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author fgiacomoni
date Wed, 23 Nov 2016 09:31:50 -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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7
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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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18
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19 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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20
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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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25
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26 =head1 NAME
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27
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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}) {
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274
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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 else {
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293 next ;
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294 }
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295 } ## end foreach
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296
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297 ## manage per query_mzs (keep query masses order by array)
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298 my @results = () ;
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299 foreach (@{$masses}) {
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300 if ($result_by_entry{$_}) {
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301
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302 ## cut all entries > $max_query
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303 my @temp_entries = @{$result_by_entry{$_}} ;
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304 my @temp_cut = () ;
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305 my $current_query = 0 ;
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306 foreach (@temp_entries) {
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307 $current_query ++ ;
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308 if ($current_query > $max_query) {
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309 last ;
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310 }
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311 else {
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312 push (@temp_cut, $_) ;
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313 }
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314 }
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315 push (@results, \@temp_cut) ;
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316 # push (@results, $result_by_entry{$_}) ;
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317 }
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318 else {push (@results, [] ) ;} ;
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319
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320 }
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321 return(\@results) ;
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322 }
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323 ## END of SUB
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324
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325 =head2 METHOD parse_hmdb_page_results
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326
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327 ## Description : [DEPRECATED] old HMDB html page parser
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328 ## Input : $page
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329 ## Output : $results
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330 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
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331
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332 =cut
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333 ## START of SUB
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334 sub parse_hmdb_page_results {
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335 ## Retrieve Values
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336 my $self = shift ;
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337 my ( $page ) = @_ ;
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338
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339 my @results = () ;
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340 my ($catch_table, $catch_name) = (0, 0) ;
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341 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
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342
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343 if ( defined $page ) {
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344
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345 my @page = @{$page} ;
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346 my $ID = undef ;
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347 my @result_by_mz = () ;
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348 my %result_by_entry = () ;
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349
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350 foreach my $line (@page) {
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351
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352 #Section de la page contenant les resultat
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353 if( $line =~/<table>/ ) { $catch_table = 1 ; }
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354
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355 ## Si il existe un resultat :
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356 if($catch_table == 1) {
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357
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358 #Id de la molecule, et creation du lien
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359 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
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fgiacomoni
parents:
diff changeset
360 $ID = $1 ;
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fgiacomoni
parents:
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361 $catch_name = 0 ;
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fgiacomoni
parents:
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362 next ;
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fgiacomoni
parents:
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363 }
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fgiacomoni
parents:
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364 #Nom de la molecule ONLY!!
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fgiacomoni
parents:
diff changeset
365 if ( $catch_name == 0 ) {
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fgiacomoni
parents:
diff changeset
366
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fgiacomoni
parents:
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367 if( $line =~ /<td>(.+)<\/td>/ ) {
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fgiacomoni
parents:
diff changeset
368
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fgiacomoni
parents:
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369 if ( !defined $name ) {
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fgiacomoni
parents:
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370 $name = $1 ;
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fgiacomoni
parents:
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371 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
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fgiacomoni
parents:
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372 $result_by_entry{'ENTRY_NAME'} = $name ;
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fgiacomoni
parents:
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373 next ;
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fgiacomoni
parents:
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374 }
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fgiacomoni
parents:
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375 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
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fgiacomoni
parents:
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376 if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; }
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fgiacomoni
parents:
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377 if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; }
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fgiacomoni
parents:
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378 if ( !defined $delta ) {
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fgiacomoni
parents:
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379 $delta = $1 ;
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fgiacomoni
parents:
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380 $result_by_entry{'ENTRY_DELTA'} = $delta ;
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fgiacomoni
parents:
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381 $catch_name = 1 ;
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fgiacomoni
parents:
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382 my %tmp = %result_by_entry ;
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fgiacomoni
parents:
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383 push (@result_by_mz, \%tmp) ;
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fgiacomoni
parents:
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384 %result_by_entry = () ;
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fgiacomoni
parents:
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385 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
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fgiacomoni
parents:
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386 next ;
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fgiacomoni
parents:
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387 }
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fgiacomoni
parents:
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388 }
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fgiacomoni
parents:
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389 }
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fgiacomoni
parents:
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390 }
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fgiacomoni
parents:
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391 #Fin de la section contenant les resultats
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fgiacomoni
parents:
diff changeset
392 if( $line =~ /<\/table>/ ) {
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fgiacomoni
parents:
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393 $catch_table = 0 ;
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fgiacomoni
parents:
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394 my @Tmp = @result_by_mz ;
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fgiacomoni
parents:
diff changeset
395 push(@results, \@Tmp) ;
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fgiacomoni
parents:
diff changeset
396 @result_by_mz = () ;
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fgiacomoni
parents:
diff changeset
397 }
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fgiacomoni
parents:
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398 }
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fgiacomoni
parents:
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399 }
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fgiacomoni
parents:
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400 return(\@results) ;
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fgiacomoni
parents:
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401 }
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fgiacomoni
parents:
diff changeset
402 ## END of SUB
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fgiacomoni
parents:
diff changeset
403
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fgiacomoni
parents:
diff changeset
404
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fgiacomoni
parents:
diff changeset
405 =head2 METHOD get_unik_ids_from_results
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fgiacomoni
parents:
diff changeset
406
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fgiacomoni
parents:
diff changeset
407 ## Description : get all unik ids from the hmdb result object
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fgiacomoni
parents:
diff changeset
408 ## Input : $results
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fgiacomoni
parents:
diff changeset
409 ## Output : $ids
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fgiacomoni
parents:
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410 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
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fgiacomoni
parents:
diff changeset
411
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fgiacomoni
parents:
diff changeset
412 =cut
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fgiacomoni
parents:
diff changeset
413 ## START of SUB
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fgiacomoni
parents:
diff changeset
414 sub get_unik_ids_from_results {
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fgiacomoni
parents:
diff changeset
415 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
416 my $self = shift ;
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fgiacomoni
parents:
diff changeset
417 my ( $results ) = @_;
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fgiacomoni
parents:
diff changeset
418 my ( %ids ) = ( () ) ;
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fgiacomoni
parents:
diff changeset
419
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fgiacomoni
parents:
diff changeset
420 foreach my $result (@{$results}) {
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fgiacomoni
parents:
diff changeset
421
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fgiacomoni
parents:
diff changeset
422 foreach my $entries (@{$result}) {
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fgiacomoni
parents:
diff changeset
423
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fgiacomoni
parents:
diff changeset
424 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
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fgiacomoni
parents:
diff changeset
425 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
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fgiacomoni
parents:
diff changeset
426 }
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fgiacomoni
parents:
diff changeset
427 }
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fgiacomoni
parents:
diff changeset
428 }
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fgiacomoni
parents:
diff changeset
429
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fgiacomoni
parents:
diff changeset
430 return (\%ids) ;
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fgiacomoni
parents:
diff changeset
431 }
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fgiacomoni
parents:
diff changeset
432 ### END of SUB
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fgiacomoni
parents:
diff changeset
433
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fgiacomoni
parents:
diff changeset
434
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fgiacomoni
parents:
diff changeset
435
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fgiacomoni
parents:
diff changeset
436 =head2 METHOD get_hmdb_metabocard_from_id
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fgiacomoni
parents:
diff changeset
437
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
438 ## Description : get a metabocard (xml format from an ID on HMDB)
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fgiacomoni
parents:
diff changeset
439 ## Input : $ids
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fgiacomoni
parents:
diff changeset
440 ## Output : $metabocard_features
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fgiacomoni
parents:
diff changeset
441 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
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fgiacomoni
parents:
diff changeset
442
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
443 =cut
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fgiacomoni
parents:
diff changeset
444 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
445 sub get_hmdb_metabocard_from_id {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
446 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
447 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
448 my ( $ids, $hmdb_url ) = @_;
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fgiacomoni
parents:
diff changeset
449 my ( %metabocard_features ) = ( () ) ;
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fgiacomoni
parents:
diff changeset
450 my $query = undef ;
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fgiacomoni
parents:
diff changeset
451
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
452 ## structure %metabocard_features
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fgiacomoni
parents:
diff changeset
453 # metabolite_id = (
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fgiacomoni
parents:
diff changeset
454 # 'metabolite_name' => '__name__',
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fgiacomoni
parents:
diff changeset
455 # 'metabolite_inchi' => '__inchi__',
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fgiacomoni
parents:
diff changeset
456 # 'metabolite_logp' => '__logp-ALOGPS__',
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fgiacomoni
parents:
diff changeset
457 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
458 # )
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fgiacomoni
parents:
diff changeset
459
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
460
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
461 if( (defined $ids) and ($ids > 0 ) ) {
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fgiacomoni
parents:
diff changeset
462
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
463 foreach my $id (keys %{$ids}) {
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fgiacomoni
parents:
diff changeset
464
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
465 # print "\n============== > $id **********************\n " ;
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fgiacomoni
parents:
diff changeset
466 my $twig = undef ;
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fgiacomoni
parents:
diff changeset
467
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fgiacomoni
parents:
diff changeset
468 if (defined $hmdb_url) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
469 $query = $hmdb_url.$id.'.xml' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
470
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
471 ## test the header if exists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
472 my $response = head($query) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
473
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
474 if (!defined $response) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
475 $metabocard_features{$id}{'metabolite_name'} = undef ;
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fgiacomoni
parents:
diff changeset
476 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
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fgiacomoni
parents:
diff changeset
477 $metabocard_features{$id}{'metabolite_logp'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
478 ## Need to be improve to manage http 404 or other response diff than 200
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fgiacomoni
parents:
diff changeset
479 }
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fgiacomoni
parents:
diff changeset
480 elsif ($response->is_success) {
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fgiacomoni
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481
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482 $twig = XML::Twig->nparse_ppe(
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fgiacomoni
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483
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fgiacomoni
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484 twig_handlers => {
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fgiacomoni
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485 # metabolite name
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486 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; } ,
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fgiacomoni
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487 # metabolite inchi
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488 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; } ,
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fgiacomoni
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489 ## metabolite logP
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490 'metabolite/predicted_properties/property' => sub {
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491
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fgiacomoni
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492 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
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493
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494 if (defined $_->children ) {
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495 foreach my $field ($_->children) {
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496 if ( $field->name eq 'kind') { $kind = $field->text ; }
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fgiacomoni
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497 elsif ( $field->name eq 'source') { $source = $field->text ; }
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498 elsif ( $field->name eq 'value') { $value = $field->text ; }
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fgiacomoni
parents:
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499
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fgiacomoni
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500 if (defined $source ) {
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501 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
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fgiacomoni
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502 $metabocard_features{$id}{'metabolite_logp'} = $value ;
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fgiacomoni
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503 }
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fgiacomoni
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504 ($kind, $source, $value ) = ( undef, undef, undef ) ;
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fgiacomoni
parents:
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505 }
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fgiacomoni
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506 }
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fgiacomoni
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507 }
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fgiacomoni
parents:
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508 }
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fgiacomoni
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509 },
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fgiacomoni
parents:
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510 pretty_print => 'indented',
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fgiacomoni
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511 error_context => 1, $query
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512 );
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fgiacomoni
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513
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fgiacomoni
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514 # $twig->print;
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fgiacomoni
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515 $twig->purge ;
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fgiacomoni
parents:
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516
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fgiacomoni
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517 if (!$@) {
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fgiacomoni
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518
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fgiacomoni
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519 }
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520 else {
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fgiacomoni
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521 warn $@ ;
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522 }
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523 }
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524 }
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fgiacomoni
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525 else {
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fgiacomoni
parents:
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526 warn "The hmdb metabocard url is not defined\n" ;
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fgiacomoni
parents:
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527 last;
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fgiacomoni
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528 }
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fgiacomoni
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529 }
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fgiacomoni
parents:
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530 }
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fgiacomoni
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531 else {
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fgiacomoni
parents:
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532 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
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fgiacomoni
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533 }
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fgiacomoni
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534
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fgiacomoni
parents:
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535 # print Dumper %metabocard_features ;
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fgiacomoni
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536 return (\%metabocard_features) ;
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fgiacomoni
parents:
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537 }
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fgiacomoni
parents:
diff changeset
538 ### END of SUB
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fgiacomoni
parents:
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539
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fgiacomoni
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540
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fgiacomoni
parents:
diff changeset
541 =head2 METHOD map_suppl_data_on_hmdb_results
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fgiacomoni
parents:
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542
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fgiacomoni
parents:
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543 ## Description : map supplementary data with already collected results with hmdb search
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fgiacomoni
parents:
diff changeset
544 ## Input : $results, $features
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fgiacomoni
parents:
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545 ## Output : $results
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fgiacomoni
parents:
diff changeset
546 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
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fgiacomoni
parents:
diff changeset
547
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fgiacomoni
parents:
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548 =cut
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fgiacomoni
parents:
diff changeset
549 ## START of SUB
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fgiacomoni
parents:
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550 sub map_suppl_data_on_hmdb_results {
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fgiacomoni
parents:
diff changeset
551 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
552 my $self = shift ;
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fgiacomoni
parents:
diff changeset
553 my ( $results, $features ) = @_;
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fgiacomoni
parents:
diff changeset
554 my ( @more_results ) = ( () ) ;
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fgiacomoni
parents:
diff changeset
555
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fgiacomoni
parents:
diff changeset
556 @more_results = @{$results} ; ## Dump array ref to map
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fgiacomoni
parents:
diff changeset
557
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
558 foreach my $result (@more_results) {
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fgiacomoni
parents:
diff changeset
559
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fgiacomoni
parents:
diff changeset
560 foreach my $entries (@{$result}) {
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fgiacomoni
parents:
diff changeset
561
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fgiacomoni
parents:
diff changeset
562 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
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fgiacomoni
parents:
diff changeset
563 ## check that we have a ID for mapping
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fgiacomoni
parents:
diff changeset
564 my $current_id = $entries->{'ENTRY_ENTRY_ID'} ;
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fgiacomoni
parents:
diff changeset
565 if ($features->{"$current_id"}) {
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fgiacomoni
parents:
diff changeset
566 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
567 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
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fgiacomoni
parents:
diff changeset
568 $entries->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
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fgiacomoni
parents:
diff changeset
569 }
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fgiacomoni
parents:
diff changeset
570 else {
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fgiacomoni
parents:
diff changeset
571 $entries->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
572 }
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fgiacomoni
parents:
diff changeset
573 ## Metabolite INCHI
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fgiacomoni
parents:
diff changeset
574 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
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fgiacomoni
parents:
diff changeset
575 $entries->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
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fgiacomoni
parents:
diff changeset
576 }
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fgiacomoni
parents:
diff changeset
577 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
578 $entries->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
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fgiacomoni
parents:
diff changeset
579 }
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fgiacomoni
parents:
diff changeset
580 ## Metabolite LOGP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
581 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
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fgiacomoni
parents:
diff changeset
582 $entries->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
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fgiacomoni
parents:
diff changeset
583 }
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fgiacomoni
parents:
diff changeset
584 else {
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fgiacomoni
parents:
diff changeset
585 $entries->{'ENTRY_ENTRY_LOGP'} = 'NA' ;
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fgiacomoni
parents:
diff changeset
586 }
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fgiacomoni
parents:
diff changeset
587 }
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fgiacomoni
parents:
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588 else {
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fgiacomoni
parents:
diff changeset
589 warn "This HMDB id doesn't match any collected ids\n" ;
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fgiacomoni
parents:
diff changeset
590 }
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fgiacomoni
parents:
diff changeset
591 }
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fgiacomoni
parents:
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592 }
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fgiacomoni
parents:
diff changeset
593 }
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fgiacomoni
parents:
diff changeset
594
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
595 return (\@more_results) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
596 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
597 ### END of SUB
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fgiacomoni
parents:
diff changeset
598
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fgiacomoni
parents:
diff changeset
599
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
600 =head2 METHOD set_html_tbody_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
601
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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602 ## Description : initializes and build the tbody object (perl array) needed to html template
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603 ## Input : $nb_pages, $nb_items_per_page
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604 ## Output : $tbody_object
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605 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
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606
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607 =cut
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608 ## START of SUB
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609 sub set_html_tbody_object {
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610 my $self = shift ;
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611 my ( $nb_pages, $nb_items_per_page ) = @_ ;
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612
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613 my ( @tbody_object ) = ( ) ;
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614
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615 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
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616
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617 my %pages = (
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618 # tbody feature
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619 PAGE_NB => $i,
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620 MASSES => [], ## end MASSES
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621 ) ; ## end TBODY N
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622 push (@tbody_object, \%pages) ;
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623 }
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624 return(\@tbody_object) ;
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625 }
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626 ## END of SUB
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627
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628 =head2 METHOD add_mz_to_tbody_object
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629
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630 ## Description : initializes and build the mz object (perl array) needed to html template
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631 ## Input : $tbody_object, $nb_items_per_page, $mz_list
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632 ## Output : $tbody_object
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633 ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
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634
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635 =cut
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fgiacomoni
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636 ## START of SUB
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637 sub add_mz_to_tbody_object {
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638 my $self = shift ;
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639 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
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640
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641 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
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642
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643 foreach my $page ( @{$tbody_object} ) {
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644
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645 my @colors = ('white', 'green') ;
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646 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
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647
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648 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
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649 #
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650 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
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651 $current_index = 0 ;
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652 last ; ##
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653 }
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654 else {
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655 $current_index++ ;
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656 if ( $icolor > 1 ) { $icolor = 0 ; }
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657
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658 if ( exists $mz_list->[$mz_index] ) {
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659
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660 my %mz = (
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661 # mass feature
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662 MASSES_ID_QUERY => $ids_list->[$mz_index],
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663 MASSES_MZ_QUERY => $mz_list->[$mz_index],
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664 MZ_COLOR => $colors[$icolor],
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665 MASSES_NB => $mz_index+1,
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666 ENTRIES => [] ,
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667 ) ;
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668 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
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669 # Html attr for mass
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670 $icolor++ ;
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671 }
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672 }
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673 $mz_index++ ;
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674 } ## foreach mz
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675
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676 $current_page++ ;
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677 }
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678 return($tbody_object) ;
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679 }
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680 ## END of SUB
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681
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682 =head2 METHOD add_entries_to_tbody_object
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683
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684 ## Description : initializes and build the entries object (perl array) needed to html template
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685 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
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686 ## Output : $tbody_object
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687 ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
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688
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689 =cut
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fgiacomoni
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690 ## START of SUB
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691 sub add_entries_to_tbody_object {
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692 ## Retrieve Values
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693 my $self = shift ;
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694 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
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695
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696 my $index_page = 0 ;
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697 my $index_mz_continous = 0 ;
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698
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699 foreach my $page (@{$tbody_object}) {
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700
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701 my $index_mz = 0 ;
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702
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703 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
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704
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705 my $index_entry = 0 ;
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706
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707 my @anti_redondant = ('N/A') ;
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708 my $check_rebond = 0 ;
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709 my $check_noentry = 0 ;
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710
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711 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
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712 $check_noentry ++ ;
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713 ## dispo anti doublons des entries
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714 foreach my $rebond (@anti_redondant) {
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715 if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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716 }
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717
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718 if ( $check_rebond == 0 ) {
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719
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720 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
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721
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diff changeset
722 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
723 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
724 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
725 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
726 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
727 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
728 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
729 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
730 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
731 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
732 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
733 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
734 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
735 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
736
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
737 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
738 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
739 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
740 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
741 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
742 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
743 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
744 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
745 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
746 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
747 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
748 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
749 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
750 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
751 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
752 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
753 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
754 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
755 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
756 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
757 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
758 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
759 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
760 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
761 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
762 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
763 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
764 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
765 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
766 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
767
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
768 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
769
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
770 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
771 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
772 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
773 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
774
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
775 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
776 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
777 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
778 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
779 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
780 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
781
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
782 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
783
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
784 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
785 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
786
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
787 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
788 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
789 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
790 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
791 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
792 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
793 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
794 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
795 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
796 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
797 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
798
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
799 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
800 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
801 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
802 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
803 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
804 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
805 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
806 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
807
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
808 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
809
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
810 ## Description : build the hmdb_row under its ref form
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
811 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
812 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
813 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
814
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
815 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
816 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
817 sub set_lm_matrix_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
818 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
819 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
820 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
821
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
822 my @hmdb_matrix = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
823
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
824 if ( defined $header ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
825 my @headers = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
826 push @headers, $header ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
827 push @hmdb_matrix, \@headers ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
828 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
829
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
830 my $index_mz = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
831
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
832 foreach my $mz ( @{$init_mzs} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
833
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
834 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
835 my @clusters = () ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
836 my $cluster_col = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
837
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
838 my @anti_redondant = ('N/A') ;
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fgiacomoni
parents:
diff changeset
839 my $check_rebond = 0 ;
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fgiacomoni
parents:
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840
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fgiacomoni
parents:
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841 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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fgiacomoni
parents:
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842
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fgiacomoni
parents:
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843 foreach my $entry (@{ $entries->[$index_mz] }) {
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fgiacomoni
parents:
diff changeset
844
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fgiacomoni
parents:
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845 ## dispo anti doublons des entries
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fgiacomoni
parents:
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846 foreach my $rebond (@anti_redondant) {
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fgiacomoni
parents:
diff changeset
847 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
parents:
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848 }
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fgiacomoni
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849
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fgiacomoni
parents:
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850 if ( $check_rebond == 0 ) {
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fgiacomoni
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851
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fgiacomoni
parents:
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852 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
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853
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fgiacomoni
parents:
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854 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
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fgiacomoni
parents:
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855 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
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fgiacomoni
parents:
diff changeset
856 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
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fgiacomoni
parents:
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857
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fgiacomoni
parents:
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858 ## METLIN data display model
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fgiacomoni
parents:
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859 ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
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fgiacomoni
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860 # manage final pipe
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fgiacomoni
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861 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; }
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fgiacomoni
parents:
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862 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
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fgiacomoni
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863
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fgiacomoni
parents:
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864 }
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fgiacomoni
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865 $check_rebond = 0 ; ## reinit double control
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fgiacomoni
parents:
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866 $index_entries++ ;
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fgiacomoni
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867 } ## end foreach
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fgiacomoni
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868 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
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fgiacomoni
parents:
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869 push (@clusters, $cluster_col) ;
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fgiacomoni
parents:
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870 push (@hmdb_matrix, \@clusters) ;
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fgiacomoni
parents:
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871 $index_mz++ ;
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fgiacomoni
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872 }
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fgiacomoni
parents:
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873 return(\@hmdb_matrix) ;
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fgiacomoni
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874 }
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fgiacomoni
parents:
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875 ## END of SUB
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fgiacomoni
parents:
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876
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fgiacomoni
parents:
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877 =head2 METHOD set_hmdb_matrix_object_with_ids
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fgiacomoni
parents:
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878
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fgiacomoni
parents:
diff changeset
879 ## Description : build the hmdb_row under its ref form (IDS only)
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fgiacomoni
parents:
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880 ## Input : $header, $init_mzs, $entries
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fgiacomoni
parents:
diff changeset
881 ## Output : $hmdb_matrix
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fgiacomoni
parents:
diff changeset
882 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
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fgiacomoni
parents:
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883
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fgiacomoni
parents:
diff changeset
884 =cut
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fgiacomoni
parents:
diff changeset
885 ## START of SUB
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fgiacomoni
parents:
diff changeset
886 sub set_hmdb_matrix_object_with_ids {
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fgiacomoni
parents:
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887 ## Retrieve Values
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fgiacomoni
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888 my $self = shift ;
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fgiacomoni
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diff changeset
889 my ( $header, $init_mzs, $entries ) = @_ ;
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fgiacomoni
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diff changeset
890
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fgiacomoni
parents:
diff changeset
891 my @hmdb_matrix = () ;
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fgiacomoni
parents:
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892
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fgiacomoni
parents:
diff changeset
893 if ( defined $header ) {
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fgiacomoni
parents:
diff changeset
894 my @headers = () ;
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fgiacomoni
parents:
diff changeset
895
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fgiacomoni
parents:
diff changeset
896 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
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fgiacomoni
parents:
diff changeset
897 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
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fgiacomoni
parents:
diff changeset
898 push @headers, $header ;
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fgiacomoni
parents:
diff changeset
899 push @hmdb_matrix, \@headers ;
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fgiacomoni
parents:
diff changeset
900 }
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fgiacomoni
parents:
diff changeset
901
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fgiacomoni
parents:
diff changeset
902 my $index_mz = 0 ;
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fgiacomoni
parents:
diff changeset
903
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fgiacomoni
parents:
diff changeset
904 foreach my $mz ( @{$init_mzs} ) {
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fgiacomoni
parents:
diff changeset
905
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fgiacomoni
parents:
diff changeset
906 my $index_entries = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
907 my @clusters = () ;
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fgiacomoni
parents:
diff changeset
908 my $cluster_col = undef ;
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fgiacomoni
parents:
diff changeset
909
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fgiacomoni
parents:
diff changeset
910 my @anti_redondant = ('N/A') ;
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fgiacomoni
parents:
diff changeset
911 my $check_rebond = 0 ;
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fgiacomoni
parents:
diff changeset
912
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fgiacomoni
parents:
diff changeset
913 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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fgiacomoni
parents:
diff changeset
914
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fgiacomoni
parents:
diff changeset
915 foreach my $entry (@{ $entries->[$index_mz] }) {
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fgiacomoni
parents:
diff changeset
916
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fgiacomoni
parents:
diff changeset
917 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
918 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
919 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
parents:
diff changeset
920 }
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fgiacomoni
parents:
diff changeset
921
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fgiacomoni
parents:
diff changeset
922 if ( $check_rebond == 0 ) {
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fgiacomoni
parents:
diff changeset
923
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fgiacomoni
parents:
diff changeset
924 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
parents:
diff changeset
925 ##
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fgiacomoni
parents:
diff changeset
926 my $hmdb_name = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ;
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fgiacomoni
parents:
diff changeset
927 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
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fgiacomoni
parents:
diff changeset
928 my $hmdb_formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
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fgiacomoni
parents:
diff changeset
929 my $hmdb_cpd_mz = $entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ;
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fgiacomoni
parents:
diff changeset
930 my $hmdb_adduct = $entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ;
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fgiacomoni
parents:
diff changeset
931 my $hmdb_delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
932
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
933 ## METLIN data display model
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
934 ## 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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fgiacomoni
parents:
diff changeset
935 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
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fgiacomoni
parents:
diff changeset
936
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
937 # manage final pipe
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
938 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' | ' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
939 else { $cluster_col .= $entry ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
940
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
941 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
942 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
943 $index_entries++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
944 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
945 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
946 push (@clusters, $cluster_col) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
947 push (@hmdb_matrix, \@clusters) ;
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fgiacomoni
parents:
diff changeset
948 $index_mz++ ;
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fgiacomoni
parents:
diff changeset
949 }
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fgiacomoni
parents:
diff changeset
950 return(\@hmdb_matrix) ;
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fgiacomoni
parents:
diff changeset
951 }
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fgiacomoni
parents:
diff changeset
952 ## END of SUB
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fgiacomoni
parents:
diff changeset
953
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954 =head2 METHOD add_lm_matrix_to_input_matrix
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fgiacomoni
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955
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fgiacomoni
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956 ## Description : build a full matrix (input + lm column)
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957 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
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958 ## Output : $output_matrix_object
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959 ## 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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960
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fgiacomoni
parents:
diff changeset
961 =cut
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fgiacomoni
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diff changeset
962 ## START of SUB
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fgiacomoni
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963 sub add_lm_matrix_to_input_matrix {
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fgiacomoni
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964 ## Retrieve Values
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fgiacomoni
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965 my $self = shift ;
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fgiacomoni
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966 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
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fgiacomoni
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967
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968 my @output_matrix_object = () ;
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969 my $index_row = 0 ;
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fgiacomoni
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970 my $line = 0 ;
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fgiacomoni
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971
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fgiacomoni
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972 foreach my $row ( @{$input_matrix_object} ) {
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fgiacomoni
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973 my @init_row = @{$row} ;
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974 $line++;
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fgiacomoni
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975
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fgiacomoni
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976 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
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fgiacomoni
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977 push (@output_matrix_object, \@init_row) ;
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fgiacomoni
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978 next ;
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fgiacomoni
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979 }
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980
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981 if ( $lm_matrix_object->[$index_row] ) {
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fgiacomoni
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982 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
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fgiacomoni
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983
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fgiacomoni
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984 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
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fgiacomoni
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985 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
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fgiacomoni
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986
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987 push (@init_row, $lm_col) ;
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988 $index_row++ ;
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989 }
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990 push (@output_matrix_object, \@init_row) ;
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991 }
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992 return(\@output_matrix_object) ;
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993 }
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994 ## END of SUB
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fgiacomoni
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995
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fgiacomoni
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996 =head2 METHOD write_csv_skel
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fgiacomoni
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997
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fgiacomoni
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998 ## Description : prepare and write csv output file
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fgiacomoni
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999 ## Input : $csv_file, $rows
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1000 ## Output : $csv_file
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fgiacomoni
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1001 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
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fgiacomoni
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1002
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fgiacomoni
parents:
diff changeset
1003 =cut
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fgiacomoni
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1004 ## START of SUB
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fgiacomoni
parents:
diff changeset
1005 sub write_csv_skel {
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fgiacomoni
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1006 ## Retrieve Values
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1007 my $self = shift ;
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fgiacomoni
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1008 my ( $csv_file, $rows ) = @_ ;
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fgiacomoni
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1009
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1010 my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
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fgiacomoni
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1011 my $csv = $ocsv->get_csv_object("\t") ;
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fgiacomoni
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1012 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
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fgiacomoni
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1013
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1014 return($csv_file) ;
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1015 }
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fgiacomoni
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1016 ## END of SUB
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fgiacomoni
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1017
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fgiacomoni
parents:
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1018 =head2 METHOD write_csv_one_mass
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fgiacomoni
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1019
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fgiacomoni
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diff changeset
1020 ## Description : print a cvs file
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fgiacomoni
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1021 ## Input : $masses, $ids, $results, $file
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fgiacomoni
parents:
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1022 ## Output : N/A
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fgiacomoni
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1023 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
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fgiacomoni
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1024
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fgiacomoni
parents:
diff changeset
1025 =cut
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fgiacomoni
parents:
diff changeset
1026 ## START of SUB
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fgiacomoni
parents:
diff changeset
1027 sub write_csv_one_mass {
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fgiacomoni
parents:
diff changeset
1028 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
1029 my $self = shift ;
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fgiacomoni
parents:
diff changeset
1030 my ( $masses, $ids, $results, $file, ) = @_ ;
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fgiacomoni
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diff changeset
1031
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1032 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
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fgiacomoni
parents:
diff changeset
1033 print CSV "ID\tQuery(Da)\tDelta\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
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fgiacomoni
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diff changeset
1034
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fgiacomoni
parents:
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1035 my $i = 0 ;
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fgiacomoni
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diff changeset
1036
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fgiacomoni
parents:
diff changeset
1037 foreach my $id (@{$ids}) {
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fgiacomoni
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1038 my $mass = undef ;
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fgiacomoni
parents:
diff changeset
1039 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
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fgiacomoni
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diff changeset
1040 else { last ; }
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fgiacomoni
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diff changeset
1041
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fgiacomoni
parents:
diff changeset
1042 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
1043
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fgiacomoni
parents:
diff changeset
1044 my @anti_redondant = ('N/A') ;
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fgiacomoni
parents:
diff changeset
1045 my $check_rebond = 0 ;
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fgiacomoni
parents:
diff changeset
1046 my $check_noentry = 0 ;
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fgiacomoni
parents:
diff changeset
1047
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fgiacomoni
parents:
diff changeset
1048 foreach my $entry (@{$results->[$i]}) {
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fgiacomoni
parents:
diff changeset
1049 $check_noentry ++ ;
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fgiacomoni
parents:
diff changeset
1050 ## dispo anti doublons des entries
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fgiacomoni
parents:
diff changeset
1051 foreach my $rebond (@anti_redondant) {
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fgiacomoni
parents:
diff changeset
1052 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
parents:
diff changeset
1053 }
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fgiacomoni
parents:
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1054 # print "\n-----------------------" ;
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fgiacomoni
parents:
diff changeset
1055 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
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fgiacomoni
parents:
diff changeset
1056 # print "-------------------------$check_rebond\n" ;
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fgiacomoni
parents:
diff changeset
1057 # print Dumper @anti_redondant ;
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fgiacomoni
parents:
diff changeset
1058 if ( $check_rebond == 0 ) {
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fgiacomoni
parents:
diff changeset
1059
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fgiacomoni
parents:
diff changeset
1060 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
parents:
diff changeset
1061
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fgiacomoni
parents:
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1062 print CSV "$id\t$mass\t" ;
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fgiacomoni
parents:
diff changeset
1063
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fgiacomoni
parents:
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1064 ## print delta
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fgiacomoni
parents:
diff changeset
1065 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
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fgiacomoni
parents:
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1066 else { print CSV "0\t" ; }
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fgiacomoni
parents:
diff changeset
1067
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fgiacomoni
parents:
diff changeset
1068 ## print cpd name
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fgiacomoni
parents:
diff changeset
1069 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
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fgiacomoni
parents:
diff changeset
1070 else { print CSV "UNKNOWN\t" ; }
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fgiacomoni
parents:
diff changeset
1071
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fgiacomoni
parents:
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1072 ## print cpd mz
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fgiacomoni
parents:
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1073 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
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parents:
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1074 else { print CSV "N/A\t" ; }
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1075
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fgiacomoni
parents:
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1076 ## print cpd formula
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fgiacomoni
parents:
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1077 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
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fgiacomoni
parents:
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1078 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
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1079
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1080 ## print adduct
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fgiacomoni
parents:
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1081 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
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fgiacomoni
parents:
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1082 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
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1083
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fgiacomoni
parents:
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1084 ## print adduct mz
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fgiacomoni
parents:
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1085 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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1086 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
diff changeset
1087
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fgiacomoni
parents:
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1088 ## print cpd id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1089 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
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fgiacomoni
parents:
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1090 else { print CSV "N/A\n" ; }
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fgiacomoni
parents:
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1091 }
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fgiacomoni
parents:
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1092 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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1093 } ## end foreach
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fgiacomoni
parents:
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1094 if ($check_noentry == 0 ) {
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fgiacomoni
parents:
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1095 print CSV "$id\t$mass\t0\tUNKNOWN\tN/A\tN/A\tN/A\tN/A\tN/A\n" ;
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fgiacomoni
parents:
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1096 }
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fgiacomoni
parents:
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1097 }
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fgiacomoni
parents:
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1098 $i++ ;
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fgiacomoni
parents:
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1099 }
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fgiacomoni
parents:
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1100 close(CSV) ;
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fgiacomoni
parents:
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1101 return() ;
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fgiacomoni
parents:
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1102 }
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fgiacomoni
parents:
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1103 ## END of SUB
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fgiacomoni
parents:
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1104
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fgiacomoni
parents:
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1105 1 ;
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fgiacomoni
parents:
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1106
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fgiacomoni
parents:
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1107
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fgiacomoni
parents:
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1108 __END__
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fgiacomoni
parents:
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1109
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fgiacomoni
parents:
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1110 =head1 SUPPORT
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fgiacomoni
parents:
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1111
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fgiacomoni
parents:
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1112 You can find documentation for this module with the perldoc command.
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fgiacomoni
parents:
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1113
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fgiacomoni
parents:
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1114 perldoc hmdb.pm
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fgiacomoni
parents:
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1115
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fgiacomoni
parents:
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1116 =head1 Exports
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fgiacomoni
parents:
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1117
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fgiacomoni
parents:
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1118 =over 4
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fgiacomoni
parents:
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1119
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fgiacomoni
parents:
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1120 =item :ALL is ...
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fgiacomoni
parents:
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1121
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fgiacomoni
parents:
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1122 =back
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fgiacomoni
parents:
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1123
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fgiacomoni
parents:
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1124 =head1 AUTHOR
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fgiacomoni
parents:
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1125
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fgiacomoni
parents:
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1126 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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fgiacomoni
parents:
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1127
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fgiacomoni
parents:
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1128 =head1 LICENSE
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fgiacomoni
parents:
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1129
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fgiacomoni
parents:
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1130 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
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1131
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fgiacomoni
parents:
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1132 =head1 VERSION
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fgiacomoni
parents:
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1133
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fgiacomoni
parents:
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1134 version 1 : 06 / 06 / 2013
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fgiacomoni
parents:
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1135
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fgiacomoni
parents:
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1136 version 2 : 27 / 01 / 2014
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fgiacomoni
parents:
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1137
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fgiacomoni
parents:
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1138 version 3 : 19 / 11 / 2014
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fgiacomoni
parents:
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1139
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fgiacomoni
parents:
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1140 version 4 : 28 / 01 / 2016
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fgiacomoni
parents:
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1141
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fgiacomoni
parents:
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1142 version 5 : 02 / 11 /2016
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fgiacomoni
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1143
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fgiacomoni
parents:
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1144 =cut