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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
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15 use Data::Dumper ;
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16
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17 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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18
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19 our $VERSION = "1.0";
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20 our @ISA = qw(Exporter);
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21 our @EXPORT = qw( 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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22 our %EXPORT_TAGS = ( ALL => [qw( 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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23
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24 =head1 NAME
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25
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26 My::Module - An example module
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27
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28 =head1 SYNOPSIS
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29
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30 use My::Module;
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31 my $object = My::Module->new();
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32 print $object->as_string;
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33
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34 =head1 DESCRIPTION
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35
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36 This module does not really exist, it
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37 was made for the sole purpose of
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38 demonstrating how POD works.
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39
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40 =head1 METHODS
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41
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42 Methods are :
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43
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44 =head2 METHOD new
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45
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46 ## Description : new
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47 ## Input : $self
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48 ## Ouput : bless $self ;
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49 ## Usage : new() ;
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50
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51 =cut
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52
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53 sub new {
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54 ## Variables
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55 my $self={};
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56 bless($self) ;
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57 return $self ;
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58 }
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59 ### END of SUB
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60
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61
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62 =head2 METHOD extract_sub_mz_lists
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63
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64 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
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65 ## Input : $HMDB_LIMITS, $masses
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66 ## Output : $sublists
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67 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
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68
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69 =cut
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70 ## START of SUB
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71 sub extract_sub_mz_lists {
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72 ## Retrieve Values
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73 my $self = shift ;
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74 my ( $masses, $HMDB_LIMITS ) = @_ ;
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75
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76 my ( @sublists, @sublist ) = ( (), () ) ;
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77 my $nb_mz = 0 ;
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78 my $nb_total_mzs = scalar(@{$masses}) ;
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79
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80 if ($nb_total_mzs == 0) {
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81 die "The provided mzs list is empty" ;
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82 }
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83
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84 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
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85
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86 if ( $nb_mz < $HMDB_LIMITS ) {
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87 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
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88 }
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89 elsif ( $nb_mz == $HMDB_LIMITS ) {
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90 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
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91 $current_pos-- ;
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92 }
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93 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
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94 }
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95 return(\@sublists) ;
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96 }
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97 ## END of SUB
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98
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99 =head2 METHOD prepare_multi_masses_query
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100
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101 ## Description : Generate the adapted format of the mz list for HMDB
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102 ## Input : $masses
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103 ## Output : $hmdb_masses
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104 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
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105
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106 =cut
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107 ## START of SUB
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108 sub prepare_multi_masses_query {
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109 ## Retrieve Values
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110 my $self = shift ;
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111 my ( $masses ) = @_ ;
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112
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113 my $hmdb_masses = undef ;
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114 my $sep = '%0D%0A' ; ## retour chariot encode
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115 my ($nb_masses, $i) = (0, 0) ;
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116
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117 if ( defined $masses ) {
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118 my @masses = @{$masses} ;
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119 my $nb_masses = scalar ( @masses ) ;
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120 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
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121 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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122
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123 foreach my $mass (@masses) {
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124
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125 if ($i < $nb_masses) {
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126 $hmdb_masses .= $mass.$sep ;
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127 }
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128 elsif ( $i == $nb_masses ) {
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129 $hmdb_masses .= $mass ;
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130 }
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131 else {
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132 last ;
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133 }
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134 $i ++ ;
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135 }
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136 }
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137 else {
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138 croak "No mass list found \n" ;
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139 }
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140 return($hmdb_masses, $nb_masses) ;
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141 }
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142 ## END of SUB
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143
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144 =head2 METHOD test_matches_from_hmdb_ua
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145
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146 ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
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147 ## Input : none
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148 ## Output : $status_line
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149 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
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150
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151 =cut
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152 ## START of SUB
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153 sub test_matches_from_hmdb_ua {
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154 ## Retrieve Values
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155 my $self = shift ;
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156
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157 my @page = () ;
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158
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159 my $ua = new LWP::UserAgent;
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160 $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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161
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162 my $req = HTTP::Request->new(
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163 POST => 'http://specdb.wishartlab.com/ms/search.csv');
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164
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165 $req->content_type('application/x-www-form-urlencoded');
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166 $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV');
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167
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168 my $res = $ua->request($req);
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169 # print $res->as_string;
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170 my $status_line = $res->status_line ;
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171 ($status_line) = ($status_line =~ /(\d+)/);
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172
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173
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174 return (\$status_line) ;
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175 }
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176 ## END of SUB
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177
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178 =head2 METHOD check_state_from_hmdb_ua
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179
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180 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
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181 ## Input : $status
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182 ## Output : none
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183 ## Usage : check_state_from_hmdb_ua($status) ;
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184
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185 =cut
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186 ## START of SUB
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187 sub check_state_from_hmdb_ua {
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188 ## Retrieve Values
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189 my $self = shift ;
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190 my ($status) = @_ ;
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191
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192 if (!defined $$status) {
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193 croak "No http status is defined for the distant server" ;
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194 }
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195 else {
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196 unless ( $$status == 200 ) {
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197 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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198 else {
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199 ## None supported http code error ##
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200 }
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201 }
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202 }
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203
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204 return (1) ;
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205 }
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206 ## END of SUB
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207
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208 =head2 METHOD get_matches_from_hmdb_ua
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209
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210 ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
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211 ## Input : $mass, $delta, $mode
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212 ## Output : $results
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213 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
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214
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215 =cut
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216 ## START of SUB
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217 sub get_matches_from_hmdb_ua {
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218 ## Retrieve Values
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219 my $self = shift ;
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220 my ( $masses, $delta, $mode ) = @_ ;
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221
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222 my @page = () ;
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223
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224 my $ua = new LWP::UserAgent;
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225 $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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226
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227 my $req = HTTP::Request->new(
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228 POST => 'http://specdb.wishartlab.com/ms/search.csv');
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229
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230 $req->content_type('application/x-www-form-urlencoded');
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231 $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
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232
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233 my $res = $ua->request($req);
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234 # print $res->as_string;
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235 if ($res->is_success) {
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236 @page = split ( /\n/, $res->decoded_content ) ;
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237 } else {
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238 my $status_line = $res->status_line ;
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239 ($status_line) = ($status_line =~ /(\d+)/);
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240 croak "HMDB service none available !! Status of the HMDB server is : $status_line\n" ;
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241 }
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242
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243
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244 return (\@page) ;
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245 }
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246 ## END of SUB
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247
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248 =head2 METHOD parse_hmdb_csv_results
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249
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250 ## Description : parse the csv results and get data
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251 ## Input : $csv
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252 ## Output : $results
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253 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
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254
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255 =cut
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256 ## START of SUB
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257 sub parse_hmdb_csv_results {
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258 ## Retrieve Values
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259 my $self = shift ;
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260 my ( $csv, $masses ) = @_ ;
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261
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262 my $test = 0 ;
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263 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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264
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265 my %result_by_entry = () ;
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266 my %features = () ;
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267
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268 # print Dumper $csv ;
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269
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270 foreach my $line (@{$csv}) {
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271
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272 if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
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273 my @entry = split(/,/, $line) ;
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274
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275 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
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276
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277 $features{ENTRY_ENTRY_ID} = $entry[1] ;
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278 $features{ENTRY_FORMULA} = $entry[2] ;
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279 $features{ENTRY_CPD_MZ} = $entry[3] ;
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280 $features{ENTRY_ADDUCT} = $entry[4] ;
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281 $features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
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282 $features{ENTRY_ADDUCT_MZ} = $entry[6] ;
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283 $features{ENTRY_DELTA} = $entry[7] ;
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284
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285 my %temp = %features ;
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286
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287 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
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288 }
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289 else {
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290 next ;
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291 }
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292 } ## end foreach
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293
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294 ## manage per query_mzs (keep query masses order by array)
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295 my @results = () ;
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296 foreach (@{$masses}) {
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297 if ($result_by_entry{$_}) { push (@results, $result_by_entry{$_}) ; }
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298 else {push (@results, [] ) ;} ;
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299 }
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300 return(\@results) ;
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301 }
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302 ## END of SUB
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303
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304 =head2 METHOD parse_hmdb_page_results
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305
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306 ## Description : [DEPRECATED] old HMDB html page parser
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307 ## Input : $page
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308 ## Output : $results
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309 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
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310
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311 =cut
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312 ## START of SUB
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313 sub parse_hmdb_page_results {
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314 ## Retrieve Values
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315 my $self = shift ;
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316 my ( $page ) = @_ ;
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317
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318 my @results = () ;
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319 my ($catch_table, $catch_name) = (0, 0) ;
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320 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
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321
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322 if ( defined $page ) {
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323
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324 my @page = @{$page} ;
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325 my $ID = undef ;
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326 my @result_by_mz = () ;
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327 my %result_by_entry = () ;
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328
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329 foreach my $line (@page) {
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330
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331 #Section de la page contenant les resultat
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332 if( $line =~/<table>/ ) { $catch_table = 1 ; }
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333
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334 ## Si il existe un resultat :
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335 if($catch_table == 1) {
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336
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337 #Id de la molecule, et creation du lien
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338 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
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339 $ID = $1 ;
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340 $catch_name = 0 ;
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341 next ;
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342 }
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343 #Nom de la molecule ONLY!!
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344 if ( $catch_name == 0 ) {
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345
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346 if( $line =~ /<td>(.+)<\/td>/ ) {
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347
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348 if ( !defined $name ) {
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349 $name = $1 ;
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350 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
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351 $result_by_entry{'ENTRY_NAME'} = $name ;
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352 next ;
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353 }
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354 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
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355 if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; }
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356 if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; }
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357 if ( !defined $delta ) {
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358 $delta = $1 ;
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359 $result_by_entry{'ENTRY_DELTA'} = $delta ;
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360 $catch_name = 1 ;
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361 my %tmp = %result_by_entry ;
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362 push (@result_by_mz, \%tmp) ;
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363 %result_by_entry = () ;
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364 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
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365 next ;
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366 }
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367 }
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368 }
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369 }
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370 #Fin de la section contenant les resultats
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371 if( $line =~ /<\/table>/ ) {
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372 $catch_table = 0 ;
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373 my @Tmp = @result_by_mz ;
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374 push(@results, \@Tmp) ;
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375 @result_by_mz = () ;
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376 }
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377 }
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378 }
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379 return(\@results) ;
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380 }
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381 ## END of SUB
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382
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383 =head2 METHOD set_html_tbody_object
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384
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385 ## Description : initializes and build the tbody object (perl array) needed to html template
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386 ## Input : $nb_pages, $nb_items_per_page
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387 ## Output : $tbody_object
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388 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
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389
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390 =cut
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391 ## START of SUB
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392 sub set_html_tbody_object {
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393 my $self = shift ;
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394 my ( $nb_pages, $nb_items_per_page ) = @_ ;
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395
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396 my ( @tbody_object ) = ( ) ;
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397
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398 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
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399
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400 my %pages = (
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401 # tbody feature
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402 PAGE_NB => $i,
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403 MASSES => [], ## end MASSES
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404 ) ; ## end TBODY N
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405 push (@tbody_object, \%pages) ;
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406 }
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407 return(\@tbody_object) ;
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408 }
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409 ## END of SUB
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410
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411 =head2 METHOD add_mz_to_tbody_object
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412
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413 ## Description : initializes and build the mz object (perl array) needed to html template
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414 ## Input : $tbody_object, $nb_items_per_page, $mz_list
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415 ## Output : $tbody_object
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416 ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
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417
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418 =cut
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419 ## START of SUB
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420 sub add_mz_to_tbody_object {
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421 my $self = shift ;
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422 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
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423
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424 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
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425
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426 foreach my $page ( @{$tbody_object} ) {
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427
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428 my @colors = ('white', 'green') ;
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429 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
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430
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431 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
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432 #
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433 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
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434 $current_index = 0 ;
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435 last ; ##
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436 }
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437 else {
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438 $current_index++ ;
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439 if ( $icolor > 1 ) { $icolor = 0 ; }
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440
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441 if ( exists $mz_list->[$mz_index] ) {
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442
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443 my %mz = (
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444 # mass feature
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445 MASSES_ID_QUERY => $ids_list->[$mz_index],
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446 MASSES_MZ_QUERY => $mz_list->[$mz_index],
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447 MZ_COLOR => $colors[$icolor],
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448 MASSES_NB => $mz_index+1,
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449 ENTRIES => [] ,
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450 ) ;
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451 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
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452 # Html attr for mass
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453 $icolor++ ;
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454 }
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455 }
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456 $mz_index++ ;
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457 } ## foreach mz
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458
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459 $current_page++ ;
|
|
460 }
|
|
461 return($tbody_object) ;
|
|
462 }
|
|
463 ## END of SUB
|
|
464
|
|
465 =head2 METHOD add_entries_to_tbody_object
|
|
466
|
|
467 ## Description : initializes and build the entries object (perl array) needed to html template
|
|
468 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
|
|
469 ## Output : $tbody_object
|
|
470 ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
|
|
471
|
|
472 =cut
|
|
473 ## START of SUB
|
|
474 sub add_entries_to_tbody_object {
|
|
475 ## Retrieve Values
|
|
476 my $self = shift ;
|
|
477 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
|
|
478
|
|
479 my $index_page = 0 ;
|
|
480 my $index_mz_continous = 0 ;
|
|
481
|
|
482 foreach my $page (@{$tbody_object}) {
|
|
483
|
|
484 my $index_mz = 0 ;
|
|
485
|
|
486 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
|
|
487
|
|
488 my $index_entry = 0 ;
|
|
489
|
|
490 my @anti_redondant = ('N/A') ;
|
|
491 my $check_rebond = 0 ;
|
|
492 my $check_noentry = 0 ;
|
|
493
|
|
494 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
|
|
495 $check_noentry ++ ;
|
|
496 ## dispo anti doublons des entries
|
|
497 foreach my $rebond (@anti_redondant) {
|
|
498 if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
|
|
499 }
|
|
500
|
|
501 if ( $check_rebond == 0 ) {
|
|
502
|
|
503 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
|
|
504
|
|
505 my %entry = (
|
|
506 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
|
|
507 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
|
|
508 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
|
|
509 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
|
|
510 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
|
|
511 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
|
|
512 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
|
|
513 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
|
|
514 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
|
|
515 ) ;
|
|
516
|
|
517 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
|
|
518 }
|
|
519 $check_rebond = 0 ; ## reinit double control
|
|
520 $index_entry++ ;
|
|
521 } ## end foreach
|
|
522 if ($check_noentry == 0 ) {
|
|
523 my %entry = (
|
|
524 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
|
|
525 ENTRY_ENTRY_ID => 'No_result_found_on_HMDB',
|
|
526 ENTRY_ENTRY_ID2 => '',
|
|
527 ENTRY_FORMULA => 'n/a',
|
|
528 ENTRY_CPD_MZ => 'n/a',
|
|
529 ENTRY_ADDUCT => 'n/a',
|
|
530 ENTRY_ADDUCT_TYPE => 'n/a',
|
|
531 ENTRY_ADDUCT_MZ => 'n/a',
|
|
532 ENTRY_DELTA => 0,
|
|
533 ) ;
|
|
534 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
|
|
535 }
|
|
536 $index_mz ++ ;
|
|
537 $index_mz_continous ++ ;
|
|
538 }
|
|
539 $index_page++ ;
|
|
540 }
|
|
541 return($tbody_object) ;
|
|
542 }
|
|
543 ## END of SUB
|
|
544
|
|
545 =head2 METHOD write_html_skel
|
|
546
|
|
547 ## Description : prepare and write the html output file
|
|
548 ## Input : $html_file_name, $html_object, $html_template
|
|
549 ## Output : $html_file_name
|
|
550 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
|
|
551
|
|
552 =cut
|
|
553 ## START of SUB
|
|
554 sub write_html_skel {
|
|
555 ## Retrieve Values
|
|
556 my $self = shift ;
|
|
557 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
|
|
558
|
|
559 my $html_file = $$html_file_name ;
|
|
560
|
|
561 if ( defined $html_file ) {
|
|
562 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
|
|
563
|
|
564 if (-e $html_template) {
|
|
565 my $ohtml = HTML::Template->new(filename => $html_template);
|
|
566 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
|
|
567 $ohtml->param( CONDITIONS => $search_condition ) ;
|
|
568 $ohtml->param( PAGES_NB => $pages ) ;
|
|
569 $ohtml->param( PAGES => $html_object ) ;
|
|
570 print HTML $ohtml->output ;
|
|
571 }
|
|
572 else {
|
|
573 croak "Can't fill any html output : No template available ($html_template)\n" ;
|
|
574 }
|
|
575
|
|
576 close (HTML) ;
|
|
577 }
|
|
578 else {
|
|
579 croak "No output file name available to write HTML file\n" ;
|
|
580 }
|
|
581 return(\$html_file) ;
|
|
582 }
|
|
583 ## END of SUB
|
|
584
|
|
585 =head2 METHOD set_lm_matrix_object
|
|
586
|
|
587 ## Description : build the hmdb_row under its ref form
|
|
588 ## Input : $header, $init_mzs, $entries
|
|
589 ## Output : $hmdb_matrix
|
|
590 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
|
|
591
|
|
592 =cut
|
|
593 ## START of SUB
|
|
594 sub set_lm_matrix_object {
|
|
595 ## Retrieve Values
|
|
596 my $self = shift ;
|
|
597 my ( $header, $init_mzs, $entries ) = @_ ;
|
|
598
|
|
599 my @hmdb_matrix = () ;
|
|
600
|
|
601 if ( defined $header ) {
|
|
602 my @headers = () ;
|
|
603 push @headers, $header ;
|
|
604 push @hmdb_matrix, \@headers ;
|
|
605 }
|
|
606
|
|
607 my $index_mz = 0 ;
|
|
608
|
|
609 foreach my $mz ( @{$init_mzs} ) {
|
|
610
|
|
611 my $index_entries = 0 ;
|
|
612 my @clusters = () ;
|
|
613 my $cluster_col = undef ;
|
|
614
|
|
615 my @anti_redondant = ('N/A') ;
|
|
616 my $check_rebond = 0 ;
|
|
617
|
|
618 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
|
|
619
|
|
620 foreach my $entry (@{ $entries->[$index_mz] }) {
|
|
621
|
|
622 ## dispo anti doublons des entries
|
|
623 foreach my $rebond (@anti_redondant) {
|
|
624 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
|
|
625 }
|
|
626
|
|
627 if ( $check_rebond == 0 ) {
|
|
628
|
|
629 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
|
|
630
|
|
631 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
|
|
632 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
|
|
633 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
|
|
634
|
|
635 ## METLIN data display model
|
|
636 ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
|
|
637 # manage final pipe
|
|
638 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; }
|
|
639 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
|
|
640
|
|
641 }
|
|
642 $check_rebond = 0 ; ## reinit double control
|
|
643 $index_entries++ ;
|
|
644 } ## end foreach
|
|
645 if ( !defined $cluster_col ) { $cluster_col = 'No_result_found_on_HMDB' ; }
|
|
646 push (@clusters, $cluster_col) ;
|
|
647 push (@hmdb_matrix, \@clusters) ;
|
|
648 $index_mz++ ;
|
|
649 }
|
|
650 return(\@hmdb_matrix) ;
|
|
651 }
|
|
652 ## END of SUB
|
|
653
|
|
654 =head2 METHOD set_hmdb_matrix_object_with_ids
|
|
655
|
|
656 ## Description : build the hmdb_row under its ref form (IDS only)
|
|
657 ## Input : $header, $init_mzs, $entries
|
|
658 ## Output : $hmdb_matrix
|
|
659 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
|
|
660
|
|
661 =cut
|
|
662 ## START of SUB
|
|
663 sub set_hmdb_matrix_object_with_ids {
|
|
664 ## Retrieve Values
|
|
665 my $self = shift ;
|
|
666 my ( $header, $init_mzs, $entries ) = @_ ;
|
|
667
|
|
668 my @hmdb_matrix = () ;
|
|
669
|
|
670 if ( defined $header ) {
|
|
671 my @headers = () ;
|
|
672 push @headers, $header ;
|
|
673 push @hmdb_matrix, \@headers ;
|
|
674 }
|
|
675
|
|
676 my $index_mz = 0 ;
|
|
677
|
|
678 foreach my $mz ( @{$init_mzs} ) {
|
|
679
|
|
680 my $index_entries = 0 ;
|
|
681 my @clusters = () ;
|
|
682 my $cluster_col = undef ;
|
|
683
|
|
684 my @anti_redondant = ('N/A') ;
|
|
685 my $check_rebond = 0 ;
|
|
686
|
|
687 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
|
|
688
|
|
689 foreach my $entry (@{ $entries->[$index_mz] }) {
|
|
690
|
|
691 ## dispo anti doublons des entries
|
|
692 foreach my $rebond (@anti_redondant) {
|
|
693 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
|
|
694 }
|
|
695
|
|
696 if ( $check_rebond == 0 ) {
|
|
697
|
|
698 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
|
|
699 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
|
|
700
|
|
701 ## METLIN data display model -- IDs ONLY !!
|
|
702 ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
|
|
703 # manage final pipe
|
|
704 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $hmdb_id.'|' ; }
|
|
705 else { $cluster_col .= $hmdb_id ; }
|
|
706
|
|
707 }
|
|
708 $check_rebond = 0 ; ## reinit double control
|
|
709 $index_entries++ ;
|
|
710 } ## end foreach
|
|
711 if ( !defined $cluster_col ) { $cluster_col = 'No_result_found_on_HMDB' ; }
|
|
712 push (@clusters, $cluster_col) ;
|
|
713 push (@hmdb_matrix, \@clusters) ;
|
|
714 $index_mz++ ;
|
|
715 }
|
|
716 return(\@hmdb_matrix) ;
|
|
717 }
|
|
718 ## END of SUB
|
|
719
|
|
720 =head2 METHOD add_lm_matrix_to_input_matrix
|
|
721
|
|
722 ## Description : build a full matrix (input + lm column)
|
|
723 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
|
|
724 ## Output : $output_matrix_object
|
|
725 ## Usage : my ( $output_matrix_object ) = add_lm_matrix_to_input_matrix( $input_matrix_object, $lm_matrix_object, $nb_header ) ;
|
|
726
|
|
727 =cut
|
|
728 ## START of SUB
|
|
729 sub add_lm_matrix_to_input_matrix {
|
|
730 ## Retrieve Values
|
|
731 my $self = shift ;
|
|
732 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
|
|
733
|
|
734 my @output_matrix_object = () ;
|
|
735 my $index_row = 0 ;
|
|
736 my $line = 0 ;
|
|
737
|
|
738 foreach my $row ( @{$input_matrix_object} ) {
|
|
739 my @init_row = @{$row} ;
|
|
740 $line++;
|
|
741
|
|
742 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
|
|
743 push (@output_matrix_object, \@init_row) ;
|
|
744 next ;
|
|
745 }
|
|
746
|
|
747 if ( $lm_matrix_object->[$index_row] ) {
|
|
748 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
|
|
749
|
|
750 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
|
|
751 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
|
|
752
|
|
753 push (@init_row, $lm_col) ;
|
|
754 $index_row++ ;
|
|
755 }
|
|
756 push (@output_matrix_object, \@init_row) ;
|
|
757 }
|
|
758 return(\@output_matrix_object) ;
|
|
759 }
|
|
760 ## END of SUB
|
|
761
|
|
762 =head2 METHOD write_csv_skel
|
|
763
|
|
764 ## Description : prepare and write csv output file
|
|
765 ## Input : $csv_file, $rows
|
|
766 ## Output : $csv_file
|
|
767 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
|
|
768
|
|
769 =cut
|
|
770 ## START of SUB
|
|
771 sub write_csv_skel {
|
|
772 ## Retrieve Values
|
|
773 my $self = shift ;
|
|
774 my ( $csv_file, $rows ) = @_ ;
|
|
775
|
|
776 my $ocsv = lib::csv::new() ;
|
|
777 my $csv = $ocsv->get_csv_object("\t") ;
|
|
778 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
|
|
779
|
|
780 return($csv_file) ;
|
|
781 }
|
|
782 ## END of SUB
|
|
783
|
|
784 =head2 METHOD write_csv_one_mass
|
|
785
|
|
786 ## Description : print a cvs file
|
|
787 ## Input : $masses, $ids, $results, $file
|
|
788 ## Output : N/A
|
|
789 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
|
|
790
|
|
791 =cut
|
|
792 ## START of SUB
|
|
793 sub write_csv_one_mass {
|
|
794 ## Retrieve Values
|
|
795 my $self = shift ;
|
|
796 my ( $masses, $ids, $results, $file, ) = @_ ;
|
|
797
|
|
798 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
|
|
799 print CSV "ID\tMASS_SUBMIT\tHMDB_ID\tCPD_FORMULA\tCPD_MW\tDELTA\n" ;
|
|
800
|
|
801 my $i = 0 ;
|
|
802
|
|
803 foreach my $id (@{$ids}) {
|
|
804 my $mass = undef ;
|
|
805 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
|
|
806 else { last ; }
|
|
807
|
|
808 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
|
|
809
|
|
810 my @anti_redondant = ('N/A') ;
|
|
811 my $check_rebond = 0 ;
|
|
812 my $check_noentry = 0 ;
|
|
813
|
|
814 foreach my $entry (@{$results->[$i]}) {
|
|
815 $check_noentry ++ ;
|
|
816 ## dispo anti doublons des entries
|
|
817 foreach my $rebond (@anti_redondant) {
|
|
818 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
|
|
819 }
|
|
820 # print "\n-----------------------" ;
|
|
821 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
|
|
822 # print "-------------------------$check_rebond\n" ;
|
|
823 # print Dumper @anti_redondant ;
|
|
824 if ( $check_rebond == 0 ) {
|
|
825
|
|
826 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
|
|
827
|
|
828 print CSV "$id\t$mass\t$entry->{ENTRY_ENTRY_ID}\t" ;
|
|
829 ## print cpd name
|
|
830 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
|
|
831 else { print CSV "N/A\t" ; }
|
|
832 ## print cpd mw
|
|
833 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
|
|
834 else { print CSV "N/A\t" ; }
|
|
835 ## print delta
|
|
836 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\n" ; }
|
|
837 else { print CSV "N/A\n" ; }
|
|
838 }
|
|
839 $check_rebond = 0 ; ## reinit double control
|
|
840 } ## end foreach
|
|
841 if ($check_noentry == 0 ) {
|
|
842 print CSV "$id\t$mass\t".'No_result_found_on_HMDB'."\tn/a\tn/a\t0\n" ;
|
|
843 }
|
|
844 }
|
|
845 $i++ ;
|
|
846 }
|
|
847 close(CSV) ;
|
|
848 return() ;
|
|
849 }
|
|
850 ## END of SUB
|
|
851
|
|
852 1 ;
|
|
853
|
|
854
|
|
855 __END__
|
|
856
|
|
857 =head1 SUPPORT
|
|
858
|
|
859 You can find documentation for this module with the perldoc command.
|
|
860
|
|
861 perldoc hmdb.pm
|
|
862
|
|
863 =head1 Exports
|
|
864
|
|
865 =over 4
|
|
866
|
|
867 =item :ALL is ...
|
|
868
|
|
869 =back
|
|
870
|
|
871 =head1 AUTHOR
|
|
872
|
|
873 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
|
|
874
|
|
875 =head1 LICENSE
|
|
876
|
|
877 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
|
|
878
|
|
879 =head1 VERSION
|
|
880
|
|
881 version 1 : 06 / 06 / 2013
|
|
882
|
|
883 version 2 : 27 / 01 / 2014
|
|
884
|
|
885 version 3 : 19 / 11 / 2014
|
|
886
|
|
887 version 4 : 28 / 01 / 2016
|
|
888
|
|
889 =cut
|