
1062 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
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fgiacomoni
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diff changeset
1063 else { last ; }
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fgiacomoni
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diff changeset
1064
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fgiacomoni
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1065 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
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fgiacomoni
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diff changeset
1066
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fgiacomoni
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1067 my @anti_redondant = ('N/A') ;
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1068 my $check_rebond = 0 ;
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1069 my $check_noentry = 0 ;
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1070
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1071 foreach my $entry (@{$results->[$i]}) {
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1072 $check_noentry ++ ;
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1073 ## dispo anti doublons des entries
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1074 foreach my $rebond (@anti_redondant) {
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1075 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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1076 }
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1077 # print "\n-----------------------" ;
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1078 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
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1079 # print "-------------------------$check_rebond\n" ;
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1080 # print Dumper @anti_redondant ;
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1081 if ( $check_rebond == 0 ) {
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1082
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1083 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
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1084
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1085 print CSV "$id\t$mass\t" ;
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fgiacomoni
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1086
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fgiacomoni
parents:
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1087 ## print delta
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parents:
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1088 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
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parents:
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1089 else { print CSV "0\t" ; }
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1090
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fgiacomoni
parents:
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1091 ## print cpd name
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fgiacomoni
parents:
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1092 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
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parents:
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1093 else { print CSV "UNKNOWN\t" ; }
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parents:
diff changeset
1094
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fgiacomoni
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1095 ## print cpd mz
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fgiacomoni
parents:
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1096 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
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parents:
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1097 else { print CSV "N/A\t" ; }
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parents:
diff changeset
1098
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parents:
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1099 ## print cpd formula
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parents:
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1100 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
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parents:
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1101 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
diff changeset
1102
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parents:
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1103 ## print adduct
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fgiacomoni
parents:
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1104 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
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fgiacomoni
parents:
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1105 else { print CSV "N/A\t" ; }
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parents:
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1106
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fgiacomoni
parents:
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1107 ## print adduct mz
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fgiacomoni
parents:
diff changeset
1108 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
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fgiacomoni
parents:
diff changeset
1109 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
diff changeset
1110
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fgiacomoni
parents:
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1111 ## print cpd id
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fgiacomoni
parents:
diff changeset
1112 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
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fgiacomoni
parents:
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1113 else { print CSV "N/A\n" ; }
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fgiacomoni
parents:
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1114 }
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fgiacomoni
parents:
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1115 $check_rebond = 0 ; ## reinit double control
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fgiacomoni
parents:
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1116 } ## end foreach
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fgiacomoni
parents:
diff changeset
1117 if ($check_noentry == 0 ) {
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fgiacomoni
parents:
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1118 print CSV "$id\t$mass\t0\tUNKNOWN\tN/A\tN/A\tN/A\tN/A\tN/A\n" ;
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fgiacomoni
parents:
diff changeset
1119 }
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fgiacomoni
parents:
diff changeset
1120 }
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fgiacomoni
parents:
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1121 $i++ ;
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fgiacomoni
parents:
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1122 }
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fgiacomoni
parents:
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1123 close(CSV) ;
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fgiacomoni
parents:
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1124 return() ;
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fgiacomoni
parents:
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1125 }
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fgiacomoni
parents:
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1126 ## END of SUB
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fgiacomoni
parents:
diff changeset
1127
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fgiacomoni
parents:
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1128 1 ;
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fgiacomoni
parents:
diff changeset
1129
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fgiacomoni
parents:
diff changeset
1130
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fgiacomoni
parents:
diff changeset
1131 __END__
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fgiacomoni
parents:
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1132
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fgiacomoni
parents:
diff changeset
1133 =head1 SUPPORT
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fgiacomoni
parents:
diff changeset
1134
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fgiacomoni
parents:
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1135 You can find documentation for this module with the perldoc command.
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fgiacomoni
parents:
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1136
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fgiacomoni
parents:
diff changeset
1137 perldoc hmdb.pm
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fgiacomoni
parents:
diff changeset
1138
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fgiacomoni
parents:
diff changeset
1139 =head1 Exports
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fgiacomoni
parents:
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1140
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fgiacomoni
parents:
diff changeset
1141 =over 4
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fgiacomoni
parents:
diff changeset
1142
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fgiacomoni
parents:
diff changeset
1143 =item :ALL is ...
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fgiacomoni
parents:
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1144
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fgiacomoni
parents:
diff changeset
1145 =back
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fgiacomoni
parents:
diff changeset
1146
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fgiacomoni
parents:
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1147 =head1 AUTHOR
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fgiacomoni
parents:
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1148
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fgiacomoni
parents:
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1149 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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fgiacomoni
parents:
diff changeset
1150
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fgiacomoni
parents:
diff changeset
1151 =head1 LICENSE
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fgiacomoni
parents:
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1152
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fgiacomoni
parents:
diff changeset
1153 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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fgiacomoni
parents:
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1154
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fgiacomoni
parents:
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1155 =head1 VERSION
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fgiacomoni
parents:
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1156
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fgiacomoni
parents:
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1157 version 1 : 06 / 06 / 2013
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fgiacomoni
parents:
diff changeset
1158
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fgiacomoni
parents:
diff changeset
1159 version 2 : 27 / 01 / 2014
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fgiacomoni
parents:
diff changeset
1160
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fgiacomoni
parents:
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1161 version 3 : 19 / 11 / 2014
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fgiacomoni
parents:
diff changeset
1162
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fgiacomoni
parents:
diff changeset
1163 version 4 : 28 / 01 / 2016
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fgiacomoni
parents:
diff changeset
1164
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fgiacomoni
parents:
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1165 version 5 : 02 / 11 /2016
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fgiacomoni
parents:
diff changeset
1166
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fgiacomoni
parents:
diff changeset
1167 =cut