annotate lib/hmdb.pm @ 20:b5a1d5e43685 draft

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author fgiacomoni
date Wed, 23 Jan 2019 07:49:34 -0500
parents 49f87ddb2c78
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1 package lib::hmdb ;
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3 use strict;
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4 use warnings ;
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5 use Exporter ;
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6 use Carp ;
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8 use LWP::Simple;
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9 use LWP::UserAgent;
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10 use WWW::Mechanize qw();
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11 use URI::URL;
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12 use SOAP::Lite;
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13 use Encode qw(encode_utf8);
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14 use HTML::Template ;
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15 use XML::Twig ;
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16 use Text::CSV ;
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18 use Data::Dumper ;
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20 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
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22 our $VERSION = "1.0";
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23 our @ISA = qw(Exporter);
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24 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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25 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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27 =head1 NAME
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29 My::Module - An example module
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31 =head1 SYNOPSIS
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32
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33 use My::Module;
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34 my $object = My::Module->new();
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35 print $object->as_string;
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37 =head1 DESCRIPTION
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38
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39 This module does not really exist, it
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40 was made for the sole purpose of
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41 demonstrating how POD works.
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42
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43 =head1 METHODS
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44
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45 Methods are :
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46
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47 =head2 METHOD new
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48
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49 ## Description : new
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50 ## Input : $self
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51 ## Ouput : bless $self ;
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52 ## Usage : new() ;
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53
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54 =cut
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55
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56 sub new {
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57 ## Variables
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58 my $self={};
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59 bless($self) ;
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60 return $self ;
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61 }
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62 ### END of SUB
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63
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64
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65 =head2 METHOD extract_sub_mz_lists
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66
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67 ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS)
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68 ## Input : $HMDB_LIMITS, $masses
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69 ## Output : $sublists
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70 ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ;
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71
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72 =cut
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73 ## START of SUB
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74 sub extract_sub_mz_lists {
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75 ## Retrieve Values
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76 my $self = shift ;
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77 my ( $masses, $HMDB_LIMITS ) = @_ ;
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78
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79 my ( @sublists, @sublist ) = ( (), () ) ;
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80 my $nb_mz = 0 ;
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81 my $nb_total_mzs = scalar(@{$masses}) ;
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82
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83 if ($nb_total_mzs == 0) {
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84 die "The provided mzs list is empty" ;
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85 }
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86
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87 for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) {
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88
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89 if ( $nb_mz < $HMDB_LIMITS ) {
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90 if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list
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91 }
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92 elsif ( $nb_mz == $HMDB_LIMITS ) {
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93 my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ;
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94 $current_pos-- ;
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95 }
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96 if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; }
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97 }
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98 return(\@sublists) ;
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99 }
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100 ## END of SUB
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101
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102 =head2 METHOD prepare_multi_masses_query
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103
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104 ## Description : Generate the adapted format of the mz list for HMDB
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105 ## Input : $masses
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106 ## Output : $hmdb_masses
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107 ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ;
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108
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109 =cut
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110 ## START of SUB
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111 sub prepare_multi_masses_query {
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112 ## Retrieve Values
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113 my $self = shift ;
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114 my ( $masses ) = @_ ;
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115
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116 my $hmdb_masses = undef ;
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117 my $sep = '%0D%0A' ; ## retour chariot encode
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118 my ($nb_masses, $i) = (0, 0) ;
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119
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120 if ( defined $masses ) {
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121 my @masses = @{$masses} ;
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122 my $nb_masses = scalar ( @masses ) ;
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123 if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; }
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124 elsif ( $nb_masses >= 700 ) { croak "Your mass list is too long : HMDB allows maximum 700 query masses per request \n" ; } ## Del it --- temporary patch
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125
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126 foreach my $mass (@masses) {
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127
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128 if ($i < $nb_masses) {
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129 $hmdb_masses .= $mass.$sep ;
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130 }
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131 elsif ( $i == $nb_masses ) {
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132 $hmdb_masses .= $mass ;
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133 }
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134 else {
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135 last ;
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136 }
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137 $i ++ ;
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138 }
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139 }
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140 else {
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141 croak "No mass list found \n" ;
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142 }
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143 return($hmdb_masses, $nb_masses) ;
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144 }
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145 ## END of SUB
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146
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147 =head2 METHOD test_matches_from_hmdb_ua DEPRECATED
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148
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149 ## Description : [DEPRECATED]test a single query with tests parameters on hmdb - get the status of the complete server infra.
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150 ## Input : none
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151 ## Output : $status_line
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152 ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ;
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153
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154 =cut
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155 ## START of SUB
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156 sub test_matches_from_hmdb_ua {
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157 ## Retrieve Values
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158 my $self = shift ;
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159
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160 my @page = () ;
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161
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162 my $ua = new LWP::UserAgent;
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163 $ua->agent("Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:64.0) Gecko/20100101 Firefox/64.0");
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164
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165 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
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166 my $header = ['Connection' => 'keep-alive', 'Content-Type' => 'application/x-www-form-urlencoded', 'Referer' => 'http://www.hmdb.ca/spectra/ms/search', 'Accept' => 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'];
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167
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168 my $req = HTTP::Request->new('POST', $url, $header);
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169 # print Dumper $req ;
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170
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171 ## Query format for HMDB 4.0
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172 #"utf8=✓&authenticity_token=K1Ys7oyMKmVNm9n8p0jiTxBlh4G4OO0cqKZYnQKDCw0pM6zmm/CiBxv+/cXhuRsVFV98LLeAMJRN5dCyhIWlAA==&query_masses=175.01 238.19 420.16 780.32 956.25 1100.45&ms_search_ion_mode=positive&adduct_type[]=Unknown&tolerance=0.05&tolerance_units=Da&commit=Search"
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173
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174 $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV');
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175 # print Dumper $req ;
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176 my $res = $ua->request($req);
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177
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178 print $res->as_string;
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179 my $status_line = $res->status_line ;
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180 ($status_line) = ($status_line =~ /(\d+)/);
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181
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182 return (\$status_line) ;
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183 }
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184 ## END of SUB
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185
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186 =head2 METHOD testMatchesFromHmdbWithUA
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187
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188 ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra.
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189 ## Input : none
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190 ## Output : $status_line
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191 ## Usage : my ( $status_line ) = testMatchesFromHmdbWithUA( ) ;
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192
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193 =cut
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194 ## START of SUB
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195 sub testMatchesFromHmdbWithUA {
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196 ## Retrieve Values
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197 my $self = shift ;
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198
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199 my @page = () ;
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200 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
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201
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202 my $mech = WWW::Mechanize->new(
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203 agent => 'wonderbot for W4M 1.01',
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204 autocheck => 1,
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205 );
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206
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207 my $statusGetLine = 0 ;
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208 my $statusPostLine = 0 ;
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209
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210 #receiving cookies and authentication token (CFRS)
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211 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
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212 $statusGetLine = $mech->status() ;
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213
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214 if ($statusGetLine == 200 ) {
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215 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
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216 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
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217 my $csrftoken = $1;
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218 # print "\nTOKEN: $csrftoken\n" ;
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219 $mech->add_header("X-CSRFToken", $csrftoken);
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220 $mech->add_header('Connection', 'keep-alive');
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221 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
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222 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
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223 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
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224 }
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225
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226 ## POST test
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227 my $top = 1 ;
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228 while ($statusPostLine != 200 ) {
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229
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230 # Fix a limit at 3 tries...
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231 if ($top < 4) {
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232 print "\tTesting HMDB server connexion ($top time(s) )...\n" ;
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233 $mech->post(
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234 "http://specdb.wishartlab.com/ms/search.csv",
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235 Content => 'utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV'
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236 );
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237
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238 # print Dumper $mech ;
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239 $statusPostLine = $mech->status() ;
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240 }
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241 else {
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242 last ;
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243 }
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244 $top++ ;
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245 }## End While
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246
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247 return (\$statusPostLine) ;
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248 }
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249 ## END of SUB
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250
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251
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252
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253
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254 =head2 METHOD check_state_from_hmdb_ua
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255
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256 ## Description : check the thhp status of hmdb and kill correctly the script if necessary.
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257 ## Input : $status
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258 ## Output : none
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259 ## Usage : check_state_from_hmdb_ua($status) ;
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260
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261 =cut
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262 ## START of SUB
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263 sub check_state_from_hmdb_ua {
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264 ## Retrieve Values
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265 my $self = shift ;
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266 my ($status) = @_ ;
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267
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268 if (!defined $$status) {
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269 croak "No http status is defined for the distant server" ;
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270 }
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271 else {
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272 unless ( $$status == 200 ) {
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273 if ( $$status == 502 ) { croak "Bad Gateway (502): The HMDB server, while acting as a gateway or proxy, received an invalid response from the upstream server. The Hmdb tool is stopped with error." ; }
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274 if ( $$status == 504 ) { croak "Gateway Timeout (504): The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server. The Hmdb tool is stopped with error." ; }
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275 if ( $$status == 500 ) { croak "Internal Server Error (500): The HMDB server returns an unexpected internal server error. The Hmdb tool is stopped with error." ; }
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276 else {
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277 ## None supported http code error ##
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278 croak "Internal Server Error $$status..." ;
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279 }
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280 }
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281 if ( $$status == 200 ) { print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ; }
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282 }
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283
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284 return (1) ;
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285 }
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286 ## END of SUB
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287
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288 =head2 METHOD get_matches_from_hmdb_ua DEPRECATED
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289
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290 ## Description : [DEPRECATED]HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
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291 ## Input : $mass, $delta, $mode
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292 ## Output : $results
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293 ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ;
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294
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295 =cut
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296 ## START of SUB
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297 sub get_matches_from_hmdb_ua {
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298 ## Retrieve Values
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299 my $self = shift ;
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300 my ( $masses, $delta, $mode ) = @_ ;
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301
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302 my @page = () ;
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303
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304 my $ua = LWP::UserAgent->new( keep_alive => 10 );
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305 $ua->agent("Mozilla/5.0 (Macintosh; Intel Mac OS X 10.11; rv:64.0) Gecko/20100101 Firefox/64.0");
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306 $ua->timeout(2400) ;
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307
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308 # Cookies
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309 # my $cookie = new HTTP::Cookies( ignore_discard => 1 );
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310 # $ua->cookie_jar( $cookie );
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311
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312 # my $req = HTTP::Request->new(
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313 # POST => 'http://specdb.wishartlab.com/ms/search.csv');
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314
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315 my $url = 'http://specdb.wishartlab.com/ms/search.csv';
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316 my $header = ['Content-Type' => 'application/x-www-form-urlencoded', 'Referer' => 'http://www.hmdb.ca/spectra/ms/search', 'Accept' => 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'];
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317 my $data = {mode => $mode, query_masses => $masses, 'tolerance' => $delta, database => 'HMDB', commit => 'Download Results As CSV'};
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318 my $encoded_data = encode_utf8($data);
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319
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320 my $req = HTTP::Request->new('POST', $url, $header, $encoded_data);
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321
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322 # $req->content_type('application/x-www-form-urlencoded');
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323 $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV');
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324 # print Dumper $req ;
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325 my $res = $ua->request($req);
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326 my $status_line = undef ;
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327 print $res->as_string;
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328 if ($res->is_success) {
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329 @page = split ( /\n/, $res->decoded_content ) ;
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330 $status_line = 'OK' ;
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331 } else {
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332 $status_line = $res->status_line ;
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333 ($status_line) = ($status_line =~ /(\d+)/);
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334 warn "\t[HMDB service issue !! the server returned a $status_line HTTP error]" ;
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335 }
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336
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337
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338 return (\@page, $status_line) ;
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339 }
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340 ## END of SUB
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341
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342 =head2 METHOD getMatchesFromHmdbWithUA
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343
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344 ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg)
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345 ## Input : $mass, $delta, $mode
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346 ## Output : $results
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347 ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ;
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348
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349 =cut
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350 ## START of SUB
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351 sub getMatchesFromHmdbWithUA {
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352 ## Retrieve Values
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353 my $self = shift ;
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354 my ( $masses, $delta, $mode ) = @_ ;
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355
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356 my @page = () ;
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357
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358 #based on https://stackoverflow.com/questions/17732916/perl-post-automation-and
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359
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360 my $mech = WWW::Mechanize->new(
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361 agent => 'wonderbot for W4M 1.01',
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362 autocheck => 1,
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363 timeout => 2400,
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364 );
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365
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366 my $statusGetLine = 0 ;
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367 my $statusPostLine = 0 ;
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368
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369 #receiving cookies and authentication token (CFRS)
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370 my $reqInit = $mech->get("http://www.hmdb.ca/spectra/ms/search");
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371 $statusGetLine = $mech->status() ;
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372
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373 if ($statusGetLine == 200 ) {
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374 die 'no CSRF_REQUEST_TOKEN_VALUE in page found'
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375 unless ($reqInit->decoded_content =~ /\"csrf-token\"\s+content=\"(.*)\"/) ;
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376 my $csrftoken = $1;
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377 # print "\nTOKEN: $csrftoken\n" ;
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378 $mech->add_header("X-CSRFToken", $csrftoken);
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379 $mech->add_header('Connection', 'keep-alive');
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380 $mech->add_header('Content-Type', 'application/x-www-form-urlencoded');
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381 $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search');
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382 $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8');
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383 }
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384
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385 my $res = $mech->post(
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386 "http://specdb.wishartlab.com/ms/search.csv",
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387 Content => 'utf8=TRUE&mode='
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388 .$mode.'&query_masses='
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389 .$masses.'&tolerance='
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390 .$delta.'&database=HMDB&commit=Download Results As CSV'
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391 );
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392
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393 if ($mech->success) {
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394 @page = split ( /\n/, $res->decoded_content ) ;
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395 $statusPostLine = 'OK' ;
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396 }
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397 else {
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398 $statusPostLine = $mech->status() ;
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399 warn "\t[HMDB service issue !! the server returned a $statusPostLine HTTP error]" ;
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400 }
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401
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402 # print Dumper $res->decoded_content ;
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403
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404 return (\@page, $statusPostLine) ;
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405 }
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406 ## END of SUB
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407
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408
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409 =head2 METHOD parse_hmdb_csv_results
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410
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411 ## Description : parse the csv results and get data
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412 ## Input : $csv
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413 ## Output : $results
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414 ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ;
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415
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416 =cut
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417 ## START of SUB
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418 sub parse_hmdb_csv_results {
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419 ## Retrieve Values
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420 my $self = shift ;
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421 my ( $csv, $masses, $max_query ) = @_ ;
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422
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423 my $test = 0 ;
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424 my ($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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425
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426 my %result_by_entry = () ;
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427 my %features = () ;
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428
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429 # print Dumper $csv ;
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430 # print Dumper $masses ;
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431 # print Dumper $max_query ;
1
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432
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433 foreach my $line (@{$csv}) {
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434 ## NEW HMDB format V4.0 - dec2017
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435 if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) {
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436
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437 if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a|\s+]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) {
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438 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
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439
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440 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
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441
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442 $features{ENTRY_ENTRY_ID} = $entry[1] ;
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443 $features{ENTRY_ENTRY_NAME} = $entry[2] ;
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444 $features{ENTRY_FORMULA} = $entry[4] ;
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445 $features{ENTRY_CPD_MZ} = $entry[5] ;
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446 $features{ENTRY_ADDUCT} = $entry[6] ;
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447 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
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448 $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
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449 $features{ENTRY_DELTA} = $entry[9] ;
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450
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451 my %temp = %features ;
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452 push (@{$result_by_entry{$entry[0]} }, \%temp) ;
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453 }
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454 # elsif ($line =~ /(\d+\.\d+)/) { #
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455 # ## 288.082286511284,HMDB0002255,R-Methylmalonyl-CoA, C01213 ,C25H40N7O19P3S,867.131252359,M-3H,-,288.036475,159
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456 # ## 283.108004472276,"Bicyclo_3,1,1heptane-2,3-diol,2,6,6_trimethyl","2,3-Pinanediol",n/a,C10H18O2,170.13067982,M+TFA-H,-,283.116266,29
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457 # ## 174.034120330029,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M-H20-H,-,174.055503,123
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458 # ## 193.139160745841,HMDB0012109,"7-[(1R,2R,3R,5S)-3,5-Dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid", C06475,C20H36O7,388.246103506,M-2H,-,193.115776,121
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459 # ## 214.018826827064,HMDB0011723,2-Methylhippuric acid, C01586,C10H11NO3,193.073893223,M+Na-2H,-,214.048559,139
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460 # }
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461 # else {
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462 #
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463 # warn "The parsed line ($line) does not match your pattern\n " ;
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464 # }
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465 }
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466 else {
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467 next ;
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468 }
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469 } ## end foreach
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470
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471 ## manage per query_mzs (keep query masses order by array)
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472 my @results = () ;
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473 foreach (@{$masses}) {
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474 if ($result_by_entry{$_}) {
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475
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476 ## cut all entries > $max_query
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477 my @temp_entries = @{$result_by_entry{$_}} ;
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478 my @temp_cut = () ;
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479 my $current_query = 0 ;
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480 foreach (@temp_entries) {
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481 $current_query ++ ;
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482 if ($current_query > $max_query) {
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483 last ;
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484 }
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485 else {
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486 push (@temp_cut, $_) ;
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487 }
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488 }
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489 push (@results, \@temp_cut) ;
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490 # push (@results, $result_by_entry{$_}) ;
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491 }
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492 else {push (@results, [] ) ;} ;
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493
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494 }
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495
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496 return(\@results) ;
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497 }
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498 ## END of SUB
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499
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500 =head2 METHOD parse_hmdb_page_results
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501
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502 ## Description : [DEPRECATED] old HMDB html page parser
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503 ## Input : $page
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504 ## Output : $results
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505 ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ;
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506
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507 =cut
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508 ## START of SUB
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509 sub parse_hmdb_page_results {
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510 ## Retrieve Values
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511 my $self = shift ;
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512 my ( $page ) = @_ ;
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513
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514 my @results = () ;
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515 my ($catch_table, $catch_name) = (0, 0) ;
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516 my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ;
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517
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518 if ( defined $page ) {
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519
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520 my @page = @{$page} ;
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521 my $ID = undef ;
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522 my @result_by_mz = () ;
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fgiacomoni
parents:
diff changeset
523 my %result_by_entry = () ;
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fgiacomoni
parents:
diff changeset
524
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fgiacomoni
parents:
diff changeset
525 foreach my $line (@page) {
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fgiacomoni
parents:
diff changeset
526
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fgiacomoni
parents:
diff changeset
527 #Section de la page contenant les resultat
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
528 if( $line =~/<table>/ ) { $catch_table = 1 ; }
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fgiacomoni
parents:
diff changeset
529
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fgiacomoni
parents:
diff changeset
530 ## Si il existe un resultat :
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
531 if($catch_table == 1) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
532
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
533 #Id de la molecule, et creation du lien
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fgiacomoni
parents:
diff changeset
534 if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
535 $ID = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
536 $catch_name = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
537 next ;
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fgiacomoni
parents:
diff changeset
538 }
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fgiacomoni
parents:
diff changeset
539 #Nom de la molecule ONLY!!
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
540 if ( $catch_name == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
541
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
542 if( $line =~ /<td>(.+)<\/td>/ ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
543
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fgiacomoni
parents:
diff changeset
544 if ( !defined $name ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
545 $name = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
546 $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ;
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fgiacomoni
parents:
diff changeset
547 $result_by_entry{'ENTRY_NAME'} = $name ;
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fgiacomoni
parents:
diff changeset
548 next ;
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fgiacomoni
parents:
diff changeset
549 }
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fgiacomoni
parents:
diff changeset
550 if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; }
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fgiacomoni
parents:
diff changeset
551 if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; }
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fgiacomoni
parents:
diff changeset
552 if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
553 if ( !defined $delta ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
554 $delta = $1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
555 $result_by_entry{'ENTRY_DELTA'} = $delta ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
556 $catch_name = 1 ;
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fgiacomoni
parents:
diff changeset
557 my %tmp = %result_by_entry ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
558 push (@result_by_mz, \%tmp) ;
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fgiacomoni
parents:
diff changeset
559 %result_by_entry = () ;
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fgiacomoni
parents:
diff changeset
560 ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ;
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fgiacomoni
parents:
diff changeset
561 next ;
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fgiacomoni
parents:
diff changeset
562 }
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fgiacomoni
parents:
diff changeset
563 }
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fgiacomoni
parents:
diff changeset
564 }
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fgiacomoni
parents:
diff changeset
565 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
566 #Fin de la section contenant les resultats
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
567 if( $line =~ /<\/table>/ ) {
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fgiacomoni
parents:
diff changeset
568 $catch_table = 0 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
569 my @Tmp = @result_by_mz ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
570 push(@results, \@Tmp) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
571 @result_by_mz = () ;
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fgiacomoni
parents:
diff changeset
572 }
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fgiacomoni
parents:
diff changeset
573 }
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fgiacomoni
parents:
diff changeset
574 }
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fgiacomoni
parents:
diff changeset
575 return(\@results) ;
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fgiacomoni
parents:
diff changeset
576 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
577 ## END of SUB
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fgiacomoni
parents:
diff changeset
578
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
579
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
580 =head2 METHOD get_unik_ids_from_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
581
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
582 ## Description : get all unik ids from the hmdb result object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
583 ## Input : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
584 ## Output : $ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
585 ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
586
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
587 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
588 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
589 sub get_unik_ids_from_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
590 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
591 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
592 my ( $results ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
593 my ( %ids ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
594
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
595 foreach my $result (@{$results}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
596
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
597 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
598
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
599 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
600 $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
601 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
602 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
603 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
604
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
605 return (\%ids) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
606 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
607 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
608
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
609
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
610
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
611 =head2 METHOD get_hmdb_metabocard_from_id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
612
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
613 ## Description : get a metabocard (xml format from an ID on HMDB)
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
614 ## Input : $ids
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
615 ## Output : $metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
616 ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
617
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
618 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
619 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
620 sub get_hmdb_metabocard_from_id {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
621 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
622 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
623 my ( $ids, $hmdb_url ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
624 my ( %metabocard_features ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
625 my $query = undef ;
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fgiacomoni
parents:
diff changeset
626
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
627 ## structure %metabocard_features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
628 # metabolite_id = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
629 # 'metabolite_name' => '__name__',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
630 # 'metabolite_inchi' => '__inchi__',
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fgiacomoni
parents:
diff changeset
631 # 'metabolite_logp' => '__logp-ALOGPS__',
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fgiacomoni
parents:
diff changeset
632 #
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
633 # )
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fgiacomoni
parents:
diff changeset
634
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
635
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
636 if( (defined $ids) and ($ids > 0 ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
637
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
638 foreach my $id (keys %{$ids}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
639
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
640 # print "\n============== > $id **********************\n " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
641 my $twig = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
642
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
643 if (defined $hmdb_url) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
644 $query = $hmdb_url.$id.'.xml' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
645
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
646 ## test the header if exists
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
647 my $response = head($query) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
648
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
649 if (!defined $response) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
650 $metabocard_features{$id}{'metabolite_name'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
651 $metabocard_features{$id}{'metabolite_inchi'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
652 $metabocard_features{$id}{'metabolite_logp'} = undef ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
653 ## Need to be improve to manage http 404 or other response diff than 200
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fgiacomoni
parents:
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654 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
655 elsif ($response->is_success) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
656
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
657 $twig = XML::Twig->nparse_ppe(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
658
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
659 twig_handlers => {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
660 # metabolite name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
661 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; } ,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
662 # metabolite inchi
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
663 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; } ,
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fgiacomoni
parents:
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664 ## metabolite logP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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665 'metabolite/predicted_properties/property' => sub {
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fgiacomoni
parents:
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666
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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667 my ($kind, $source, $value ) = ( undef, undef, undef ) ;
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fgiacomoni
parents:
diff changeset
668
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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669 if (defined $_->children ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
670 foreach my $field ($_->children) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
671 if ( $field->name eq 'kind') { $kind = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
672 elsif ( $field->name eq 'source') { $source = $field->text ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
673 elsif ( $field->name eq 'value') { $value = $field->text ; }
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fgiacomoni
parents:
diff changeset
674
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
675 if (defined $source ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
676 if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
677 $metabocard_features{$id}{'metabolite_logp'} = $value ;
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fgiacomoni
parents:
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678 }
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fgiacomoni
parents:
diff changeset
679 ($kind, $source, $value ) = ( undef, undef, undef ) ;
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fgiacomoni
parents:
diff changeset
680 }
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fgiacomoni
parents:
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681 }
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fgiacomoni
parents:
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682 }
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fgiacomoni
parents:
diff changeset
683 }
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fgiacomoni
parents:
diff changeset
684 },
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
685 pretty_print => 'indented',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
686 error_context => 1, $query
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
687 );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
688
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
689 # $twig->print;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
690 $twig->purge ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
691
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
692 if (!$@) {
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fgiacomoni
parents:
diff changeset
693
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
694 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
695 else {
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fgiacomoni
parents:
diff changeset
696 warn $@ ;
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fgiacomoni
parents:
diff changeset
697 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
698 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
699 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
700 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
701 warn "The hmdb metabocard url is not defined\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
702 last;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
703 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
704 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
705 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
706 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
707 warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
708 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
709
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
710 # print Dumper %metabocard_features ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
711 return (\%metabocard_features) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
712 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
713 ### END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
714
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
715
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
716 =head2 METHOD map_suppl_data_on_hmdb_results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
717
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
718 ## Description : map supplementary data with already collected results with hmdb search
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
719 ## Input : $results, $features
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
720 ## Output : $results
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
721 ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
722
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
723 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
724 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
725 sub map_suppl_data_on_hmdb_results {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
726 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
727 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
728 my ( $results, $features ) = @_;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
729 my ( @more_results ) = ( () ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
730
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
731 @more_results = @{$results} ; ## Dump array ref to map
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
732
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
733 foreach my $result (@more_results) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
734
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
735 foreach my $entries (@{$result}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
736
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
737 if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
738 ## check that we have a ID for mapping
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
739 my $current_id = $entries->{'ENTRY_ENTRY_ID'} ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
740 if ($features->{"$current_id"}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
741 ## Metabolite NAME
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
742 if (defined $features->{"$current_id"}{'metabolite_name'} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
743 $entries->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
744 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
745 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
746 $entries->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
747 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
748 ## Metabolite INCHI
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
749 if (defined $features->{"$current_id"}{'metabolite_inchi'} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
750 $entries->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
751 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
752 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
753 $entries->{'ENTRY_ENTRY_INCHI'} = 'NA' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
754 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
755 ## Metabolite LOGP
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
756 if (defined $features->{"$current_id"}{'metabolite_logp'} ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
757 $entries->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
758 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
759 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
760 $entries->{'ENTRY_ENTRY_LOGP'} = 'NA' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
761 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
762 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
763 else {
15
beb9619263b0 Master branch Updating - - Fxx
fgiacomoni
parents: 14
diff changeset
764 # if ($features) {
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fgiacomoni
parents: 14
diff changeset
765 # warn "This HMDB id doesn't match any collected ids\n" ;
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766 # }
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767 $entries->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ;
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diff changeset
768 $entries->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ;
1
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769 }
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770 }
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771 }
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772 }
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773
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774 return (\@more_results) ;
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fgiacomoni
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775 }
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776 ### END of SUB
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fgiacomoni
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777
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fgiacomoni
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778
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779 =head2 METHOD set_html_tbody_object
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780
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781 ## Description : initializes and build the tbody object (perl array) needed to html template
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782 ## Input : $nb_pages, $nb_items_per_page
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fgiacomoni
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783 ## Output : $tbody_object
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784 ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ;
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785
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fgiacomoni
parents:
diff changeset
786 =cut
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fgiacomoni
parents:
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787 ## START of SUB
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788 sub set_html_tbody_object {
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789 my $self = shift ;
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790 my ( $nb_pages, $nb_items_per_page ) = @_ ;
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791
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792 my ( @tbody_object ) = ( ) ;
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793
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794 for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) {
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fgiacomoni
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795
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796 my %pages = (
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fgiacomoni
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797 # tbody feature
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798 PAGE_NB => $i,
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799 MASSES => [], ## end MASSES
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800 ) ; ## end TBODY N
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801 push (@tbody_object, \%pages) ;
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fgiacomoni
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802 }
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803 return(\@tbody_object) ;
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fgiacomoni
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804 }
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fgiacomoni
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805 ## END of SUB
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fgiacomoni
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806
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807 =head2 METHOD add_mz_to_tbody_object
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fgiacomoni
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808
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fgiacomoni
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809 ## Description : initializes and build the mz object (perl array) needed to html template
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fgiacomoni
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810 ## Input : $tbody_object, $nb_items_per_page, $mz_list
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fgiacomoni
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811 ## Output : $tbody_object
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fgiacomoni
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812 ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ;
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813
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fgiacomoni
parents:
diff changeset
814 =cut
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fgiacomoni
parents:
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815 ## START of SUB
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fgiacomoni
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816 sub add_mz_to_tbody_object {
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817 my $self = shift ;
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818 my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ;
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819
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820 my ( $current_page, $mz_index ) = ( 0, 0 ) ;
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821
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822 foreach my $page ( @{$tbody_object} ) {
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823
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824 my @colors = ('white', 'green') ;
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825 my ( $current_index, , $icolor ) = ( 0, 0 ) ;
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826
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827 for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) {
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fgiacomoni
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828 #
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829 if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page
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830 $current_index = 0 ;
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fgiacomoni
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831 last ; ##
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832 }
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833 else {
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834 $current_index++ ;
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fgiacomoni
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835 if ( $icolor > 1 ) { $icolor = 0 ; }
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fgiacomoni
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diff changeset
836
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837 if ( exists $mz_list->[$mz_index] ) {
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fgiacomoni
parents:
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838
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fgiacomoni
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diff changeset
839 my %mz = (
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fgiacomoni
parents:
diff changeset
840 # mass feature
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fgiacomoni
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841 MASSES_ID_QUERY => $ids_list->[$mz_index],
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fgiacomoni
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842 MASSES_MZ_QUERY => $mz_list->[$mz_index],
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843 MZ_COLOR => $colors[$icolor],
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fgiacomoni
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844 MASSES_NB => $mz_index+1,
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fgiacomoni
parents:
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845 ENTRIES => [] ,
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fgiacomoni
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846 ) ;
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fgiacomoni
parents:
diff changeset
847 push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ;
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fgiacomoni
parents:
diff changeset
848 # Html attr for mass
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849 $icolor++ ;
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850 }
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851 }
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852 $mz_index++ ;
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fgiacomoni
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853 } ## foreach mz
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fgiacomoni
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854
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diff changeset
855 $current_page++ ;
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fgiacomoni
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856 }
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857 return($tbody_object) ;
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fgiacomoni
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858 }
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fgiacomoni
parents:
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859 ## END of SUB
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860
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fgiacomoni
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861 =head2 METHOD add_entries_to_tbody_object
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fgiacomoni
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862
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fgiacomoni
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diff changeset
863 ## Description : initializes and build the entries object (perl array) needed to html template
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fgiacomoni
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diff changeset
864 ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries
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fgiacomoni
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865 ## Output : $tbody_object
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fgiacomoni
parents:
diff changeset
866 ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ;
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fgiacomoni
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diff changeset
867
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fgiacomoni
parents:
diff changeset
868 =cut
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fgiacomoni
parents:
diff changeset
869 ## START of SUB
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fgiacomoni
parents:
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870 sub add_entries_to_tbody_object {
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fgiacomoni
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871 ## Retrieve Values
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fgiacomoni
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diff changeset
872 my $self = shift ;
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fgiacomoni
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diff changeset
873 my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ;
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fgiacomoni
parents:
diff changeset
874
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fgiacomoni
parents:
diff changeset
875 my $index_page = 0 ;
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fgiacomoni
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876 my $index_mz_continous = 0 ;
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fgiacomoni
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diff changeset
877
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fgiacomoni
parents:
diff changeset
878 foreach my $page (@{$tbody_object}) {
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879
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880 my $index_mz = 0 ;
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881
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fgiacomoni
parents:
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882 foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) {
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fgiacomoni
parents:
diff changeset
883
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fgiacomoni
parents:
diff changeset
884 my $index_entry = 0 ;
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fgiacomoni
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885
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fgiacomoni
parents:
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886 my @anti_redondant = ('N/A') ;
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fgiacomoni
parents:
diff changeset
887 my $check_rebond = 0 ;
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fgiacomoni
parents:
diff changeset
888 my $check_noentry = 0 ;
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fgiacomoni
parents:
diff changeset
889
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
890 foreach my $entry (@{ $entries->[$index_mz_continous] }) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
891 $check_noentry ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
892 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
893 foreach my $rebond (@anti_redondant) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
894 if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
parents:
diff changeset
895 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
896
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
897 if ( $check_rebond == 0 ) {
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fgiacomoni
parents:
diff changeset
898
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
899 push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
parents:
diff changeset
900
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
901 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
902 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
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fgiacomoni
parents:
diff changeset
903 ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
904 ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
905 ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
906 ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
907 ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
908 ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
909 ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
910 ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ},
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fgiacomoni
parents:
diff changeset
911 ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
912 ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI},
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fgiacomoni
parents:
diff changeset
913 ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
914 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
915
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
916 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
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fgiacomoni
parents:
diff changeset
917 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
918 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
919 $index_entry++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
920 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
921 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
922 my %entry = (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
923 ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR},
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
924 ENTRY_ENTRY_NAME => 'UNKNOWN',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
925 ENTRY_ENTRY_ID => 'NONE',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
926 ENTRY_ENTRY_ID2 => '',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
927 ENTRY_FORMULA => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
928 ENTRY_CPD_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
929 ENTRY_ADDUCT => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
930 ENTRY_ADDUCT_TYPE => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
931 ENTRY_ADDUCT_MZ => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
932 ENTRY_DELTA => 0,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
933 ENTRY_ENTRY_INCHI => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
934 ENTRY_ENTRY_LOGP => 'n/a',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
935 ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
936 push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ;
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fgiacomoni
parents:
diff changeset
937 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
938 $index_mz ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
939 $index_mz_continous ++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
940 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
941 $index_page++ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
942 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
943 return($tbody_object) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
944 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
945 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
946
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
947 =head2 METHOD write_html_skel
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
948
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
949 ## Description : prepare and write the html output file
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
950 ## Input : $html_file_name, $html_object, $html_template
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
951 ## Output : $html_file_name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
952 ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
953
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
954 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
955 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
956 sub write_html_skel {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
957 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
958 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
959 my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
960
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
961 my $html_file = $$html_file_name ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
962
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
963 if ( defined $html_file ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
964 open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
965
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
966 if (-e $html_template) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
967 my $ohtml = HTML::Template->new(filename => $html_template);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
968 $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
969 $ohtml->param( CONDITIONS => $search_condition ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
970 $ohtml->param( PAGES_NB => $pages ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
971 $ohtml->param( PAGES => $html_object ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
972 print HTML $ohtml->output ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
973 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
974 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
975 croak "Can't fill any html output : No template available ($html_template)\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
976 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
977
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
978 close (HTML) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
979 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
980 else {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
981 croak "No output file name available to write HTML file\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
982 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
983 return(\$html_file) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
984 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
985 ## END of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
986
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
987 =head2 METHOD set_lm_matrix_object
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
988
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
989 ## Description : build the hmdb_row under its ref form
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
990 ## Input : $header, $init_mzs, $entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
991 ## Output : $hmdb_matrix
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
992 ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
993
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
994 =cut
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
995 ## START of SUB
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
996 sub set_lm_matrix_object {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
997 ## Retrieve Values
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
998 my $self = shift ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
999 my ( $header, $init_mzs, $entries ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1000
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1001 my @hmdb_matrix = () ;
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1002
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1003 if ( defined $header ) {
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1004 my @headers = () ;
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1005 push @headers, $header ;
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1006 push @hmdb_matrix, \@headers ;
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1007 }
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1008
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1009 my $index_mz = 0 ;
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1010
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1011 foreach my $mz ( @{$init_mzs} ) {
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1012
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1013 my $index_entries = 0 ;
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1014 my @clusters = () ;
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1015 my $cluster_col = undef ;
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1016
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1017 my @anti_redondant = ('N/A') ;
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1018 my $check_rebond = 0 ;
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1019
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1020 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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1021
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1022 foreach my $entry (@{ $entries->[$index_mz] }) {
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1023
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1024 ## dispo anti doublons des entries
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1025 foreach my $rebond (@anti_redondant) {
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1026 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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1027 }
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1028
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1029 if ( $check_rebond == 0 ) {
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1030
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1031 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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1032
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1033 my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ;
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1034 my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ;
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1035 my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ;
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1036
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1037 ## METLIN data display model
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1038 ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|...
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1039 # manage final pipe
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1040 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; }
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1041 else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; }
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1042
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1043 }
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1044 $check_rebond = 0 ; ## reinit double control
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1045 $index_entries++ ;
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1046 } ## end foreach
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1047 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
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1048 push (@clusters, $cluster_col) ;
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1049 push (@hmdb_matrix, \@clusters) ;
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1050 $index_mz++ ;
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1051 }
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1052 return(\@hmdb_matrix) ;
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1053 }
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1054 ## END of SUB
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1055
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1056 =head2 METHOD set_hmdb_matrix_object_with_ids
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1057
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1058 ## Description : build the hmdb_row under its ref form (IDS only)
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1059 ## Input : $header, $init_mzs, $entries
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1060 ## Output : $hmdb_matrix
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1061 ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ;
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1062
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1063 =cut
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1064 ## START of SUB
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1065 sub set_hmdb_matrix_object_with_ids {
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1066 ## Retrieve Values
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1067 my $self = shift ;
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1068 my ( $header, $init_mzs, $entries ) = @_ ;
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1069
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1070 # print Dumper $entries ;
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1071
1
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1072 my @hmdb_matrix = () ;
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1073
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1074 if ( defined $header ) {
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1075 my @headers = () ;
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1076
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1077 ## redefined the header hmdb(delta::name::mz::formula::adduct::id)
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1078 $header = 'hmdb(delta::name::mz::formula::adduct::id)' ;
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1079 push @headers, $header ;
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1080 push @hmdb_matrix, \@headers ;
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1081 }
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1082
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1083 my $index_mz = 0 ;
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1084
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1085 foreach my $mz ( @{$init_mzs} ) {
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1086
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1087 my $index_entries = 0 ;
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1088 my @clusters = () ;
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1089 my $cluster_col = undef ;
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1090
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1091 my @anti_redondant = ('N/A') ;
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1092 my $check_rebond = 0 ;
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1093
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1094 my $nb_entries = scalar (@{ $entries->[$index_mz] }) ;
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1095
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1096 foreach my $entry (@{ $entries->[$index_mz] }) {
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1097
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1098 ## dispo anti doublons des entries
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1099 foreach my $rebond (@anti_redondant) {
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1100 if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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1101 }
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1102
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1103 if ( $check_rebond == 0 ) {
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1104
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1105 push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ;
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1106 ##
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1107
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1108 my ($hmdb_name, $hmdb_id, $hmdb_formula, $hmdb_cpd_mz, $hmdb_adduct, $hmdb_delta) = (undef, undef, undef, undef, undef, undef) ;
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1109
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1110 if ($entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ) { $hmdb_name = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ; }
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1111 else { $hmdb_name = 'UNKNOWN' ; }
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1112
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1113 if ($entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; }
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1114 else { $hmdb_id = 0 ; }
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1115
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1116 if ($entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ) { $hmdb_formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ; }
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1117 else { $hmdb_formula = 'N/A' ; }
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1118
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1119 if ($entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ) { $hmdb_cpd_mz = $entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ; }
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1120 else { $hmdb_cpd_mz = 'N/A' ; }
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1121
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1122 if ($entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ) { $hmdb_adduct = $entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ; }
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diff changeset
1123 else { $hmdb_adduct = 'N/A' ; }
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diff changeset
1124
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diff changeset
1125 if ($entries->[$index_mz][$index_entries]{ENTRY_DELTA} ) { $hmdb_delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ; }
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diff changeset
1126 else { $hmdb_delta = 0 ; }
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diff changeset
1127
1
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diff changeset
1128
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fgiacomoni
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1129 ## METLIN data display model
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fgiacomoni
parents:
diff changeset
1130 ## 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
1131 my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ;
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parents:
diff changeset
1132
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fgiacomoni
parents:
diff changeset
1133 # manage final pipe
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fgiacomoni
parents:
diff changeset
1134 if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' | ' ; }
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fgiacomoni
parents:
diff changeset
1135 else { $cluster_col .= $entry ; }
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fgiacomoni
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diff changeset
1136
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fgiacomoni
parents:
diff changeset
1137 }
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fgiacomoni
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diff changeset
1138 $check_rebond = 0 ; ## reinit double control
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fgiacomoni
parents:
diff changeset
1139 $index_entries++ ;
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fgiacomoni
parents:
diff changeset
1140 } ## end foreach
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fgiacomoni
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diff changeset
1141 if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; }
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fgiacomoni
parents:
diff changeset
1142 push (@clusters, $cluster_col) ;
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fgiacomoni
parents:
diff changeset
1143 push (@hmdb_matrix, \@clusters) ;
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fgiacomoni
parents:
diff changeset
1144 $index_mz++ ;
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fgiacomoni
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diff changeset
1145 }
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diff changeset
1146 return(\@hmdb_matrix) ;
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fgiacomoni
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diff changeset
1147 }
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fgiacomoni
parents:
diff changeset
1148 ## END of SUB
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diff changeset
1149
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fgiacomoni
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diff changeset
1150 =head2 METHOD add_lm_matrix_to_input_matrix
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fgiacomoni
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diff changeset
1151
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fgiacomoni
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1152 ## Description : build a full matrix (input + lm column)
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fgiacomoni
parents:
diff changeset
1153 ## Input : $input_matrix_object, $lm_matrix_object, $nb_header
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fgiacomoni
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diff changeset
1154 ## Output : $output_matrix_object
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fgiacomoni
parents:
diff changeset
1155 ## 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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diff changeset
1156
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fgiacomoni
parents:
diff changeset
1157 =cut
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fgiacomoni
parents:
diff changeset
1158 ## START of SUB
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fgiacomoni
parents:
diff changeset
1159 sub add_lm_matrix_to_input_matrix {
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fgiacomoni
parents:
diff changeset
1160 ## Retrieve Values
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fgiacomoni
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1161 my $self = shift ;
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fgiacomoni
parents:
diff changeset
1162 my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ;
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fgiacomoni
parents:
diff changeset
1163
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fgiacomoni
parents:
diff changeset
1164 my @output_matrix_object = () ;
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fgiacomoni
parents:
diff changeset
1165 my $index_row = 0 ;
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fgiacomoni
parents:
diff changeset
1166 my $line = 0 ;
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fgiacomoni
parents:
diff changeset
1167
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fgiacomoni
parents:
diff changeset
1168 foreach my $row ( @{$input_matrix_object} ) {
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fgiacomoni
parents:
diff changeset
1169 my @init_row = @{$row} ;
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fgiacomoni
parents:
diff changeset
1170 $line++;
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fgiacomoni
parents:
diff changeset
1171
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fgiacomoni
parents:
diff changeset
1172 if ( ( defined $nb_header ) and ( $line <= $nb_header) ) {
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fgiacomoni
parents:
diff changeset
1173 push (@output_matrix_object, \@init_row) ;
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fgiacomoni
parents:
diff changeset
1174 next ;
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fgiacomoni
parents:
diff changeset
1175 }
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fgiacomoni
parents:
diff changeset
1176
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fgiacomoni
parents:
diff changeset
1177 if ( $lm_matrix_object->[$index_row] ) {
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fgiacomoni
parents:
diff changeset
1178 my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ;
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fgiacomoni
parents:
diff changeset
1179
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fgiacomoni
parents:
diff changeset
1180 if ($dim > 1) { warn "the add method can't manage more than one column\n" ;}
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fgiacomoni
parents:
diff changeset
1181 my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ;
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fgiacomoni
parents:
diff changeset
1182
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fgiacomoni
parents:
diff changeset
1183 push (@init_row, $lm_col) ;
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fgiacomoni
parents:
diff changeset
1184 $index_row++ ;
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fgiacomoni
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diff changeset
1185 }
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fgiacomoni
parents:
diff changeset
1186 push (@output_matrix_object, \@init_row) ;
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fgiacomoni
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diff changeset
1187 }
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fgiacomoni
parents:
diff changeset
1188 return(\@output_matrix_object) ;
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fgiacomoni
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diff changeset
1189 }
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fgiacomoni
parents:
diff changeset
1190 ## END of SUB
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fgiacomoni
parents:
diff changeset
1191
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fgiacomoni
parents:
diff changeset
1192 =head2 METHOD write_csv_skel
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fgiacomoni
parents:
diff changeset
1193
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fgiacomoni
parents:
diff changeset
1194 ## Description : prepare and write csv output file
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fgiacomoni
parents:
diff changeset
1195 ## Input : $csv_file, $rows
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fgiacomoni
parents:
diff changeset
1196 ## Output : $csv_file
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fgiacomoni
parents:
diff changeset
1197 ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ;
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fgiacomoni
parents:
diff changeset
1198
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fgiacomoni
parents:
diff changeset
1199 =cut
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fgiacomoni
parents:
diff changeset
1200 ## START of SUB
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fgiacomoni
parents:
diff changeset
1201 sub write_csv_skel {
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fgiacomoni
parents:
diff changeset
1202 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
1203 my $self = shift ;
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fgiacomoni
parents:
diff changeset
1204 my ( $csv_file, $rows ) = @_ ;
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fgiacomoni
parents:
diff changeset
1205
14
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diff changeset
1206 # my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ;
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diff changeset
1207 my $ocsv = lib::csv::new() ;
1
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fgiacomoni
parents:
diff changeset
1208 my $csv = $ocsv->get_csv_object("\t") ;
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fgiacomoni
parents:
diff changeset
1209 $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ;
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fgiacomoni
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diff changeset
1210
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fgiacomoni
parents:
diff changeset
1211 return($csv_file) ;
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fgiacomoni
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diff changeset
1212 }
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fgiacomoni
parents:
diff changeset
1213 ## END of SUB
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fgiacomoni
parents:
diff changeset
1214
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fgiacomoni
parents:
diff changeset
1215 =head2 METHOD write_csv_one_mass
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fgiacomoni
parents:
diff changeset
1216
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fgiacomoni
parents:
diff changeset
1217 ## Description : print a cvs file
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fgiacomoni
parents:
diff changeset
1218 ## Input : $masses, $ids, $results, $file
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fgiacomoni
parents:
diff changeset
1219 ## Output : N/A
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fgiacomoni
parents:
diff changeset
1220 ## Usage : write_csv_one_mass( $ids, $results, $file ) ;
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fgiacomoni
parents:
diff changeset
1221
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fgiacomoni
parents:
diff changeset
1222 =cut
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fgiacomoni
parents:
diff changeset
1223 ## START of SUB
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fgiacomoni
parents:
diff changeset
1224 sub write_csv_one_mass {
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fgiacomoni
parents:
diff changeset
1225 ## Retrieve Values
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fgiacomoni
parents:
diff changeset
1226 my $self = shift ;
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fgiacomoni
parents:
diff changeset
1227 my ( $masses, $ids, $results, $file, ) = @_ ;
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fgiacomoni
parents:
diff changeset
1228
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fgiacomoni
parents:
diff changeset
1229 open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ;
14
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diff changeset
1230 print CSV "ID\tQuery(Da)\tDelta(ppm)\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ;
1
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fgiacomoni
parents:
diff changeset
1231
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fgiacomoni
parents:
diff changeset
1232 my $i = 0 ;
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fgiacomoni
parents:
diff changeset
1233
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fgiacomoni
parents:
diff changeset
1234 foreach my $id (@{$ids}) {
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fgiacomoni
parents:
diff changeset
1235 my $mass = undef ;
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fgiacomoni
parents:
diff changeset
1236 if ( $masses->[$i] ) { $mass = $masses->[$i] ; }
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fgiacomoni
parents:
diff changeset
1237 else { last ; }
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fgiacomoni
parents:
diff changeset
1238
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fgiacomoni
parents:
diff changeset
1239 if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results.
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fgiacomoni
parents:
diff changeset
1240
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1241 my @anti_redondant = ('N/A') ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1242 my $check_rebond = 0 ;
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fgiacomoni
parents:
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1243 my $check_noentry = 0 ;
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fgiacomoni
parents:
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1244
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fgiacomoni
parents:
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1245 foreach my $entry (@{$results->[$i]}) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
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1246 $check_noentry ++ ;
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fgiacomoni
parents:
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1247 ## dispo anti doublons des entries
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1248 foreach my $rebond (@anti_redondant) {
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fgiacomoni
parents:
diff changeset
1249 if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; }
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fgiacomoni
parents:
diff changeset
1250 }
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fgiacomoni
parents:
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1251 # print "\n-----------------------" ;
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fgiacomoni
parents:
diff changeset
1252 # print Dumper $entry->{ENTRY_ENTRY_ID} ;
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fgiacomoni
parents:
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1253 # print "-------------------------$check_rebond\n" ;
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fgiacomoni
parents:
diff changeset
1254 # print Dumper @anti_redondant ;
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fgiacomoni
parents:
diff changeset
1255 if ( $check_rebond == 0 ) {
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fgiacomoni
parents:
diff changeset
1256
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1257 push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ;
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fgiacomoni
parents:
diff changeset
1258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1259 print CSV "$id\t$mass\t" ;
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fgiacomoni
parents:
diff changeset
1260
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1261 ## print delta
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1262 if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; }
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fgiacomoni
parents:
diff changeset
1263 else { print CSV "0\t" ; }
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fgiacomoni
parents:
diff changeset
1264
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1265 ## print cpd name
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1266 if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1267 else { print CSV "UNKNOWN\t" ; }
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fgiacomoni
parents:
diff changeset
1268
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1269 ## print cpd mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1270 if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1271 else { print CSV "N/A\t" ; }
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fgiacomoni
parents:
diff changeset
1272
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1273 ## print cpd formula
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1274 if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1275 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1276
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1277 ## print adduct
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1278 if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1279 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1280
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1281 ## print adduct mz
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1282 if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1283 else { print CSV "N/A\t" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1284
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1285 ## print cpd id
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1286 if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1287 else { print CSV "N/A\n" ; }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1288 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1289 $check_rebond = 0 ; ## reinit double control
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1290 } ## end foreach
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1291 if ($check_noentry == 0 ) {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1292 print CSV "$id\t$mass\t0\tUNKNOWN\tN/A\tN/A\tN/A\tN/A\tN/A\n" ;
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fgiacomoni
parents:
diff changeset
1293 }
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fgiacomoni
parents:
diff changeset
1294 }
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fgiacomoni
parents:
diff changeset
1295 $i++ ;
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fgiacomoni
parents:
diff changeset
1296 }
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fgiacomoni
parents:
diff changeset
1297 close(CSV) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1298 return() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1299 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1300 ## END of SUB
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fgiacomoni
parents:
diff changeset
1301
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1302 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1303
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1304
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1305 __END__
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1306
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1307 =head1 SUPPORT
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fgiacomoni
parents:
diff changeset
1308
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1309 You can find documentation for this module with the perldoc command.
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1310
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1311 perldoc hmdb.pm
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fgiacomoni
parents:
diff changeset
1312
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1313 =head1 Exports
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fgiacomoni
parents:
diff changeset
1314
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1315 =over 4
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fgiacomoni
parents:
diff changeset
1316
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1317 =item :ALL is ...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1318
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1319 =back
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1320
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1321 =head1 AUTHOR
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1322
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1323 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
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fgiacomoni
parents:
diff changeset
1324
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1325 =head1 LICENSE
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fgiacomoni
parents:
diff changeset
1326
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1327 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
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fgiacomoni
parents:
diff changeset
1328
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1329 =head1 VERSION
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1330
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1331 version 1 : 06 / 06 / 2013
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fgiacomoni
parents:
diff changeset
1332
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1333 version 2 : 27 / 01 / 2014
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fgiacomoni
parents:
diff changeset
1334
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fgiacomoni
parents:
diff changeset
1335 version 3 : 19 / 11 / 2014
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fgiacomoni
parents:
diff changeset
1336
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1337 version 4 : 28 / 01 / 2016
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fgiacomoni
parents:
diff changeset
1338
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1339 version 5 : 02 / 11 /2016
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fgiacomoni
parents:
diff changeset
1340
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1341 =cut