Repository 'hmdb_ms_search'
hg clone https://toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search

Changeset 4:6091a80df951 (2018-01-19)
Previous changeset 3:505956db90c5 (2017-02-20) Next changeset 5:520778e357cc (2018-01-19)
Commit message:
planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98
modified:
lib/hmdb.pm
t/hmdb_managerTest.pl
t/lib/hmdbTest.pm
test-data/out_test02.html
test-data/out_test02.tabular
test-data/out_test02.txt
test-data/out_test03.html
test-data/out_test03.tabular
test-data/out_test03.txt
wsdl_hmdb.pl
b
diff -r 505956db90c5 -r 6091a80df951 lib/hmdb.pm
--- a/lib/hmdb.pm Mon Feb 20 09:55:54 2017 -0500
+++ b/lib/hmdb.pm Fri Jan 19 09:38:17 2018 -0500
[
@@ -271,23 +271,46 @@
 #    print Dumper $csv ;
     
     foreach my $line (@{$csv}) {
-    
-     if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
-     my @entry = split(/,/, $line) ;
-    
-     if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
+     ## HMDB csv output - [DEPRECATED]...
+#     if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) {
+#     my @entry = split(/,/, $line) ;
+#    
+#     if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
+#    
+#     $features{ENTRY_ENTRY_ID} = $entry[1] ;
+#     $features{ENTRY_FORMULA} = $entry[2] ;
+#     $features{ENTRY_CPD_MZ} = $entry[3] ;
+#     $features{ENTRY_ADDUCT} = $entry[4] ;
+#     $features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
+#     $features{ENTRY_ADDUCT_MZ} = $entry[6] ;
+#     $features{ENTRY_DELTA} = $entry[7] ;
+#    
+#     my %temp = %features ;
+#    
+#     push (@{$result_by_entry{$entry[0]} }, \%temp) ;
+#     }
+     ## NEW HMDB format V4.0 - dec2017
+ if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) {
     
-     $features{ENTRY_ENTRY_ID} = $entry[1] ;
-     $features{ENTRY_FORMULA} = $entry[2] ;
-     $features{ENTRY_CPD_MZ} = $entry[3] ;
-     $features{ENTRY_ADDUCT} = $entry[4] ;
-     $features{ENTRY_ADDUCT_TYPE} = $entry[5] ;
-     $features{ENTRY_ADDUCT_MZ} = $entry[6] ;
-     $features{ENTRY_DELTA} = $entry[7] ;
-    
-     my %temp = %features ;
-    
-     push (@{$result_by_entry{$entry[0]} }, \%temp) ;
+     if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/  ) {
+     my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ;
+
+     if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
+         
+      $features{ENTRY_ENTRY_ID} = $entry[1] ;
+      $features{ENTRY_FORMULA} = $entry[4] ;
+      $features{ENTRY_CPD_MZ} = $entry[5] ;
+      $features{ENTRY_ADDUCT} = $entry[6] ;
+      $features{ENTRY_ADDUCT_TYPE} = $entry[7] ;
+      $features{ENTRY_ADDUCT_MZ} = $entry[8] ;
+      $features{ENTRY_DELTA} = $entry[9] ;
+     
+      my %temp = %features ;
+      push (@{$result_by_entry{$entry[0]} }, \%temp) ;
+     }
+     else {
+     warn "The parsed line ($line) does not match your pattern\n " ;
+     }
      }
      else {
      next ;
b
diff -r 505956db90c5 -r 6091a80df951 t/hmdb_managerTest.pl
--- a/t/hmdb_managerTest.pl Mon Feb 20 09:55:54 2017 -0500
+++ b/t/hmdb_managerTest.pl Fri Jan 19 09:38:17 2018 -0500
[
b'@@ -48,14 +48,22 @@\n \tis_deeply( get_matches_from_hmdb_uaTest(\n \t\t\'175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A\', 0.001, \'positive\'),\n \t\t[\n-          \'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta\',\n-          \'175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125\',\n-          \'175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676\',\n-          \'175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895\',\n-          \'175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-          \'175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-          \'420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\',\n-          \'420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\'\n+          \'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)\',\n+#          \'175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125\',\n+#          \'175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676\',\n+#          \'175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895\',\n+#          \'175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n+#          \'175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n+#          \'420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\',\n+#          \'420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\'\n+\t\t\t## Update format - 2018-01-19... HMDB V04\n+\t\t\t\'175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1\',\n+\t\t\t\'175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4\',\n+\t\t\t\'175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5\',\n+\t\t\t\'175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5\',\n+\t\t\t\'175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5\',\n+\t\t\t\'420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n+\t\t\t\'420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n         ],\n \t\t\'Method \\\'get_matches_from_hmdb_ua\\\' works with a well-formated string of mzs and return a complete csv from hmdb\');\n \t\n@@ -77,29 +85,38 @@\n \tprint "\\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\\n" ; $current_test++;\n \tis_deeply ( parse_hmdb_csv_resultsTest (\n \t\t[\n-          \'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta\',\n-          \'175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125\',\n-          \'175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676\',\n-          \'175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895\',\n-          \'175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-          \'175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n-          \'420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\',\n-          \'420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683\'\n+          \'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)\',\n+#          \'175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125\',\n+#          \'175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676\',\n+#          \'175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895\',\n+#          \'175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914\',\n+#          \'175.01,HM'..b'M+H+K,+,175.009086,5\',\n+\t\t\t\'175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5\',\n+\t\t\t\'420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n+\t\t\t\'420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2\',\n         ],\n-        [\'175.01\', \'238.19\', \'420.16\']\n+        [\'175.01\', \'238.19\', \'420.16\'],\n+        10\n \t),\n \t\t[\n           [\n-\t\t\t{ \'ENTRY_ADDUCT\' => \'M+IsoProp+H\', \'ENTRY_DELTA\' => \'0.000125\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_FORMULA\' => \'H2O3S2\', \'ENTRY_ENTRY_ID\' => \'HMDB60293\', \'ENTRY_ADDUCT_MZ\' => \'175.009875\', \'ENTRY_CPD_MZ\' => \'113.94453531\' },\n-\t\t\t{ \'ENTRY_ADDUCT\' => \'M+CH3OH+H\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_DELTA\' => \'0.000676\', \'ENTRY_FORMULA\' => \'C2H6O3S2\', \'ENTRY_ENTRY_ID\' => \'HMDB03745\', \'ENTRY_ADDUCT_MZ\' => \'175.009324\', \'ENTRY_CPD_MZ\' => \'141.975835438\' },\n-\t\t\t{ \'ENTRY_CPD_MZ\' => \'95.987885149\', \'ENTRY_FORMULA\' => \'H4O4Si\', \'ENTRY_ENTRY_ID\' => \'HMDB31436\', \'ENTRY_ADDUCT_MZ\' => \'175.009105\', \'ENTRY_DELTA\' => \'0.000895\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_ADDUCT\' => \'M+DMSO+H\' },\n-\t\t\t{ \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_DELTA\' => \'0.000914\', \'ENTRY_ADDUCT\' => \'M+H+K\', \'ENTRY_CPD_MZ\' => \'310.047738052\', \'ENTRY_ENTRY_ID\' => \'HMDB33657\', \'ENTRY_ADDUCT_MZ\' => \'175.009086\', \'ENTRY_FORMULA\' => \'C17H10O6\' },\n-\t\t\t{ \'ENTRY_ADDUCT\' => \'M+H+K\', \'ENTRY_DELTA\' => \'0.000914\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_FORMULA\' => \'C17H10O6\', \'ENTRY_ADDUCT_MZ\' => \'175.009086\', \'ENTRY_ENTRY_ID\' => \'HMDB35230\', \'ENTRY_CPD_MZ\' => \'310.047738052\' }\n+            { \'ENTRY_CPD_MZ\' => \'113.94453531\', \'ENTRY_ENTRY_ID\' => \'HMDB0060293\', \'ENTRY_FORMULA\' => \'H2O3S2\', \'ENTRY_ADDUCT_MZ\' => \'175.009875\', \'ENTRY_DELTA\' => \'1\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_ADDUCT\' => \'M+IsoProp+H\' },\n+            {\'ENTRY_DELTA\' => \'4\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_ADDUCT\' => \'M+CH3OH+H\',\'ENTRY_CPD_MZ\' => \'141.975835438\',\'ENTRY_ENTRY_ID\' => \'HMDB0003745\',\'ENTRY_FORMULA\' => \'C2H6O3S2\',\'ENTRY_ADDUCT_MZ\' => \'175.009324\'},\n+            {\'ENTRY_ENTRY_ID\' => \'HMDB0031436\',\'ENTRY_CPD_MZ\' => \'95.987885149\',\'ENTRY_ADDUCT_MZ\' => \'175.009105\',\'ENTRY_FORMULA\' => \'H4O4Si\',\'ENTRY_DELTA\' => \'5\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_ADDUCT\' => \'M+DMSO+H\'},\n+            {\'ENTRY_ADDUCT_MZ\' => \'175.009086\',\'ENTRY_FORMULA\' => \'C17H10O6\',\'ENTRY_ENTRY_ID\' => \'HMDB0033657\',\'ENTRY_CPD_MZ\' => \'310.047738052\',\'ENTRY_ADDUCT\' => \'M+H+K\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_DELTA\' => \'5\'},\n+            {\'ENTRY_ADDUCT_MZ\' => \'175.009086\',\'ENTRY_FORMULA\' => \'C17H10O6\',\'ENTRY_ENTRY_ID\' => \'HMDB0035230\',\'ENTRY_CPD_MZ\' => \'310.047738052\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_ADDUCT\' => \'M+H+K\',\'ENTRY_DELTA\' => \'5\'}\n           ],\n           [],\n           [\n-            { \'ENTRY_ADDUCT\' => \'M+IsoProp+H\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_DELTA\' => \'0.000683\', \'ENTRY_ENTRY_ID\' => \'HMDB60838\', \'ENTRY_ADDUCT_MZ\' => \'420.159317\', \'ENTRY_FORMULA\' => \'C17H17N3O4S\', \'ENTRY_CPD_MZ\' => \'359.093976737\' }, \n-            { \'ENTRY_CPD_MZ\' => \'359.093976737\', \'ENTRY_FORMULA\' => \'C17H17N3O4S\', \'ENTRY_ENTRY_ID\' => \'HMDB60836\', \'ENTRY_ADDUCT_MZ\' => \'420.159317\', \'ENTRY_ADDUCT_TYPE\' => \'+\', \'ENTRY_DELTA\' => \'0.000683\', \'ENTRY_ADDUCT\' => \'M+IsoProp+H\' }\n+            {\'ENTRY_FORMULA\' => \'C17H17N3O4S\',\'ENTRY_ADDUCT_MZ\' => \'420.159317\',\'ENTRY_CPD_MZ\' => \'359.093976737\',\'ENTRY_ENTRY_ID\' => \'HMDB0060838\',\'ENTRY_ADDUCT\' => \'M+IsoProp+H\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_DELTA\' => \'2\'},\n+            {\'ENTRY_DELTA\' => \'2\',\'ENTRY_ADDUCT_TYPE\' => \'+\',\'ENTRY_ADDUCT\' => \'M+IsoProp+H\',\'ENTRY_ENTRY_ID\' => \'HMDB0060836\',\'ENTRY_CPD_MZ\' => \'359.093976737\',\'ENTRY_ADDUCT_MZ\' => \'420.159317\',\'ENTRY_FORMULA\' => \'C17H17N3O4S\'}\n           ]\n         ],\n \t\t\'Method \\\'parse_hmdb_csv_results\\\' works with a well-formated csv output and returns a a well formated array\' ) ;\n'
b
diff -r 505956db90c5 -r 6091a80df951 t/lib/hmdbTest.pm
--- a/t/lib/hmdbTest.pm Mon Feb 20 09:55:54 2017 -0500
+++ b/t/lib/hmdbTest.pm Fri Jan 19 09:38:17 2018 -0500
b
@@ -71,10 +71,10 @@
 
 ## sub
 sub parse_hmdb_csv_resultsTest {
- my ($hmdb_pages, $mzs ) = @_ ;
+ my ($hmdb_pages, $mzs, $max ) = @_ ;
 
  my $oHmdb = lib::hmdb->new() ;
- my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result
+ my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max) ; ## hash format result
 
  return($result) ;
 }
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.html
--- a/test-data/out_test02.html Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test02.html Fri Jan 19 09:38:17 2018 -0500
b
b'@@ -1,1 +1,1 @@\n-<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><!-- JavaScript --><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style type="text/css">body {padding-top: 70px}div.lm-table-warning {  font-size: 1.4em;  font-weight: bold;  padding-right: 25px;  color: #21536a;  margin-left: 3px;}tr.green td  {background-color: #eaf2d3; color: black;}tr.blank td {background-color: #9999CC; color: black;}table {font-family:\'Trebuchet MS\',Arial,Helvetica,sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size: 1.2em;text-align: center;padding-top: 5px;padding-bottom: 10px;background-color: #a7c942;color: #ffffff;}td.ca {text-align:center;}footer {  margin: 50px 0;}</style><script>function test(pageNumber){  var page="#page-id-"+pageNumber;  $(\'.select\').hide() ; $(page).show()}</script></head><body><div class="container"><div class="lm-table-warning">Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><!-- HeadRows--><table id="detail_table" class="detail"><col style="width:30px;"><!-- Ids (m/z)--><col style="width:30px;"><!-- Mass (m/z)--><col style="width:120px;"><!-- Met name--><col style="width:50px;"><!-- Cpd ID--><col style="width:40px;"><!-- formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- adduct --><col style="width:20px;"><!-- adduct type--><col style="width:60px;"><!-- adduct mw--><col style="width:50px;"><!-- delta--><col style="width:120px;"><!-- INCHI--><col style="width:20;"><!-- logP--><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >7.02080998</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">UNKNOWN</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/" target="_blank" class="btn">NONE</a></td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">n/a</td><td class="ca">0</td><td class="ca">n/a</td><td class="ca">n/a</td></tr><tr class="green"><td class="ca" >mz_00002</td><td id="2" class="ca" >75.05547146</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Nitrosodimethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB31419" target="_blank" class="btn">HMDB31419</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012824</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">0.00018246</td><td class="ca">InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3</td><td class="ca">-0.53</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Acetylhydrazine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB60428" target="_blank" class="btn">HMDB60428</a></td><td class='..b' target="_blank" class="btn">HMDB0142449</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">2</td><td class="ca">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">2</td><td class="ca">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Allyl alcohol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031652" target="_blank" class="btn">HMDB0031652</a></td><td class="ca">C3H6O</td><td class="ca">58.041864814</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">2</td><td class="ca">InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2</td><td class="ca">-0.03</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >76.07593168</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">3-aminopropan-1-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0140038" target="_blank" class="btn">HMDB0140038</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2</td><td class="ca">-1.01</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-Amino-propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0012136" target="_blank" class="btn">HMDB0012136</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3</td><td class="ca">-1.03</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-(methylamino)ethan-1-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0142449" target="_blank" class="btn">HMDB0142449</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413914</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3</td><td class="ca">-1.05</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Trimethylamine N-oxide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000925" target="_blank" class="btn">HMDB0000925</a></td><td class="ca">C3H9NO</td><td class="ca">75.068413915</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.07569</td><td class="ca">3</td><td class="ca">InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3</td><td class="ca">-2.01</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Allyl alcohol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0031652" target="_blank" class="btn">HMDB0031652</a></td><td class="ca">C3H6O</td><td class="ca">58.041864814</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.075688</td><td class="ca">3</td><td class="ca">InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2</td><td class="ca">-0.03</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row">  <div class="col-lg-12"><p>Copyright &copy; INRA, N Paulhe, F Giacomoni 2014 </p>  </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.tabular
--- a/test-data/out_test02.tabular Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test02.tabular Fri Jan 19 09:38:17 2018 -0500
[
@@ -1,7 +1,7 @@
 id mz rt hmdb(delta::name::mz::formula::adduct::id)
 1 7.02080998 49.38210915 NONE
-2 75.05547146 0.658528069 0.00018246::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB31419 | 0.00018246::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB60428 | 0.00018346::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB00064 | 0.00018346::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB13222 | 0.00018446::[Nitrogen oxides]::33.021463723::H3NO::[M+ACN+H]::HMDB32439
-3 75.08059797 1743.94267 0.00015697::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB04327 | 0.00015697::[UNKNOWN]::74.073164942::C4H10O::[M+H]::HMDB62103 | 0.00015697::[2-Butanol]::74.073164942::C4H10O::[M+H]::HMDB11469 | 0.00015697::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB06006 | 0.00015697::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB31456
-4 76.03942694 51.23158899 0.00012294::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB00191 | 0.00012294::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB31239 | 0.00012294::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB00123 | 0.00012294::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB14691 | 0.00012294::[Iminodiacetic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB11753
-5 76.07584477 50.51249853 0.00015477::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB12136 | 0.00015477::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB00925 | 0.00015677::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB31652 | 0.00015677::[UNKNOWN]::58.041864813::C3H6O::[M+NH4]::HMDB62143 | 0.00015677::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB31558
-6 76.07593168 0.149308136 0.00024168::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB12136 | 0.00024168::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB00925 | 0.00024368::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB31652 | 0.00024368::[UNKNOWN]::58.041864813::C3H6O::[M+NH4]::HMDB62143 | 0.00024368::[Methyloxirane]::58.041864814::C3H6O::[M+NH4]::HMDB31558
+2 75.05547146 0.658528069 2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222
+3 75.08059797 1743.94267 0::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[UNKNOWN]::74.073164942::C4H10O::[M+H]::HMDB0062103 | 2::[1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether]::74.073164942::C4H10O::[M+H]::HMDB0062326 | 2::[2-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0011469
+4 76.03942694 51.23158899 2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Glycine]::75.032028409::C2H5NO2::[M+H]::HMDB0000123 | 2::[Acetohydroxamic Acid]::75.032028409::C2H5NO2::[M+H]::HMDB0014691
+5 76.07584477 50.51249853 2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652
+6 76.07593168 0.149308136 3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[Allyl alcohol]::58.041864814::C3H6O::[M+NH4]::HMDB0031652
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test02.txt
--- a/test-data/out_test02.txt Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test02.txt Fri Jan 19 09:38:17 2018 -0500
[
@@ -1,27 +1,27 @@
 ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
 mz_00001 7.02080998 0 UNKNOWN N/A N/A N/A N/A N/A
-mz_00002 75.05547146 0.00018246 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB31419
-mz_00002 75.05547146 0.00018246 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB60428
-mz_00002 75.05547146 0.00018346 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB00064
-mz_00002 75.05547146 0.00018346 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB13222
-mz_00002 75.05547146 0.00018446 [Nitrogen oxides] 33.021463723 H3NO [M+ACN+H] 75.055287 HMDB32439
-mz_00003 75.08059797 0.00015697 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB04327
-mz_00003 75.08059797 0.00015697 [UNKNOWN] 74.073164942 C4H10O [M+H] 75.080441 HMDB62103
-mz_00003 75.08059797 0.00015697 [2-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB11469
-mz_00003 75.08059797 0.00015697 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB06006
-mz_00003 75.08059797 0.00015697 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB31456
-mz_00004 76.03942694 0.00012294 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB00191
-mz_00004 76.03942694 0.00012294 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB31239
-mz_00004 76.03942694 0.00012294 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB00123
-mz_00004 76.03942694 0.00012294 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB14691
-mz_00004 76.03942694 0.00012294 [Iminodiacetic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB11753
-mz_00005 76.07584477 0.00015477 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB12136
-mz_00005 76.07584477 0.00015477 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB00925
-mz_00005 76.07584477 0.00015677 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31652
-mz_00005 76.07584477 0.00015677 [UNKNOWN] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB62143
-mz_00005 76.07584477 0.00015677 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31558
-mz_00006 76.07593168 0.00024168 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB12136
-mz_00006 76.07593168 0.00024168 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB00925
-mz_00006 76.07593168 0.00024368 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31652
-mz_00006 76.07593168 0.00024368 [UNKNOWN] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB62143
-mz_00006 76.07593168 0.00024368 [Methyloxirane] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB31558
+mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419
+mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428
+mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472
+mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064
+mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222
+mz_00003 75.08059797 0 [UNKNOWN] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221
+mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327
+mz_00003 75.08059797 2 [UNKNOWN] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062103
+mz_00003 75.08059797 2 [1-hydroperoxy-8-carboxyoctyl 3,4-epoxynon-(2E)-enyl ether] 74.073164942 C4H10O [M+H] 75.080441 HMDB0062326
+mz_00003 75.08059797 2 [2-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0011469
+mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191
+mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239
+mz_00004 76.03942694 2 [1-deoxy-1-(N6-lysino)-D-fructose] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186
+mz_00004 76.03942694 2 [Glycine] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0000123
+mz_00004 76.03942694 2 [Acetohydroxamic Acid] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0014691
+mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
+mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
+mz_00005 76.07584477 2 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
+mz_00005 76.07584477 2 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031652
+mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038
+mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136
+mz_00006 76.07593168 3 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449
+mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925
+mz_00006 76.07593168 3 [Allyl alcohol] 58.041864814 C3H6O [M+NH4] 76.075688 HMDB0031652
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.html
--- a/test-data/out_test03.html Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test03.html Fri Jan 19 09:38:17 2018 -0500
b
b'@@ -1,1 +1,1 @@\n-<?xml version="1.0" encoding="UTF-8" ?><!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="description" content=""><meta name="author" content="INRA de Clermont-Ferrand"><title>Galaxy HMDB queries - All results</title><link rel="stylesheet" type="text/css" href="css.php" media="all"><link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style/simplePagination.css"/><!-- JavaScript --><script src="https://ajax.googleapis.com/ajax/libs/jquery/1.7.2/jquery.min.js"></script><script src="https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts/jquery.simplePagination.js"></script><style type="text/css">body {padding-top: 70px}div.lm-table-warning {  font-size: 1.4em;  font-weight: bold;  padding-right: 25px;  color: #21536a;  margin-left: 3px;}tr.green td  {background-color: #eaf2d3; color: black;}tr.blank td {background-color: #9999CC; color: black;}table {font-family:\'Trebuchet MS\',Arial,Helvetica,sans-serif;width:100%;border-collapse:collapse;}table.detail, table.detail tr.parent, table.detail td, table.detail th, table.detail tr.category {border-collapse:collapse;border:1px solid #98bf21;}table.detail th {font-size: 1.2em;text-align: center;padding-top: 5px;padding-bottom: 10px;background-color: #a7c942;color: #ffffff;}td.ca {text-align:center;}footer {  margin: 50px 0;}</style><script>function test(pageNumber){  var page="#page-id-"+pageNumber;  $(\'.select\').hide() ; $(page).show()}</script></head><body><div class="container"><div class="lm-table-warning">Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05</div><div id="detail_table_source" style="display:none"></div><p><div id="choose"></div><p><div id="ms_search_0" class="ms-search-table"></div><!-- HeadRows--><table id="detail_table" class="detail"><col style="width:30px;"><!-- Ids (m/z)--><col style="width:30px;"><!-- Mass (m/z)--><col style="width:120px;"><!-- Met name--><col style="width:50px;"><!-- Cpd ID--><col style="width:40px;"><!-- formula--><col style="width:60px;"><!-- cpd mw--><col style="width:50px;"><!-- adduct --><col style="width:20px;"><!-- adduct type--><col style="width:60px;"><!-- adduct mw--><col style="width:50px;"><!-- delta--><col style="width:120px;"><!-- INCHI--><col style="width:20;"><!-- logP--><thead><th>ID from input</th><th>Mass (m/z)</th><th>Metabolite_Name</th><th>Compound_ID</th><th>Formula</th><th>Compound MW (Da)</th><th>Adduct</th><th>Adduct_Type</th><th>Adduct MW (Da)</th><th>Delta</th><th>InChI Identifier</th><th>Predicted LogP (ALOGPS)</th></thead><tbody class="select" id="page-id-1"><tr class="white"><td class="ca" >mz_00001</td><td id="1" class="ca" >175.01</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Hydroxidodioxidosulfidosulfate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB60293" target="_blank" class="btn">HMDB60293</a></td><td class="ca">H2O3S2</td><td class="ca">113.94453531</td><td class="ca">M+IsoProp+H</td><td class="ca">+</td><td class="ca">175.009875</td><td class="ca">0.000125</td><td class="ca">InChI=1S/H2O3S2/c1-5(2,3)4/h(H2,1,2,3,4)</td><td class="ca">NA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Mesna</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB03745" target="_blank" class="btn">HMDB03745</a></td><td class="ca">C2H6O3S2</td><td class="ca">141.975835438</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">175.009324</td><td class="ca">0.000676</td><td class="ca">InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)</td><td class="ca">-1.53</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Silicic acid</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB31436" target="_blank" class="btn">HMDB31436</a></td><td class="ca">H4O4Si</td><td'..b'(17)24)15-8-14(25)12-4-3-11(7-16(12)31-15)30-22-21(28)20(27)19(26)18(9-23)32-22/h2-8,18-24,26-28H,9H2,1H3</td><td class="ca">0.81</td></tr><tr class="green"><td class="ca" >mz_00006</td><td id="6" class="ca" >1100.45</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">NPC</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0060499" target="_blank" class="btn">HMDB0060499</a></td><td class="ca">C28H30N4O6</td><td class="ca">518.216534712</td><td class="ca">2M+ACN+Na</td><td class="ca">+</td><td class="ca">1100.448834</td><td class="ca">1</td><td class="ca">InChI=1S/C28H30N4O6/c1-3-17-18-11-16(38-27(35)31-9-7-15(29)8-10-31)5-6-22(18)30-24-19(17)13-32-23(24)12-21-20(25(32)33)14-37-26(34)28(21,36)4-2/h5-6,11-12,15,36H,3-4,7-10,13-14,29H2,1-2H3/t28-/m0/s1</td><td class="ca">2.40</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Cellulose triacetate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0032198" target="_blank" class="btn">HMDB0032198</a></td><td class="ca">C30H34Cl2N4O</td><td class="ca">536.210967144</td><td class="ca">2M+3H2O+2H</td><td class="ca">+</td><td class="ca">1100.445054</td><td class="ca">4</td><td class="ca">InChI=1S/C30H34Cl2N4O/c31-21-17-24(32)29-27(18-21)36-26-12-7-5-10-23(26)30(29)34-15-8-2-1-3-13-28(37)33-16-14-20-19-35-25-11-6-4-9-22(20)25/h4,6,9,11,17-19,35H,1-3,5,7-8,10,12-16H2,(H,33,37)(H,34,36)</td><td class="ca">7.37</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Lewis X trisaccharide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0006568" target="_blank" class="btn">HMDB0006568</a></td><td class="ca">C20H35NO15</td><td class="ca">529.200669455</td><td class="ca">2M+ACN+H</td><td class="ca">+</td><td class="ca">1100.435162</td><td class="ca">13</td><td class="ca">InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)35-17(8(3-22)21-7(2)25)18(9(26)4-23)36-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1</td><td class="ca">-2.26</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0002060" target="_blank" class="btn">HMDB0002060</a></td><td class="ca">C20H35NO15</td><td class="ca">529.200669455</td><td class="ca">2M+ACN+H</td><td class="ca">+</td><td class="ca">1100.435162</td><td class="ca">13</td><td class="ca">InChI=1S/C20H35NO15/c1-6-11(27)14(30)16(32)19(33-6)36-18-15(31)13(29)10(5-24)34-20(18)35-17(12(28)9(26)4-23)8(3-22)21-7(2)25/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13-,14+,15-,16-,17+,18+,19-,20-/m0/s1</td><td class="ca">-2.25</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Lewis a trisaccharide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0006582" target="_blank" class="btn">HMDB0006582</a></td><td class="ca">C20H35NO15</td><td class="ca">529.200669455</td><td class="ca">2M+ACN+H</td><td class="ca">+</td><td class="ca">1100.435162</td><td class="ca">13</td><td class="ca">InChI=1S/C20H35NO15/c1-6-11(27)13(29)15(31)19(33-6)36-18(9(26)4-23)17(8(3-22)21-7(2)25)35-20-16(32)14(30)12(28)10(5-24)34-20/h3,6,8-20,23-24,26-32H,4-5H2,1-2H3,(H,21,25)/t6-,8-,9+,10+,11+,12-,13+,14-,15-,16+,17+,18+,19-,20-/m0/s1</td><td class="ca">-2.27</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row">  <div class="col-lg-12"><p>Copyright &copy; INRA, N Paulhe, F Giacomoni 2014 </p>  </div> </div> </footer></div><script language="javascript">$(function() {$(\'#choose\').pagination({items: 2,itemsOnPage: 1,currentPage: 1,onInit: function () { test(1); },cssStyle: \'light-theme\',onPageClick: function(pageNumber){test(pageNumber)}}).pagination(\'redraw\');});</script></body></html>\n\\ No newline at end of file\n'
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.tabular
--- a/test-data/out_test03.tabular Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test03.tabular Fri Jan 19 09:38:17 2018 -0500
[
@@ -1,31 +1,31 @@
 ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 0.000125 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB60293
-mz_00001 175.01 0.000676 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB03745
-mz_00001 175.01 0.000895 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB31436
-mz_00001 175.01 0.000914 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB33657
-mz_00001 175.01 0.000914 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB35230
-mz_00002 238.19 0.000875 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04043
-mz_00002 238.19 0.000875 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB36086
-mz_00002 238.19 0.000875 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04472
-mz_00002 238.19 0.000875 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB05812
-mz_00002 238.19 0.000875 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB35861
-mz_00003 420.16 0.000683 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60836
-mz_00003 420.16 0.000683 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60838
-mz_00003 420.16 0.001237 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB33374
-mz_00003 420.16 0.001268 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB00590
-mz_00003 420.16 0.001268 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB01138
-mz_00004 780.32 0.001444 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB31947
-mz_00004 780.32 0.005702 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB35940
-mz_00004 780.32 0.007526 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB33906
-mz_00004 780.32 0.007526 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB39032
-mz_00004 780.32 0.007526 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB32731
-mz_00005 956.25 0.005681 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB35451
-mz_00005 956.25 0.005681 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB38095
-mz_00005 956.25 0.008359 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB40803
-mz_00005 956.25 0.008359 [Glycitin] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB02219
-mz_00005 956.25 0.008359 [Calycosin 7-galactoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB38821
-mz_00006 1100.45 0.001166 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB60499
-mz_00006 1100.45 0.004946 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB32198
-mz_00006 1100.45 0.014838 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06568
-mz_00006 1100.45 0.014838 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB02060
-mz_00006 1100.45 0.014838 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06582
+mz_00001 175.01 1 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB0060293
+mz_00001 175.01 4 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB0003745
+mz_00001 175.01 5 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB0031436
+mz_00001 175.01 5 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0033657
+mz_00001 175.01 5 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0035230
+mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043
+mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086
+mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472
+mz_00002 238.19 4 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0005812
+mz_00002 238.19 4 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0035861
+mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836
+mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838
+mz_00003 420.16 3 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB0033374
+mz_00003 420.16 3 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0000590
+mz_00003 420.16 3 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0001138
+mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
+mz_00004 780.32 7 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB0035940
+mz_00004 780.32 10 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0033906
+mz_00004 780.32 10 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0039032
+mz_00004 780.32 10 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0032731
+mz_00005 956.25 6 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0035451
+mz_00005 956.25 6 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0038095
+mz_00005 956.25 9 [UNKNOWN] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0153300
+mz_00005 956.25 9 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0040803
+mz_00005 956.25 9 [2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0141944
+mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499
+mz_00006 1100.45 4 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB0032198
+mz_00006 1100.45 13 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006568
+mz_00006 1100.45 13 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0002060
+mz_00006 1100.45 13 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006582
b
diff -r 505956db90c5 -r 6091a80df951 test-data/out_test03.txt
--- a/test-data/out_test03.txt Mon Feb 20 09:55:54 2017 -0500
+++ b/test-data/out_test03.txt Fri Jan 19 09:38:17 2018 -0500
[
@@ -1,31 +1,31 @@
 ID Query(Da) Delta Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID
-mz_00001 175.01 0.000125 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB60293
-mz_00001 175.01 0.000676 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB03745
-mz_00001 175.01 0.000895 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB31436
-mz_00001 175.01 0.000914 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB33657
-mz_00001 175.01 0.000914 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB35230
-mz_00002 238.19 0.000875 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04043
-mz_00002 238.19 0.000875 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB36086
-mz_00002 238.19 0.000875 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB04472
-mz_00002 238.19 0.000875 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB05812
-mz_00002 238.19 0.000875 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB35861
-mz_00003 420.16 0.000683 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60836
-mz_00003 420.16 0.000683 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB60838
-mz_00003 420.16 0.001237 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB33374
-mz_00003 420.16 0.001268 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB00590
-mz_00003 420.16 0.001268 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB01138
-mz_00004 780.32 0.001444 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB31947
-mz_00004 780.32 0.005702 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB35940
-mz_00004 780.32 0.007526 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB33906
-mz_00004 780.32 0.007526 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB39032
-mz_00004 780.32 0.007526 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB32731
-mz_00005 956.25 0.005681 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB35451
-mz_00005 956.25 0.005681 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB38095
-mz_00005 956.25 0.008359 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB40803
-mz_00005 956.25 0.008359 [Glycitin] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB02219
-mz_00005 956.25 0.008359 [Calycosin 7-galactoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB38821
-mz_00006 1100.45 0.001166 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB60499
-mz_00006 1100.45 0.004946 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB32198
-mz_00006 1100.45 0.014838 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06568
-mz_00006 1100.45 0.014838 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB02060
-mz_00006 1100.45 0.014838 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB06582
+mz_00001 175.01 1 [Hydroxidodioxidosulfidosulfate] 113.94453531 H2O3S2 [M+IsoProp+H] 175.009875 HMDB0060293
+mz_00001 175.01 4 [Mesna] 141.975835438 C2H6O3S2 [M+CH3OH+H] 175.009324 HMDB0003745
+mz_00001 175.01 5 [Silicic acid] 95.987885149 H4O4Si [M+DMSO+H] 175.009105 HMDB0031436
+mz_00001 175.01 5 [De-O-methylsterigmatocystin] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0033657
+mz_00001 175.01 5 [Aurantricholide B] 310.047738052 C17H10O6 [M+H+K] 175.009086 HMDB0035230
+mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043
+mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086
+mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472
+mz_00002 238.19 4 [Geraniol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0005812
+mz_00002 238.19 4 [trans-(-)-p-Menth-1-en-3-ol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0035861
+mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836
+mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838
+mz_00003 420.16 3 [Benzyl glycinate 4-methylbenzenesulfonate salt] 337.098393413 C16H19NO5S [M+2ACN+H] 420.158763 HMDB0033374
+mz_00003 420.16 3 [Glutarylglycine] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0000590
+mz_00003 420.16 3 [N-Acetylglutamic acid] 189.063722467 C7H11NO5 [2M+ACN+H] 420.161268 HMDB0001138
+mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947
+mz_00004 780.32 7 [Mulberrofuran T] 716.298533006 C44H44O9 [M+ACN+Na] 780.314298 HMDB0035940
+mz_00004 780.32 10 [2'-Hydroxy-3',4',5',7,8-pentamethoxyflavan] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0033906
+mz_00004 780.32 10 [trans-Grandmarin isovalerate] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0039032
+mz_00004 780.32 10 [(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olide] 376.152203122 C20H24O7 [2M+3H2O+2H] 780.327526 HMDB0032731
+mz_00005 956.25 6 [Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranoside] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0035451
+mz_00005 956.25 6 [Petanin] 933.266462874 C43H49O23 [M+Na] 956.255681 HMDB0038095
+mz_00005 956.25 9 [UNKNOWN] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0153300
+mz_00005 956.25 9 [Kaempferide 3-rhamnoside] 446.121296924 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0040803
+mz_00005 956.25 9 [2-(4-hydroxy-3-methoxyphenyl)-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one] 446.121296908 C22H22O10 [2M+ACN+Na] 956.258359 HMDB0141944
+mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499
+mz_00006 1100.45 4 [Cellulose triacetate] 536.210967144 C30H34Cl2N4O [2M+3H2O+2H] 1100.445054 HMDB0032198
+mz_00006 1100.45 13 [Lewis X trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006568
+mz_00006 1100.45 13 [O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-Galactose] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0002060
+mz_00006 1100.45 13 [Lewis a trisaccharide] 529.200669455 C20H35NO15 [2M+ACN+H] 1100.435162 HMDB0006582
b
diff -r 505956db90c5 -r 6091a80df951 wsdl_hmdb.pl
--- a/wsdl_hmdb.pl Mon Feb 20 09:55:54 2017 -0500
+++ b/wsdl_hmdb.pl Fri Jan 19 09:38:17 2018 -0500
[
@@ -214,12 +214,12 @@
 help of wsdl_hmdb
 
 # wsdl_hmdb is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool.
-# Input : formula or list of formula
+# Input : accurate mz or list of accurate masses
 # Author : Franck Giacomoni and Marion Landi
-# Email : fgiacomoni\@clermont.inra.fr
-# Version : 1.4
+# Email : fgiacomoni\@inra.fr
+# Version : 1.5
 # Created : 08/07/2012
-# Updated : 21/01/2016
+# Updated : 19/01/2018
 USAGE :  
  wsdl_hmdb.pl  -mass [one mass or a string list of exact masses] -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] 
 
@@ -268,7 +268,7 @@
 
 =head1 AUTHOR
 
-Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
+Franck Giacomoni E<lt>franck.giacomoni@inra.frE<gt>
 
 =head1 LICENSE
 
@@ -284,4 +284,6 @@
 
 version 1.4 : 21 / 01 / 2016 - a clean version for community
 
+version 1.5 : 19 / 01 / 2018 - modifiy parser to match HMDB V4.0 formats
+
 =cut
\ No newline at end of file