Mercurial > repos > fgiacomoni > hmdb_ms_search
changeset 25:8f7546d0b925 draft
master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author | fgiacomoni |
---|---|
date | Tue, 05 Jul 2022 12:39:15 +0000 (2022-07-05) |
parents | d8e2ede293a6 |
children | 76872ac24fb2 |
files | Dockerfile README.txt lib/hmdb.pm test-data/out_test02.html test-data/out_test02.tabular test-data/out_test02.txt wsdl_hmdb.pl wsdl_hmdb.xml |
diffstat | 8 files changed, 58 insertions(+), 66 deletions(-) [+] |
line wrap: on
line diff
--- a/Dockerfile Thu May 19 14:41:34 2022 +0000 +++ b/Dockerfile Tue Jul 05 12:39:15 2022 +0000 @@ -1,53 +1,39 @@ -# ref install: ubuntu 20.04 -FROM ubuntu:20.04 - -# init var -ARG DEBIAN_FRONTEND=noninteractive +#FROM pfem/perlfull +FROM python:3.8-buster # set author -MAINTAINER Franck Giacomoni <franck.giacomoni.fr> +LABEL maintainer="franck.giacomoni@inrae.fr" -### -### [CONTAINER CORE FUNCTIONS]: -### xxxx -### xxxx -### [NOTES] -### xxxx +ENV PLANEMO_VENV_LOCATION /planemo-venv +ENV CONDA /tmp/conda -ENV PATH /opt/conda/bin:$PATH -RUN apt-get -y update &&\ - apt-get -y install build-essential \ - cpanminus \ - gzip \ - wget \ - bzip2 \ - ca-certificates \ - libglib2.0-0 \ - libxext6 \ - libsm6 \ - libxrender1 \ - libtext-csv-perl \ - libxml-twig-perl \ - libfile-share-perl - -RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \ - /bin/bash ~/anaconda.sh -b -p /opt/conda && \ - rm ~/anaconda.sh && \ - ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \ - echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \ - echo "conda activate base" >> ~/.bashrc - -RUN cpan install ExtUtils::MakeMaker && \ - cpan install File::ShareDir::Install && \ - cpan install Module::Release && \ - cpan install Archive::Zip && \ - apt -y install git &&\ - apt -y install python3 python3-pip && \ - apt -y install virtualenv && \ - pip install "pip>=7" && \ - pip install -U git+git://github.com/galaxyproject/planemo.git && \ +RUN apt-get update &&\ + apt-get upgrade -y &&\ + apt-get install --no-install-recommends --yes build-essential \ + git \ + libgl1-mesa-glx \ + libegl1-mesa \ + libxrandr2 \ + libxss1 \ + libxcursor1 \ + libxcomposite1 \ + libasound2 \ + libxi6 \ + libxtst6 \ + python-virtualenv && \ + pip install virtualenv && \ + python3 -m virtualenv "$PLANEMO_VENV_LOCATION" && \ + . "$PLANEMO_VENV_LOCATION"/bin/activate && \ + pip install --upgrade pip setuptools && \ + pip install planemo numpy && \ + pip install -U planemo && \ + #planemo conda_init --conda_prefix "$CONDA" && \ apt-get autoremove -y && \ apt-get clean && \ - rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - + rm -rf /var/lib/apt/lists/* && \ + rm -rf /tmp/* && \ + rm -rf /var/tmp/* && \ + rm -rf /usr/bin/X11 ; + +CMD [] \ No newline at end of file
--- a/README.txt Thu May 19 14:41:34 2022 +0000 +++ b/README.txt Tue Jul 05 12:39:15 2022 +0000 @@ -1,5 +1,5 @@ ## ****** HMDB environnemnt : ****** ## -# version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team +# version June 2022 M Landi / F Giacomoni - INRAE - METABOHUB - workflow4metabolomics.org core team ## --- PERL compilator / libraries : --- ## $ perl -v
--- a/lib/hmdb.pm Thu May 19 14:41:34 2022 +0000 +++ b/lib/hmdb.pm Tue Jul 05 12:39:15 2022 +0000 @@ -709,10 +709,12 @@ if ($line !~ /query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,"delta\(ppm\),",ccs_value/) { #query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value', - if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/ ) { - #print "$line\n" ; + #if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),(\d*)/ ) { + if ( $line =~ /(\d+\.\d+),(\w+),(.*),(\w+),(\d+\.\d+),([\+|\-|\w|n\/a|\s+]+)\s*,(\+|\-),(\d+\.\d+),(\d+),.*/ ) { # works on NEG AND POS results + print "$line\n" ; #if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a|\s+]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { - my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; + my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9") ; + #my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; }
--- a/test-data/out_test02.html Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.html Tue Jul 05 12:39:15 2022 +0000 @@ -1,1 +1,1 @@ -<?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 (ppm)</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">O-Methylisourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255861" target="_blank" class="btn">HMDB0255861</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Propyl-N-nitrosourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255236" target="_blank" class="btn">HMDB0255236</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476542</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-METHYL-N-FORMYLHYDRAZINE</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255179" target="_blank" class="btn">HMDB0255179</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Asparaginamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248665" target="_blank" class="btn">HMDB0248665</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476542</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N'-Hydroxyethanimidamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243752" target="_blank" class="btn">HMDB0243752</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"Propan-2,2-diyl"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0251402" target="_blank" class="btn">HMDB0251402</a></td><td class="ca">C3H6</td><td class="ca">42.046950193</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">75.080439</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Methylene</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0249629" target="_blank" class="btn">HMDB0249629</a></td><td class="ca">CH2</td><td class="ca">14.015650064</td><td class="ca">M+IsoProp+H</td><td class="ca">+</td><td class="ca">75.08099</td><td class="ca">5</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Cyclopropane</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0250673" target="_blank" class="btn">HMDB0250673</a></td><td class="ca">C3H6</td><td class="ca">42.046950193</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">75.080439</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Pyrophosphate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000250" target="_blank" class="btn">HMDB0000250</a></td><td class="ca">H4O7P2</td><td class="ca">177.943225506</td><td class="ca">M+H+2Na</td><td class="ca">+</td><td class="ca">75.080599</td><td class="ca">0</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Propylene</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0256839" target="_blank" class="btn">HMDB0256839</a></td><td class="ca">C3H6</td><td class="ca">42.046950192</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">75.080439</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >76.03942694</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Glutamic acid diethyl ester</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0252807" target="_blank" class="btn">HMDB0252807</a></td><td class="ca">C9H17NO4</td><td class="ca">203.115758031</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">76.039843</td><td class="ca">5</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Methylcarbonyloxy</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0249651" target="_blank" class="btn">HMDB0249651</a></td><td class="ca">C2H2O2</td><td class="ca">58.005479304</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.039302</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">o-Acetylhydroxylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248304" target="_blank" class="btn">HMDB0248304</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028405</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-Hydroxyacetamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245149" target="_blank" class="btn">HMDB0245149</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028405</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">1-Carboxyethylisoleucine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0242158" target="_blank" class="btn">HMDB0242158</a></td><td class="ca">C9H17NO4</td><td class="ca">203.115758031</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">76.039843</td><td class="ca">5</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >76.07584477</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-(2-Hydroxypropan-2-ylamino)propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257796" target="_blank" class="btn">HMDB0257796</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Aminopropanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248330" target="_blank" class="btn">HMDB0248330</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Methyl vinyl ether</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0254619" target="_blank" class="btn">HMDB0254619</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</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">2-(2-Hydroxypropan-2-ylamino)propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257796" target="_blank" class="btn">HMDB0257796</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Aminopropanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248330" target="_blank" class="btn">HMDB0248330</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Methyl vinyl ether</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0254619" target="_blank" class="btn">HMDB0254619</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © 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> \ No newline at end of file +<?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 (ppm)</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">Beryllium</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0002387" target="_blank" class="btn">HMDB0002387</a></td><td class="ca">Be</td><td class="ca">9.012182135</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">7.02033</td><td class="ca">68</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</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">O-Methylisourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255861" target="_blank" class="btn">HMDB0255861</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-Propyl-N-nitrosourea</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255236" target="_blank" class="btn">HMDB0255236</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476542</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">N-METHYL-N-FORMYLHYDRAZINE</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0255179" target="_blank" class="btn">HMDB0255179</a></td><td class="ca">C2H6N2O</td><td class="ca">74.048012821</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">75.055289</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Asparaginamide</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248665" target="_blank" class="btn">HMDB0248665</a></td><td class="ca">C4H9N3O2</td><td class="ca">131.069476542</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">75.055288</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">o-Acetylhydroxylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248304" target="_blank" class="btn">HMDB0248304</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028405</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">75.054728</td><td class="ca">10</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" >mz_00003</td><td id="3" class="ca" >75.08059797</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">"Propan-2,2-diyl"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0251402" target="_blank" class="btn">HMDB0251402</a></td><td class="ca">C3H6</td><td class="ca">42.046950193</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">75.080439</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Methylene</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0249629" target="_blank" class="btn">HMDB0249629</a></td><td class="ca">CH2</td><td class="ca">14.015650064</td><td class="ca">M+IsoProp+H</td><td class="ca">+</td><td class="ca">75.08099</td><td class="ca">5</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Ethanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000108" target="_blank" class="btn">HMDB0000108</a></td><td class="ca">C2H6O</td><td class="ca">46.041864814</td><td class="ca">2M+H-H2O</td><td class="ca">+</td><td class="ca">75.08053</td><td class="ca">1</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Cyclopropane</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0250673" target="_blank" class="btn">HMDB0250673</a></td><td class="ca">C3H6</td><td class="ca">42.046950193</td><td class="ca">M+CH3OH+H</td><td class="ca">+</td><td class="ca">75.080439</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Pyrophosphate</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0000250" target="_blank" class="btn">HMDB0000250</a></td><td class="ca">H4O7P2</td><td class="ca">177.943225506</td><td class="ca">M+H+2Na</td><td class="ca">+</td><td class="ca">75.080599</td><td class="ca">0</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" >mz_00004</td><td id="4" class="ca" >76.03942694</td><td class="ca" colspan="10"></td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Tri-hydroxymethylaminomethane</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0259134" target="_blank" class="btn">HMDB0259134</a></td><td class="ca">C2H7NO3</td><td class="ca">93.042593089</td><td class="ca">M+H-H2O</td><td class="ca">+</td><td class="ca">76.039893</td><td class="ca">6</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Glutamic acid diethyl ester</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0252807" target="_blank" class="btn">HMDB0252807</a></td><td class="ca">C9H17NO4</td><td class="ca">203.115758031</td><td class="ca">M+2H+Na</td><td class="ca">+</td><td class="ca">76.039843</td><td class="ca">5</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Methylcarbonyloxy</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0249651" target="_blank" class="btn">HMDB0249651</a></td><td class="ca">C2H2O2</td><td class="ca">58.005479304</td><td class="ca">M+NH4</td><td class="ca">+</td><td class="ca">76.039302</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">o-Acetylhydroxylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248304" target="_blank" class="btn">HMDB0248304</a></td><td class="ca">C2H5NO2</td><td class="ca">75.032028405</td><td class="ca">M+H</td><td class="ca">+</td><td class="ca">76.039304</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">"2-Aminoethane-1,1,1-triol"</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0247334" target="_blank" class="btn">HMDB0247334</a></td><td class="ca">C2H7NO3</td><td class="ca">93.042593089</td><td class="ca">M+H-H2O</td><td class="ca">+</td><td class="ca">76.039893</td><td class="ca">6</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody><tbody class="select" id="page-id-2"><tr class="white"><td class="ca" >mz_00005</td><td id="5" class="ca" >76.07584477</td><td class="ca" colspan="10"></td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-(2-Hydroxypropan-2-ylamino)propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257796" target="_blank" class="btn">HMDB0257796</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">2</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Propanediol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0256813" target="_blank" class="btn">HMDB0256813</a></td><td class="ca">C3H8O2</td><td class="ca">76.052429498</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">76.075129</td><td class="ca">9</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">Aminopropanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248330" target="_blank" class="btn">HMDB0248330</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="white"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</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">2-(2-Hydroxypropan-2-ylamino)propan-2-ol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0257796" target="_blank" class="btn">HMDB0257796</a></td><td class="ca">C6H15NO2</td><td class="ca">133.110278727</td><td class="ca">M+H+NH4</td><td class="ca">+</td><td class="ca">76.075689</td><td class="ca">3</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Propanediol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0256813" target="_blank" class="btn">HMDB0256813</a></td><td class="ca">C3H8O2</td><td class="ca">76.052429498</td><td class="ca">M+NH4-H2O</td><td class="ca">+</td><td class="ca">76.075129</td><td class="ca">11</td><td class="ca">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">Aminopropanol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0248330" target="_blank" class="btn">HMDB0248330</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">2-Methoxyethylamine</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0245205" target="_blank" class="btn">HMDB0245205</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">NONEDATA</td><td class="ca">NONEDATA</td></tr><tr class="green"><td class="ca" colspan="2"></td><td class="ca">(E)-1-Propenol</td><td class="ca"><a href="http://www.hmdb.ca/metabolites/HMDB0243637" target="_blank" class="btn">HMDB0243637</a></td><td class="ca">C3H6O</td><td class="ca">58.041864813</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">NONEDATA</td><td class="ca">NONEDATA</td></tr></tbody></table></div><div class="container"><hr><footer><div class="row"> <div class="col-lg-12"><p>Copyright © 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> \ No newline at end of file
--- a/test-data/out_test02.tabular Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.tabular Tue Jul 05 12:39:15 2022 +0000 @@ -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 "2::[O-Methylisourea]::74.048012821::C2H6N2O::[M+H]::HMDB0255861 | 2::[N-Propyl-N-nitrosourea]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0255236 | 2::[N-METHYL-N-FORMYLHYDRAZINE]::74.048012821::C2H6N2O::[M+H]::HMDB0255179 | 2::[Asparaginamide]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0248665 | 2::[N'-Hydroxyethanimidamide]::74.048012821::C2H6N2O::[M+H]::HMDB0243752" -3 75.08059797 1743.94267 "2::[""Propan-2,2-diyl""]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0251402 | 5::[Methylene]::14.015650064::CH2::[M+IsoProp+H]::HMDB0249629 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 2::[Propylene]::42.046950192::C3H6::[M+CH3OH+H]::HMDB0256839" -4 76.03942694 51.23158899 "5::[Glutamic acid diethyl ester]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0252807 | 2::[Methylcarbonyloxy]::58.005479304::C2H2O2::[M+NH4]::HMDB0249651 | 2::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+H]::HMDB0248304 | 2::[2-Hydroxyacetamide]::75.032028405::C2H5NO2::[M+H]::HMDB0245149 | 5::[1-Carboxyethylisoleucine]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0242158" -5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 2::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 2::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 2::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 2::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619" -6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 3::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 3::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 3::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637 | 3::[Methyl vinyl ether]::58.041864813::C3H6O::[M+NH4]::HMDB0254619" +1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 +2 75.05547146 0.658528069 "2::[O-Methylisourea]::74.048012821::C2H6N2O::[M+H]::HMDB0255861 | 2::[N-Propyl-N-nitrosourea]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0255236 | 2::[N-METHYL-N-FORMYLHYDRAZINE]::74.048012821::C2H6N2O::[M+H]::HMDB0255179 | 2::[Asparaginamide]::131.069476542::C4H9N3O2::[M+H+NH4]::HMDB0248665 | 10::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+NH4-H2O]::HMDB0248304" +3 75.08059797 1743.94267 "2::[""Propan-2,2-diyl""]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0251402 | 5::[Methylene]::14.015650064::CH2::[M+IsoProp+H]::HMDB0249629 | 1::[Ethanol]::46.041864814::C2H6O::[2M+H-H2O]::HMDB0000108 | 2::[Cyclopropane]::42.046950193::C3H6::[M+CH3OH+H]::HMDB0250673 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250" +4 76.03942694 51.23158899 "6::[Tri-hydroxymethylaminomethane]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0259134 | 5::[Glutamic acid diethyl ester]::203.115758031::C9H17NO4::[M+2H+Na]::HMDB0252807 | 2::[Methylcarbonyloxy]::58.005479304::C2H2O2::[M+NH4]::HMDB0249651 | 2::[o-Acetylhydroxylamine]::75.032028405::C2H5NO2::[M+H]::HMDB0248304 | 6::[""2-Aminoethane-1,1,1-triol""]::93.042593089::C2H7NO3::[M+H-H2O]::HMDB0247334" +5 76.07584477 50.51249853 "2::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 9::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 2::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 2::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 2::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637" +6 76.07593168 0.149308136 "3::[2-(2-Hydroxypropan-2-ylamino)propan-2-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0257796 | 11::[Propanediol]::76.052429498::C3H8O2::[M+NH4-H2O]::HMDB0256813 | 3::[Aminopropanol]::75.068413914::C3H9NO::[M+H]::HMDB0248330 | 3::[2-Methoxyethylamine]::75.068413914::C3H9NO::[M+H]::HMDB0245205 | 3::[(E)-1-Propenol]::58.041864813::C3H6O::[M+NH4]::HMDB0243637"
--- a/test-data/out_test02.txt Thu May 19 14:41:34 2022 +0000 +++ b/test-data/out_test02.txt Tue Jul 05 12:39:15 2022 +0000 @@ -1,27 +1,27 @@ ID Query(Da) Delta(ppm) 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_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 mz_00002 75.05547146 2 [O-Methylisourea] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255861 mz_00002 75.05547146 2 [N-Propyl-N-nitrosourea] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0255236 mz_00002 75.05547146 2 [N-METHYL-N-FORMYLHYDRAZINE] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0255179 mz_00002 75.05547146 2 [Asparaginamide] 131.069476542 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0248665 -mz_00002 75.05547146 2 [N'-Hydroxyethanimidamide] 74.048012821 C2H6N2O [M+H] 75.055289 HMDB0243752 +mz_00002 75.05547146 10 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+NH4-H2O] 75.054728 HMDB0248304 mz_00003 75.08059797 2 ["Propan-2,2-diyl"] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0251402 mz_00003 75.08059797 5 [Methylene] 14.015650064 CH2 [M+IsoProp+H] 75.08099 HMDB0249629 +mz_00003 75.08059797 1 [Ethanol] 46.041864814 C2H6O [2M+H-H2O] 75.08053 HMDB0000108 mz_00003 75.08059797 2 [Cyclopropane] 42.046950193 C3H6 [M+CH3OH+H] 75.080439 HMDB0250673 mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250 -mz_00003 75.08059797 2 [Propylene] 42.046950192 C3H6 [M+CH3OH+H] 75.080439 HMDB0256839 +mz_00004 76.03942694 6 [Tri-hydroxymethylaminomethane] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0259134 mz_00004 76.03942694 5 [Glutamic acid diethyl ester] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0252807 mz_00004 76.03942694 2 [Methylcarbonyloxy] 58.005479304 C2H2O2 [M+NH4] 76.039302 HMDB0249651 mz_00004 76.03942694 2 [o-Acetylhydroxylamine] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0248304 -mz_00004 76.03942694 2 [2-Hydroxyacetamide] 75.032028405 C2H5NO2 [M+H] 76.039304 HMDB0245149 -mz_00004 76.03942694 5 [1-Carboxyethylisoleucine] 203.115758031 C9H17NO4 [M+2H+Na] 76.039843 HMDB0242158 +mz_00004 76.03942694 6 ["2-Aminoethane-1,1,1-triol"] 93.042593089 C2H7NO3 [M+H-H2O] 76.039893 HMDB0247334 mz_00005 76.07584477 2 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796 +mz_00005 76.07584477 9 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813 mz_00005 76.07584477 2 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330 mz_00005 76.07584477 2 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205 mz_00005 76.07584477 2 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637 -mz_00005 76.07584477 2 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619 mz_00006 76.07593168 3 [2-(2-Hydroxypropan-2-ylamino)propan-2-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0257796 +mz_00006 76.07593168 11 [Propanediol] 76.052429498 C3H8O2 [M+NH4-H2O] 76.075129 HMDB0256813 mz_00006 76.07593168 3 [Aminopropanol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0248330 mz_00006 76.07593168 3 [2-Methoxyethylamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0245205 mz_00006 76.07593168 3 [(E)-1-Propenol] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0243637 -mz_00006 76.07593168 3 [Methyl vinyl ether] 58.041864813 C3H6O [M+NH4] 76.075688 HMDB0254619
--- a/wsdl_hmdb.pl Thu May 19 14:41:34 2022 +0000 +++ b/wsdl_hmdb.pl Tue Jul 05 12:39:15 2022 +0000 @@ -162,6 +162,8 @@ ## Cutof will be done in next method after URI check ($result) = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, 1000) ; ## hash format result +# print Dumper $result ; + ## This previous step return results with cutoff on the number of entries returned ! ## clean/max result by testing each HMDB_ID page in HMDB @@ -275,7 +277,7 @@ # Email : fgiacomoni\@inra.fr # Version : 1.6 # Created : 08/07/2012 -# Updated : 23/01/2019 - 1.6 +# Updated : 22/06/2022 - 1.7.2 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] @@ -349,4 +351,6 @@ version 1.7.0 : 19/ 05 / 2022 - Update HMDB API client - compliant with HMDB 5.0 web portal +version 1.7.2 : 22/ 06 / 2022 - Fix issue with neg result parsing + =cut \ No newline at end of file
--- a/wsdl_hmdb.xml Thu May 19 14:41:34 2022 +0000 +++ b/wsdl_hmdb.xml Tue Jul 05 12:39:15 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.1"> +<tool id="wsdl_hmdb" name="HMDB MS search" version="1.7.2"> <description> search by masses on HMDB v5 online LCMS bank </description>