# HG changeset patch # User fgiacomoni # Date 1479911510 18000 # Node ID 6d0a0f8f672a6b737b676f241dc2b55df0df1fcb # Parent 9583f97721988ff4fa95cdc762e4eeda6b31cd46 planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 diff -r 9583f9772198 -r 6d0a0f8f672a README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,52 @@ +HMDB MS search - search by masses on HMDB online bank +===================================================== + +[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io) [![Build Status](https://travis-ci.org/workflow4metabolomics/tool-bank-golm-lib_search.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/tool-bank-golm-lib_search) + +Our project +----------- +The [Workflow4Metabolomics](http://workflow4metabolomics.org), W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform. + + +HMDB MS search - search by masses on HMDB online bank +----------------------------------------------------- + +Tool using the HMDB Library Search. + + +Galaxy +------ +Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + +Homepage: [https://galaxyproject.org/](https://galaxyproject.org/) + + +Dependencies using Conda +------------------------ +[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io) + + +[Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages. + +``` +#To install miniconda2 +#http://conda.pydata.org/miniconda.html +#To install the tool dependencies using conda: +conda install perl-lwp-simple perl-lwp-useragent perl-uri-url perl-soap-lite perl-list-moreutils perl-text-csv perl perl-html-template +#To set an environment: +conda create -n tool-bank-hmdb perl-soap-lite perl-list-moreutils perl-json perl-html-template` +#To activate the environment: +. activate tool-bank-hmdb +``` + + +Travis +------ +[![Build Status](https://travis-ci.org/workflow4metabolomics/tool-bank-golm-lib_search.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/tool-bank-golm-lib_search) + +Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes! + +Historic contributors +--------------------- +- Franck Giacomoni @fgiacomoni - [French Metabolomics and Fluxomics Infrastructure (MetaboHUB)](http://www.metabohub.fr/en) - [La plateforme "Exploration du Métabolisme" (PFEM, Clermont-Ferrand)](http://www6.clermont.inra.fr/plateforme_exploration_metabolisme) +- Marion Landi - [LIFEGRID grant](http://www.lifegrid.fr/fr/home/le-pra-lifegrid.html) - [La plateforme "Exploration du Métabolisme" (PFEM, Clermont-Ferrand)](http://www6.clermont.inra.fr/plateforme_exploration_metabolisme) diff -r 9583f9772198 -r 6d0a0f8f672a README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,68 @@ +## ****** HMDB environnemnt : ****** ## +# version Nov 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team + +## --- PERL compilator / libraries : --- ## +$ perl -v +This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi + +# libs CORE PERL : +use strict ; +use warnings ; +use Carp qw (cluck croak carp) ; +use Exporter ; +use Data::Dumper ; +use Getopt::Long ; +use FindBin ; +use Encode; + +# libs CPAN PERL : +$ perl -e 'use Text::CSV' - OK +use LWP::Simple; - OK +use LWP::UserAgent; - OK +use URI::URL; - OK +use SOAP::Lite; - OK +use HTML::Template ; - OK +use XML::Twig ; - OK + +$ sudo perl -MCPAN -e shell +cpan> install Text::CSV + +# libs pfem PERL : this lib were included in lib dir. +use conf::conf qw( :ALL ) ; +use formats::csv qw( :ALL ) ; +-- + +## --- Conda compliant --- ## +This tool and its PERL dependencies are "Conda compliant". +The requirements section in the Xml file is still commented, waiting for "Conda" deployment improvement in Galaxy project. + +## --- R bin and Packages : --- ## +No interaction with R +-- + +## --- Binary dependencies --- ## +No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?) +-- + +## --- Config : --- ## +JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed + + +PS :If Galaxy can't find the file "hmdb.tmpl", perform this command line : perl -pi -e 's/\r//g' conf_hmdb.cfg +-- + +## --- XML HELP PART --- ## +one image : +hmdb.png +-- + +## --- DATASETS OR TUTORIAL --- ## +Please find help on W4M: http://workflow4metabolomics.org/howto +-- + +## --- ??? COMMENTS ??? --- ## +If Galaxy can't find the file "hmdb.tmpl", perform this command line : " perl -pi -e 's/\r//g' " on the conf file "conf_hmdb.cfg". + +To use fully functionalities of HTML output format file : + - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE. +-- \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a conf_hmdb.cfg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conf_hmdb.cfg Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,17 @@ +## Conf file for wsdl_hmdb.pl script +# +## Version -- edited by F.Giacomoni +VERSION=2016-11-28 +# +## ARGVT +# Hmdb limits per job (max is 149) +HMDB_LIMITS=50 +## Maximum query filtered (default is 20 - min : 1 / max 50) +HMDB_MAX_QUERY=20 +## Galaxy url for HTML JS and CSS path +JS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts +CSS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style +# +## HTML OUTPUT : +HTML_ENTRIES_PER_PAGE=4 +HMDB_METABOCARD_URL=http://www.hmdb.ca/metabolites/ diff -r 9583f9772198 -r 6d0a0f8f672a hmdb.tmpl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hmdb.tmpl Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,1 @@ +Galaxy HMDB queries - All results
Results of HMDB queries -

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/README.txt --- a/hmdb/README.txt Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -## ****** HMDB environnemnt : ****** ## -# version January 2016 M Landi / F Giacomoni - INRA - METABOHUB - workflow4metabolomics.org core team - -## --- PERL compilator / libraries : --- ## -$ perl -v -This is perl, v5.10.1 (*) built for x86_64-linux-thread-multi - -# libs CORE PERL : -use strict ; -use warnings ; -use Carp qw (cluck croak carp) ; -use Exporter ; -use Data::Dumper ; -use Getopt::Long ; -use FindBin ; -use Encode; - -# libs CPAN PERL : -$ perl -e 'use Text::CSV' -$ perl -e 'use LWP::Simple' -$ perl -e 'use URI::URL' -$ perl -e 'use SOAP::Lite' -$ perl -e 'use HTML::Template' -$ sudo perl -MCPAN -e shell -cpan> install Text::CSV -cpan> install LWP::Simple -cpan> install URI::URL -cpan> install SOAP::Lite -cpan> install HTML::Template - -# libs pfem PERL : this lib were included in lib dir. -use conf::conf qw( :ALL ) ; -use formats::csv qw( :ALL ) ; --- - -## --- R bin and Packages : --- ## -No interaction with R --- - -## --- Binary dependencies --- ## -No interaction with binary - use only HMDB post method (http://www.hmdb.ca/spectra/ms/search?) --- - -## --- Config : --- ## -JS and CSS (used in HTML output format) are now hosted on cdn.rawgit.com server - no local config needed - - -PS :If Galaxy can't find the file "hmdb.tmpl", perform this command line : perl -pi -e 's/\r//g' conf_hmdb.cfg --- - -## --- XML HELP PART --- ## -one image : -hmdb.png --- - -## --- DATASETS OR TUTORIAL --- ## -Please find help on W4M : --- - -## --- ??? COMMENTS ??? --- ## -If Galaxy can't find the file "hmdb.tmpl", perform this command line : " perl -pi -e 's/\r//g' " on the conf file "conf_hmdb.cfg". - -To use fully functionalities of HTML output format file : - - check that sanitize_all_html option in universe_wsgi.ini file is uncomment and set to FALSE. --- \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/conf_hmdb.cfg --- a/hmdb/conf_hmdb.cfg Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -## Conf file for wsdl_hmdb.pl script -# -## Version -- edited by F.Giacomoni -VERSION=2015-06-08 -# -## ARGVT -# Hmdb limits per job (max is 149) -HMDB_LIMITS=50 -## Galaxy url for HTML JS and CSS path -JS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/scripts -CSS_GALAXY_PATH=https://cdn.rawgit.com/fgiacomoni/galaxy_utils/master/style -# -## HTML OUTPUT : -HTML_ENTRIES_PER_PAGE=4 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/hmdb.tmpl --- a/hmdb/hmdb.tmpl Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Galaxy HMDB queries - All results
Results of HMDB queries -

ID from inputMass (m/z)Compound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)Delta
\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/lib/conf.pm --- a/hmdb/lib/conf.pm Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,259 +0,0 @@ -package lib::conf ; - -use strict; -use warnings ; -use Exporter ; -use Carp ; -use Data::Dumper ; - -use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); - -our $VERSION = "1.0" ; -our @ISA = qw(Exporter) ; -our @EXPORT = qw( as_conf get_value_from_conf check_path_and_file ) ; -our %EXPORT_TAGS = ( ALL => [qw( as_conf get_value_from_conf )] ) ; - -=head1 NAME - -conf - A module for manage pfem conf file - -=head1 SYNOPSIS - - use conf ; - my $object = conf->new() ; - -=head1 DESCRIPTION - -This module does manage conf file (extract all or selected fields) - -=head1 METHODS - -Methods are : - -=head2 METHOD new - - ## Description : new - ## Input : $self - ## Ouput : bless $self ; - ## Usage : new() ; - -=cut -## START of SUB -sub new { - ## Variables - my $self={}; - bless($self) ; - return $self ; -} -### END of SUB - -=head2 METHOD as_conf - - ## Description : permet de cr�er l'object conf � partir d'un fichier de conf de type KEY=VALUE - ## Input : $file - ## Ouput : $oConf (a hash) - ## Usage : my ( $oConf ) = as_conf( $file ) ; - -=cut -## START of SUB -sub as_conf { - ## Retrieve Values - my $self = shift ; - my ( $file, $separator ) = @_ ; - -# if (!defined $separator) { $separator = ';' } ## set separator to ; - - if ( !defined $file ) { croak "Can't create object with an none defined file\n" ; } - - my %Conf = () ; ## Hash devant contenir l'ensemble des parametres locaux - - if (-e $file) { - open (CFG, "<$file") or die "Can't open $file\n" ; - while () { - chomp $_ ; - if ( $_ =~ /^#(.*)/) { next ; } - elsif ($_ =~/^(\w+?)=(.*)/) { ## ALPHANUMERIC OR UNDERSCORE ONLY FOR THE KEY AND ANYTHING ELSE FOR VALUE - - my ($key, $value) = ($1, $2) ; - - if (defined $separator) { - if ( $value=~/$separator/ ) { ## is a list to split - my @tmp = split(/$separator/ , $value) ; - $Conf{$key} = \@tmp ; - } - } - else { - $Conf{$key} = $value ; - } - } - } - close(CFG) ; - } - else { - croak "Can't create object with an none existing file\n" ; - } - - return ( \%Conf ) ; -} -## END of SUB - -=head2 METHOD as_conf_list - - ## Description : permet de charger une liste txt en array - ## Input : $file - ## Output : elements - ## Usage : my ( elements ) = as_conf_list( $conf_file ) ; - -=cut -## START of SUB -sub as_conf_list { - ## Retrieve Values - my $self = shift ; - my ( $file ) = @_ ; - - my @elements = () ; - if ( !defined $file ) { croak "Can't create object with an none defined file\n" ; } - - if (-e $file) { - open (CFG, "<$file") or die "Can't open $file\n" ; - while () { - chomp $_ ; - if ( $_ =~ /^#(.*)/) { next ; } - elsif ($_ =~/^(.*)/) { if (defined $1) { push (@elements, $1) ; } } - } - } - else { - croak "Can't create object with an none existing file\n" ; - } - return(\@elements) ; -} -## END of SUB - -=head2 METHOD get_value_from_conf - - ## Description : permet de retourner une valeur du hash de conf � partir d'une key - ## Input : $oConf, $Key - ## Ouput : $Value - ## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ; - -=cut -## START of SUB -sub get_value_from_conf { - ## Retrieve Values - my $self = shift ; - my ( $oConf, $Key ) = @_ ; - - my $Value = undef ; - - if ( defined $oConf ) { - if ( defined $oConf->{$Key} ) { - $Value = $oConf->{$Key} ; - } - } - else { - croak "Can't manage value with undefined object\n" ; - } - return($Value) ; -} -## END of SUB - -=head2 METHOD get_value_from_conf - - ## Description : permet de retourner une valeur du hash de conf � partir d'une key - ## Input : $oConf, $Key - ## Ouput : $Value - ## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ; - -=cut -## START of SUB -sub split_value_from_conf { - ## Retrieve Values - my $self = shift ; - my ( $oConf, $Key, $sep ) = @_ ; - - my $value = undef ; - my @values = () ; - - if ( defined $oConf ) { - if ( defined $oConf->{$Key} ) { - $value = $oConf->{$Key} ; - @values = split ( /$sep/, $value) ; - } - } - else { - croak "Can't manage value with undefined object\n" ; - } - return(\@values) ; -} -## END of SUB - - -=head2 METHOD check_path_and_file - - ## Description : permet de v�rifier les path et la pr�sence des exe d�crits dans le file conf. Bloque le script en cas de probleme - ## Input : $oConfs - ## Ouput : NA - ## Usage : &get_value_from_conf( $oConf ) ; - -=cut -## START of SUB -sub check_path_and_file { - - my $self = shift ; - my ( $oConfs ) = @_ ; - - foreach my $conf ( keys %{ $oConfs } ) { - if ( $conf =~ /^FILE/ ) { - if ( -e $oConfs->{$conf} ) { - if ( -s $oConfs->{$conf} ) { next ; } - else { carp "[Warning] : The size of file $oConfs->{$conf} is null\n" ; } - } - else { - carp "[Warning] : The file $oConfs->{$conf} doesn't exist\n" ; - } - } - elsif ( $conf =~ /^PATH/ ) { - if ( -d $oConfs->{$conf} ) { next ; } - else { carp "[Warning] : The dir $oConfs->{$conf} doesn't exist\n" ; } - } - else { next ; } - } - return ; -} -## END of SUB - -1 ; - - -__END__ - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc conf.pm - - -=head1 Exports - -=over 4 - -=item :ALL is as_conf get_value_from_conf - -=back - -=head1 AUTHOR - -Franck Giacomoni Efranck.giacomoni@clermont.inra.frE - -=head1 LICENSE - -This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. - -=head1 VERSION - -version 1 : 10 / 02 / 2013 - -version 2 : ?? - -=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/lib/csv.pm --- a/hmdb/lib/csv.pm Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,239 +0,0 @@ -package lib::csv ; - -use strict; -use warnings ; -use Exporter ; -use Carp ; - -use Text::CSV ; - -use Data::Dumper ; - -use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); - -our $VERSION = "1.0"; -our @ISA = qw(Exporter); -our @EXPORT = qw( get_csv_object get_value_from_csv_multi_header ); -our %EXPORT_TAGS = ( ALL => [qw( get_csv_object get_value_from_csv_multi_header )] ); - -=head1 NAME - -My::Module - An example module - -=head1 SYNOPSIS - - use My::Module; - my $object = My::Module->new(); - print $object->as_string; - -=head1 DESCRIPTION - -This module does not really exist, it -was made for the sole purpose of -demonstrating how POD works. - -=head1 METHODS - -Methods are : - -=head2 METHOD new - - ## Description : new - ## Input : $self - ## Ouput : bless $self ; - ## Usage : new() ; - -=cut - -sub new { - ## Variables - my $self={}; - bless($self) ; - return $self ; -} -### END of SUB - -=head2 METHOD get_csv_object - - ## Description : builds a csv object and etablishes format - ## Input : $separator - ## Output : $csv - ## Usage : my ( $csv ) = get_csv_object( $separator ) ; - -=cut -## START of SUB -sub get_csv_object { - ## Retrieve Values - my $self = shift ; - my ( $separator ) = @_ ; - -# my $csv = Text::CSV->new({'sep_char' => "$separator"}); - my $csv = Text::CSV->new ( {'sep_char' => "$separator", binary => 1 } ) # should set binary attribute. - or die "Cannot use CSV: ".Text::CSV->error_diag (); - - return($csv) ; -} -## END of SUB - -=head2 METHOD get_value_from_csv_multi_header - - ## Description : extract a targeted column in a csv file - ## Input : $csv, $file, $column, $is_header, $nb_header - ## Output : $value - ## Usage : my ( $value ) = get_value_from_csv_multi_header( $csv, $file, $column, $is_header, $nb_header ) ; - -=cut -## START of SUB -sub get_value_from_csv_multi_header { - ## Retrieve Values - my $self = shift ; - my ( $csv, $file, $column, $is_header, $nb_header ) = @_ ; - - my @value = () ; - - ## Adapte the number of the colunm : (nb of column to position in array) - $column = $column - 1 ; - - open (CSV, "<", $file) or die $! ; - - my $line = 0 ; - - while () { - $line++ ; - chomp $_ ; - # file has a header - if ( defined $is_header and $is_header eq 'yes') { if ($line <= $nb_header) { next ; } } - # parsing the targeted column - if ( $csv->parse($_) ) { - my @columns = $csv->fields(); - push ( @value, $columns[$column] ) ; - } - else { - my $err = $csv->error_input; - die "Failed to parse line: $err"; - } - } - close CSV; - return(\@value) ; -} -## END of SUB - -=head2 METHOD parse_csv_object - - ## Description : parse_all csv object and return a array of rows - ## Input : $csv, $file - ## Output : $csv_matrix - ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file ) ; - -=cut -## START of SUB -sub parse_csv_object { - ## Retrieve Values - my $self = shift ; - my ( $csv, $file ) = @_ ; - - my @csv_matrix = () ; - - open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; - - while ( my $row = $csv->getline( $fh ) ) { - push @csv_matrix, $row; - } - $csv->eof or $csv->error_diag(); - close $fh; - - return(\@csv_matrix) ; -} -## END of SUB - -=head2 METHOD parse_allcsv_object - - ## Description : parse_all csv object and return a array of rows with or without header - ## Input : $csv, $file, $keep_header - ## Output : $csv_matrix - ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file, $keep_header ) ; - -=cut -## START of SUB -sub parse_allcsv_object { - ## Retrieve Values - my $self = shift ; - my ( $csv, $file, $keep_header ) = @_ ; - - my @csv_matrix = () ; - my $line = 1 ; - - open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; - - while ( my $row = $csv->getline( $fh ) ) { - if ( ( $keep_header eq 'n' ) and ($line == 1) ) { } - else { push @csv_matrix, $row; } - $line ++ ; - } - my $status = $csv->eof or $csv->error_diag(); - close $fh; - - return(\@csv_matrix, $status) ; -} -## END of SUB - - -=head2 METHOD write_csv_from_arrays - - ## Description : write a csv file from list of rows - ## Input : $csv, $file_name, $rows - ## Output : $csv_file - ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $rows ) ; - -=cut -## START of SUB -sub write_csv_from_arrays { - ## Retrieve Values - my $self = shift ; - my ( $csv, $file_name, $rows ) = @_ ; - - my $fh = undef ; - $csv->eol ("\n"); ## end-of-line string to add to rows - open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!"; - - my $status = $csv->print ($fh, $_) for @{$rows}; - close $fh or die "$file_name: $!"; - - return(\$file_name) ; -} -## END of SUB - -1 ; - - -__END__ - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc csv.pm - -=head1 Exports - -=over 4 - -=item :ALL is get_csv_object, get_value_from_csv_multi_header - -=back - -=head1 AUTHOR - -Franck Giacomoni Efranck.giacomoni@clermont.inra.frE - -=head1 LICENSE - -This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. - -=head1 VERSION - -version 1 : 23 / 10 / 2013 - -version 2 : ?? - -=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/lib/hmdb.pm --- a/hmdb/lib/hmdb.pm Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,889 +0,0 @@ -package lib::hmdb ; - -use strict; -use warnings ; -use Exporter ; -use Carp ; - -use LWP::Simple; -use LWP::UserAgent; -use URI::URL; -use SOAP::Lite; -use Encode; -use HTML::Template ; - -use Data::Dumper ; - -use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); - -our $VERSION = "1.0"; -our @ISA = qw(Exporter); -our @EXPORT = qw( extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass ); -our %EXPORT_TAGS = ( ALL => [qw( extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] ); - -=head1 NAME - -My::Module - An example module - -=head1 SYNOPSIS - - use My::Module; - my $object = My::Module->new(); - print $object->as_string; - -=head1 DESCRIPTION - -This module does not really exist, it -was made for the sole purpose of -demonstrating how POD works. - -=head1 METHODS - -Methods are : - -=head2 METHOD new - - ## Description : new - ## Input : $self - ## Ouput : bless $self ; - ## Usage : new() ; - -=cut - -sub new { - ## Variables - my $self={}; - bless($self) ; - return $self ; -} -### END of SUB - - -=head2 METHOD extract_sub_mz_lists - - ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS) - ## Input : $HMDB_LIMITS, $masses - ## Output : $sublists - ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ; - -=cut -## START of SUB -sub extract_sub_mz_lists { - ## Retrieve Values - my $self = shift ; - my ( $masses, $HMDB_LIMITS ) = @_ ; - - my ( @sublists, @sublist ) = ( (), () ) ; - my $nb_mz = 0 ; - my $nb_total_mzs = scalar(@{$masses}) ; - - if ($nb_total_mzs == 0) { - die "The provided mzs list is empty" ; - } - - for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) { - - if ( $nb_mz < $HMDB_LIMITS ) { - if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list - } - elsif ( $nb_mz == $HMDB_LIMITS ) { - my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ; - $current_pos-- ; - } - if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; } - } - return(\@sublists) ; -} -## END of SUB - -=head2 METHOD prepare_multi_masses_query - - ## Description : Generate the adapted format of the mz list for HMDB - ## Input : $masses - ## Output : $hmdb_masses - ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ; - -=cut -## START of SUB -sub prepare_multi_masses_query { - ## Retrieve Values - my $self = shift ; - my ( $masses ) = @_ ; - - my $hmdb_masses = undef ; - my $sep = '%0D%0A' ; ## retour chariot encode - my ($nb_masses, $i) = (0, 0) ; - - if ( defined $masses ) { - my @masses = @{$masses} ; - my $nb_masses = scalar ( @masses ) ; - if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; } - elsif ( $nb_masses >= 150 ) { croak "Your mass list is too long : HMDB allows maximum 150 query masses per request \n" ; } ## Del it --- temporary patch - - foreach my $mass (@masses) { - - if ($i < $nb_masses) { - $hmdb_masses .= $mass.$sep ; - } - elsif ( $i == $nb_masses ) { - $hmdb_masses .= $mass ; - } - else { - last ; - } - $i ++ ; - } - } - else { - croak "No mass list found \n" ; - } - return($hmdb_masses, $nb_masses) ; -} -## END of SUB - -=head2 METHOD test_matches_from_hmdb_ua - - ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra. - ## Input : none - ## Output : $status_line - ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ; - -=cut -## START of SUB -sub test_matches_from_hmdb_ua { - ## Retrieve Values - my $self = shift ; - - my @page = () ; - - my $ua = new LWP::UserAgent; - $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); - - my $req = HTTP::Request->new( - POST => 'http://specdb.wishartlab.com/ms/search.csv'); - - $req->content_type('application/x-www-form-urlencoded'); - $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV'); - - my $res = $ua->request($req); -# print $res->as_string; - my $status_line = $res->status_line ; - ($status_line) = ($status_line =~ /(\d+)/); - - - return (\$status_line) ; -} -## END of SUB - -=head2 METHOD check_state_from_hmdb_ua - - ## Description : check the thhp status of hmdb and kill correctly the script if necessary. - ## Input : $status - ## Output : none - ## Usage : check_state_from_hmdb_ua($status) ; - -=cut -## START of SUB -sub check_state_from_hmdb_ua { - ## Retrieve Values - my $self = shift ; - my ($status) = @_ ; - - if (!defined $$status) { - croak "No http status is defined for the distant server" ; - } - else { - unless ( $$status == 200 ) { - if ( $$status == 504 ) { croak "Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server" ; } - else { - ## None supported http code error ## - } - } - } - - return (1) ; -} -## END of SUB - -=head2 METHOD get_matches_from_hmdb_ua - - ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg) - ## Input : $mass, $delta, $mode - ## Output : $results - ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ; - -=cut -## START of SUB -sub get_matches_from_hmdb_ua { - ## Retrieve Values - my $self = shift ; - my ( $masses, $delta, $mode ) = @_ ; - - my @page = () ; - - my $ua = new LWP::UserAgent; - $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); - - my $req = HTTP::Request->new( - POST => 'http://specdb.wishartlab.com/ms/search.csv'); - - $req->content_type('application/x-www-form-urlencoded'); - $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV'); - - my $res = $ua->request($req); -# print $res->as_string; - if ($res->is_success) { - @page = split ( /\n/, $res->decoded_content ) ; - } else { - my $status_line = $res->status_line ; - ($status_line) = ($status_line =~ /(\d+)/); - croak "HMDB service none available !! Status of the HMDB server is : $status_line\n" ; - } - - - return (\@page) ; -} -## END of SUB - -=head2 METHOD parse_hmdb_csv_results - - ## Description : parse the csv results and get data - ## Input : $csv - ## Output : $results - ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ; - -=cut -## START of SUB -sub parse_hmdb_csv_results { - ## Retrieve Values - my $self = shift ; - my ( $csv, $masses ) = @_ ; - - my $test = 0 ; - my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ; - - my %result_by_entry = () ; - my %features = () ; - -# 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]} = [] ; } - - $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) ; - } - else { - next ; - } - } ## end foreach - - ## manage per query_mzs (keep query masses order by array) - my @results = () ; - foreach (@{$masses}) { - if ($result_by_entry{$_}) { push (@results, $result_by_entry{$_}) ; } - else {push (@results, [] ) ;} ; - } - return(\@results) ; -} -## END of SUB - -=head2 METHOD parse_hmdb_page_results - - ## Description : [DEPRECATED] old HMDB html page parser - ## Input : $page - ## Output : $results - ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ; - -=cut -## START of SUB -sub parse_hmdb_page_results { - ## Retrieve Values - my $self = shift ; - my ( $page ) = @_ ; - - my @results = () ; - my ($catch_table, $catch_name) = (0, 0) ; - my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ; - - if ( defined $page ) { - - my @page = @{$page} ; - my $ID = undef ; - my @result_by_mz = () ; - my %result_by_entry = () ; - - foreach my $line (@page) { - - #Section de la page contenant les resultat - if( $line =~// ) { $catch_table = 1 ; } - - ## Si il existe un resultat : - if($catch_table == 1) { - - #Id de la molecule, et creation du lien - if( $line =~ // ) { - $ID = $1 ; - $catch_name = 0 ; - next ; - } - #Nom de la molecule ONLY!! - if ( $catch_name == 0 ) { - - if( $line =~ /
(.+)<\/td>/ ) { - - if ( !defined $name ) { - $name = $1 ; - $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ; - $result_by_entry{'ENTRY_NAME'} = $name ; - next ; - } - if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; } - if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; } - if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; } - if ( !defined $delta ) { - $delta = $1 ; - $result_by_entry{'ENTRY_DELTA'} = $delta ; - $catch_name = 1 ; - my %tmp = %result_by_entry ; - push (@result_by_mz, \%tmp) ; - %result_by_entry = () ; - ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ; - next ; - } - } - } - } - #Fin de la section contenant les resultats - if( $line =~ /<\/table>/ ) { - $catch_table = 0 ; - my @Tmp = @result_by_mz ; - push(@results, \@Tmp) ; - @result_by_mz = () ; - } - } - } - return(\@results) ; -} -## END of SUB - -=head2 METHOD set_html_tbody_object - - ## Description : initializes and build the tbody object (perl array) needed to html template - ## Input : $nb_pages, $nb_items_per_page - ## Output : $tbody_object - ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ; - -=cut -## START of SUB -sub set_html_tbody_object { - my $self = shift ; - my ( $nb_pages, $nb_items_per_page ) = @_ ; - - my ( @tbody_object ) = ( ) ; - - for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) { - - my %pages = ( - # tbody feature - PAGE_NB => $i, - MASSES => [], ## end MASSES - ) ; ## end TBODY N - push (@tbody_object, \%pages) ; - } - return(\@tbody_object) ; -} -## END of SUB - -=head2 METHOD add_mz_to_tbody_object - - ## Description : initializes and build the mz object (perl array) needed to html template - ## Input : $tbody_object, $nb_items_per_page, $mz_list - ## Output : $tbody_object - ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ; - -=cut -## START of SUB -sub add_mz_to_tbody_object { - my $self = shift ; - my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ; - - my ( $current_page, $mz_index ) = ( 0, 0 ) ; - - foreach my $page ( @{$tbody_object} ) { - - my @colors = ('white', 'green') ; - my ( $current_index, , $icolor ) = ( 0, 0 ) ; - - for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) { - # - if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page - $current_index = 0 ; - last ; ## - } - else { - $current_index++ ; - if ( $icolor > 1 ) { $icolor = 0 ; } - - if ( exists $mz_list->[$mz_index] ) { - - my %mz = ( - # mass feature - MASSES_ID_QUERY => $ids_list->[$mz_index], - MASSES_MZ_QUERY => $mz_list->[$mz_index], - MZ_COLOR => $colors[$icolor], - MASSES_NB => $mz_index+1, - ENTRIES => [] , - ) ; - push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ; - # Html attr for mass - $icolor++ ; - } - } - $mz_index++ ; - } ## foreach mz - - $current_page++ ; - } - return($tbody_object) ; -} -## END of SUB - -=head2 METHOD add_entries_to_tbody_object - - ## Description : initializes and build the entries object (perl array) needed to html template - ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries - ## Output : $tbody_object - ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ; - -=cut -## START of SUB -sub add_entries_to_tbody_object { - ## Retrieve Values - my $self = shift ; - my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ; - - my $index_page = 0 ; - my $index_mz_continous = 0 ; - - foreach my $page (@{$tbody_object}) { - - my $index_mz = 0 ; - - foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) { - - my $index_entry = 0 ; - - my @anti_redondant = ('N/A') ; - my $check_rebond = 0 ; - my $check_noentry = 0 ; - - foreach my $entry (@{ $entries->[$index_mz_continous] }) { - $check_noentry ++ ; - ## dispo anti doublons des entries - foreach my $rebond (@anti_redondant) { - if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } - } - - if ( $check_rebond == 0 ) { - - push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ; - - my %entry = ( - ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR}, - ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID}, - ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID}, - ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA}, - ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ}, - ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT}, - ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE}, - ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ}, - ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA}, - ) ; - - push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ; - } - $check_rebond = 0 ; ## reinit double control - $index_entry++ ; - } ## end foreach - if ($check_noentry == 0 ) { - my %entry = ( - ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR}, - ENTRY_ENTRY_ID => 'No_result_found_on_HMDB', - ENTRY_ENTRY_ID2 => '', - ENTRY_FORMULA => 'n/a', - ENTRY_CPD_MZ => 'n/a', - ENTRY_ADDUCT => 'n/a', - ENTRY_ADDUCT_TYPE => 'n/a', - ENTRY_ADDUCT_MZ => 'n/a', - ENTRY_DELTA => 0, - ) ; - push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ; - } - $index_mz ++ ; - $index_mz_continous ++ ; - } - $index_page++ ; - } - return($tbody_object) ; -} -## END of SUB - -=head2 METHOD write_html_skel - - ## Description : prepare and write the html output file - ## Input : $html_file_name, $html_object, $html_template - ## Output : $html_file_name - ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ; - -=cut -## START of SUB -sub write_html_skel { - ## Retrieve Values - my $self = shift ; - my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ; - - my $html_file = $$html_file_name ; - - if ( defined $html_file ) { - open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ; - - if (-e $html_template) { - my $ohtml = HTML::Template->new(filename => $html_template); - $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ; - $ohtml->param( CONDITIONS => $search_condition ) ; - $ohtml->param( PAGES_NB => $pages ) ; - $ohtml->param( PAGES => $html_object ) ; - print HTML $ohtml->output ; - } - else { - croak "Can't fill any html output : No template available ($html_template)\n" ; - } - - close (HTML) ; - } - else { - croak "No output file name available to write HTML file\n" ; - } - return(\$html_file) ; -} -## END of SUB - -=head2 METHOD set_lm_matrix_object - - ## Description : build the hmdb_row under its ref form - ## Input : $header, $init_mzs, $entries - ## Output : $hmdb_matrix - ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ; - -=cut -## START of SUB -sub set_lm_matrix_object { - ## Retrieve Values - my $self = shift ; - my ( $header, $init_mzs, $entries ) = @_ ; - - my @hmdb_matrix = () ; - - if ( defined $header ) { - my @headers = () ; - push @headers, $header ; - push @hmdb_matrix, \@headers ; - } - - my $index_mz = 0 ; - - foreach my $mz ( @{$init_mzs} ) { - - my $index_entries = 0 ; - my @clusters = () ; - my $cluster_col = undef ; - - my @anti_redondant = ('N/A') ; - my $check_rebond = 0 ; - - my $nb_entries = scalar (@{ $entries->[$index_mz] }) ; - - foreach my $entry (@{ $entries->[$index_mz] }) { - - ## dispo anti doublons des entries - foreach my $rebond (@anti_redondant) { - if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } - } - - if ( $check_rebond == 0 ) { - - push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ; - - my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ; - my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ; - my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; - - ## METLIN data display model - ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|... - # manage final pipe - if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; } - else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; } - - } - $check_rebond = 0 ; ## reinit double control - $index_entries++ ; - } ## end foreach - if ( !defined $cluster_col ) { $cluster_col = 'No_result_found_on_HMDB' ; } - push (@clusters, $cluster_col) ; - push (@hmdb_matrix, \@clusters) ; - $index_mz++ ; - } - return(\@hmdb_matrix) ; -} -## END of SUB - -=head2 METHOD set_hmdb_matrix_object_with_ids - - ## Description : build the hmdb_row under its ref form (IDS only) - ## Input : $header, $init_mzs, $entries - ## Output : $hmdb_matrix - ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ; - -=cut -## START of SUB -sub set_hmdb_matrix_object_with_ids { - ## Retrieve Values - my $self = shift ; - my ( $header, $init_mzs, $entries ) = @_ ; - - my @hmdb_matrix = () ; - - if ( defined $header ) { - my @headers = () ; - push @headers, $header ; - push @hmdb_matrix, \@headers ; - } - - my $index_mz = 0 ; - - foreach my $mz ( @{$init_mzs} ) { - - my $index_entries = 0 ; - my @clusters = () ; - my $cluster_col = undef ; - - my @anti_redondant = ('N/A') ; - my $check_rebond = 0 ; - - my $nb_entries = scalar (@{ $entries->[$index_mz] }) ; - - foreach my $entry (@{ $entries->[$index_mz] }) { - - ## dispo anti doublons des entries - foreach my $rebond (@anti_redondant) { - if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } - } - - if ( $check_rebond == 0 ) { - - push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ; - my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; - - ## METLIN data display model -- IDs ONLY !! - ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|... - # manage final pipe - if ($index_entries < $nb_entries-1 ) { $cluster_col .= $hmdb_id.'|' ; } - else { $cluster_col .= $hmdb_id ; } - - } - $check_rebond = 0 ; ## reinit double control - $index_entries++ ; - } ## end foreach - if ( !defined $cluster_col ) { $cluster_col = 'No_result_found_on_HMDB' ; } - push (@clusters, $cluster_col) ; - push (@hmdb_matrix, \@clusters) ; - $index_mz++ ; - } - return(\@hmdb_matrix) ; -} -## END of SUB - -=head2 METHOD add_lm_matrix_to_input_matrix - - ## Description : build a full matrix (input + lm column) - ## Input : $input_matrix_object, $lm_matrix_object, $nb_header - ## Output : $output_matrix_object - ## Usage : my ( $output_matrix_object ) = add_lm_matrix_to_input_matrix( $input_matrix_object, $lm_matrix_object, $nb_header ) ; - -=cut -## START of SUB -sub add_lm_matrix_to_input_matrix { - ## Retrieve Values - my $self = shift ; - my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ; - - my @output_matrix_object = () ; - my $index_row = 0 ; - my $line = 0 ; - - foreach my $row ( @{$input_matrix_object} ) { - my @init_row = @{$row} ; - $line++; - - if ( ( defined $nb_header ) and ( $line <= $nb_header) ) { - push (@output_matrix_object, \@init_row) ; - next ; - } - - if ( $lm_matrix_object->[$index_row] ) { - my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ; - - if ($dim > 1) { warn "the add method can't manage more than one column\n" ;} - my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ; - - push (@init_row, $lm_col) ; - $index_row++ ; - } - push (@output_matrix_object, \@init_row) ; - } - return(\@output_matrix_object) ; -} -## END of SUB - -=head2 METHOD write_csv_skel - - ## Description : prepare and write csv output file - ## Input : $csv_file, $rows - ## Output : $csv_file - ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ; - -=cut -## START of SUB -sub write_csv_skel { - ## Retrieve Values - my $self = shift ; - my ( $csv_file, $rows ) = @_ ; - - my $ocsv = lib::csv::new() ; - my $csv = $ocsv->get_csv_object("\t") ; - $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ; - - return($csv_file) ; -} -## END of SUB - -=head2 METHOD write_csv_one_mass - - ## Description : print a cvs file - ## Input : $masses, $ids, $results, $file - ## Output : N/A - ## Usage : write_csv_one_mass( $ids, $results, $file ) ; - -=cut -## START of SUB -sub write_csv_one_mass { - ## Retrieve Values - my $self = shift ; - my ( $masses, $ids, $results, $file, ) = @_ ; - - open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ; - print CSV "ID\tMASS_SUBMIT\tHMDB_ID\tCPD_FORMULA\tCPD_MW\tDELTA\n" ; - - my $i = 0 ; - - foreach my $id (@{$ids}) { - my $mass = undef ; - if ( $masses->[$i] ) { $mass = $masses->[$i] ; } - else { last ; } - - if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results. - - my @anti_redondant = ('N/A') ; - my $check_rebond = 0 ; - my $check_noentry = 0 ; - - foreach my $entry (@{$results->[$i]}) { - $check_noentry ++ ; - ## dispo anti doublons des entries - foreach my $rebond (@anti_redondant) { - if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } - } -# print "\n-----------------------" ; -# print Dumper $entry->{ENTRY_ENTRY_ID} ; -# print "-------------------------$check_rebond\n" ; -# print Dumper @anti_redondant ; - if ( $check_rebond == 0 ) { - - push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ; - - print CSV "$id\t$mass\t$entry->{ENTRY_ENTRY_ID}\t" ; - ## print cpd name - if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; } - else { print CSV "N/A\t" ; } - ## print cpd mw - if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; } - else { print CSV "N/A\t" ; } - ## print delta - if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\n" ; } - else { print CSV "N/A\n" ; } - } - $check_rebond = 0 ; ## reinit double control - } ## end foreach - if ($check_noentry == 0 ) { - print CSV "$id\t$mass\t".'No_result_found_on_HMDB'."\tn/a\tn/a\t0\n" ; - } - } - $i++ ; - } - close(CSV) ; - return() ; -} -## END of SUB - -1 ; - - -__END__ - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc hmdb.pm - -=head1 Exports - -=over 4 - -=item :ALL is ... - -=back - -=head1 AUTHOR - -Franck Giacomoni Efranck.giacomoni@clermont.inra.frE - -=head1 LICENSE - -This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. - -=head1 VERSION - -version 1 : 06 / 06 / 2013 - -version 2 : 27 / 01 / 2014 - -version 3 : 19 / 11 / 2014 - -version 4 : 28 / 01 / 2016 - -=cut diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/static/images/hmdb.png Binary file hmdb/static/images/hmdb.png has changed diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/t/hmdb_managerTest.pl --- a/hmdb/t/hmdb_managerTest.pl Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -#! perl -use diagnostics; -use warnings; -no warnings qw/void/; -use strict; -no strict "refs" ; -use Test::More qw( no_plan ); -use Test::Exception; -use FindBin ; -use Carp ; - -## Specific Modules -use lib $FindBin::Bin ; -my $binPath = $FindBin::Bin ; -use lib::hmdbTest qw( :ALL ) ; - - -## To launch the right sequence : API, MAPPER, THREADER, ... -#my $sequence = 'MAPPER' ; -my $sequence = 'MAIN' ; -my $current_test = 1 ; - -if ($sequence eq "MAIN") { - print "\n\t\t\t\t * * * * * * \n" ; - print "\t * * * - - - Test HMDB Main script - - - * * * \n\n" ; - - - print "\n** Test $current_test extract_sub_mz_lists with an empty list of mzs **\n" ; $current_test++; - - throws_ok{ extract_sub_mz_listsTest([], 3)} '/The provided mzs list is empty/', 'Method \'extract_sub_mz_lists\' detects empty argument and died correctly' ; - - print "\n** Test $current_test extract_sub_mz_lists with a list of mzs and a limit of 3 **\n" ; $current_test++; - is_deeply( extract_sub_mz_listsTest( - ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ], 3), - [ [ '175.01', '238.19', '420.16' ], [ '780.32', '956.25', '1100.45' ] ], - 'Method \'extract_sub_mz_lists\' works with a list and return a well formated list of sublist of mzs'); - - print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; - throws_ok{ prepare_multi_masses_queryTest([])} '/The input method parameter mass list is empty/', 'Method \'prepare_multi_masses_query\' detects empty argument and died correctly' ; - - print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++; - is_deeply( prepare_multi_masses_queryTest( - ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ), - '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', - 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying'); - - print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++; - is_deeply( get_matches_from_hmdb_uaTest( - '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'), - [ - 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', - '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', - '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', - '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', - '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', - '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' - ], - 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb'); - - print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++; - is_deeply (test_matches_from_hmdb_uaTest (), - \'200', - 'The HMDB server is available: returns successful HTTP requests' ) ; - - print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++; - is_deeply (check_state_from_hmdb_uaTest (\'200'), - 1, - 'The status 200 returns no error/warn' ) ; - - print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; - throws_ok{ check_state_from_hmdb_uaTest(\'504')} - '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/', - 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ; - - print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( - [ - 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', - '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', - '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', - '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', - '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', - '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', - '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' - ], - ['175.01', '238.19', '420.16'] - ), - [ - [ - { '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' }, - { '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' }, - { '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' }, - { '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' }, - { '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' } - ], - [], - [ - { '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' }, - { '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' } - ] - ], - 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; - - print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ), - [ [], [], [] ], - 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ; - - print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), - [], - 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; -} - - - - - - - - - - - - - - - - - -## END of the script \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/t/lib/hmdbTest.pm --- a/hmdb/t/lib/hmdbTest.pm Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -package lib::hmdbTest ; - -use diagnostics; # this gives you more debugging information -use warnings; # this warns you of bad practices -use strict; # this prevents silly errors -use Exporter ; -use Carp ; - -our $VERSION = "1.0"; -our @ISA = qw(Exporter); -our @EXPORT = qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest); -our %EXPORT_TAGS = ( ALL => [qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] ); - -use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ; -use lib::hmdb qw( :ALL ) ; - -use Data::Dumper ; - -## sub -sub extract_sub_mz_listsTest { - - my ($masses, $hmdb_limits, ) = @_ ; - - my $oHmdb = lib::hmdb->new() ; - my $submasses = $oHmdb->extract_sub_mz_lists($masses, $hmdb_limits ) ; - - return ($submasses) ; -} - -## sub -sub prepare_multi_masses_queryTest { - - my ($mzs ) = @_ ; - - my $oHmdb = lib::hmdb->new() ; - my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; - - return ($hmdb_masses) ; -} - -## sub -sub get_matches_from_hmdb_uaTest { - - my ( $hmdb_masses, $delta, $molecular_species ) = @_ ; - - my $oHmdb = lib::hmdb->new() ; - my $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; - return ($hmdb_pages) ; -} - - -## sub -sub test_matches_from_hmdb_uaTest { - - my $oHmdb = lib::hmdb->new() ; - my $status = $oHmdb->test_matches_from_hmdb_ua() ; - return ($status) ; -} - - -## sub -sub check_state_from_hmdb_uaTest { - my ($status ) = @_ ; - - my $oHmdb = lib::hmdb->new() ; - my $res = $oHmdb->check_state_from_hmdb_ua($status) ; - return($res) ; -} - - - -## sub -sub parse_hmdb_csv_resultsTest { - my ($hmdb_pages, $mzs ) = @_ ; - - my $oHmdb = lib::hmdb->new() ; - my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result - - return($result) ; -} - - -1 ; \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/._.DS_Store Binary file hmdb/test_data/._.DS_Store has changed diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/input_test01_fake-mzrt-input-with-id.tsv --- a/hmdb/test_data/input_test01_fake-mzrt-input-with-id.tsv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -id mz rt -1 7.02080998 49.38210915 -2 75.05547146 0.658528069 -3 75.08059797 1743.94267 -4 76.03942694 51.23158899 -5 76.07584477 50.51249853 -6 76.07593168 0.149308136 \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/input_test02_mzrt-input-with-id.tsv --- a/hmdb/test_data/input_test02_mzrt-input-with-id.tsv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -id mz rt -1 7.02080998 49.38210915 -2 75.05547146 0.658528069 -3 75.08059797 1743.94267 -4 76.03942694 51.23158899 -5 76.07584477 50.51249853 -6 76.07593168 0.149308136 \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test01.csv --- a/hmdb/test_data/out_test01.csv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -ID MASS_SUBMIT HMDB_ID CPD_FORMULA CPD_MW DELTA -mz_00001 7.02080998 No_result_found_on_HMDB n/a n/a 0 -mz_00002 75.05547146 No_result_found_on_HMDB n/a n/a 0 -mz_00003 75.08059797 No_result_found_on_HMDB n/a n/a 0 -mz_00004 76.03942694 No_result_found_on_HMDB n/a n/a 0 -mz_00005 76.07584477 No_result_found_on_HMDB n/a n/a 0 -mz_00006 76.07593168 No_result_found_on_HMDB n/a n/a 0 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test01.html --- a/hmdb/test_data/out_test01.html Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = neutral / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Compound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)Delta
mz_000017.02080998
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000275.05547146
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000375.08059797
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000476.03942694
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000576.07584477
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000676.07593168
No_result_found_on_HMDBn/an/an/an/an/a0

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test01.tsv --- a/hmdb/test_data/out_test01.tsv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -id mz rt hmdb -1 7.02080998 49.38210915 No_result_found_on_HMDB -2 75.05547146 0.658528069 No_result_found_on_HMDB -3 75.08059797 1743.94267 No_result_found_on_HMDB -4 76.03942694 51.23158899 No_result_found_on_HMDB -5 76.07584477 50.51249853 No_result_found_on_HMDB -6 76.07593168 0.149308136 No_result_found_on_HMDB diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test02.csv --- a/hmdb/test_data/out_test02.csv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,75 +0,0 @@ -ID MASS_SUBMIT HMDB_ID CPD_FORMULA CPD_MW DELTA -mz_00001 7.02080998 No_result_found_on_HMDB n/a n/a 0 -mz_00002 75.05547146 HMDB31419 C2H6N2O 74.048012824 0.00018246 -mz_00002 75.05547146 HMDB60428 C2H6N2O 74.048012824 0.00018246 -mz_00002 75.05547146 HMDB00064 C4H9N3O2 131.069476547 0.00018346 -mz_00002 75.05547146 HMDB13222 C4H9N3O2 131.069476547 0.00018346 -mz_00002 75.05547146 HMDB32439 H3NO 33.021463723 0.00018446 -mz_00002 75.05547146 HMDB03338 H3NO 33.021463723 0.00018446 -mz_00002 75.05547146 HMDB13162 C11H22NO2 200.165053953 0.00080354 -mz_00003 75.08059797 HMDB04327 C4H10O 74.073164942 0.00015697 -mz_00003 75.08059797 HMDB62103 C4H10O 74.073164942 0.00015697 -mz_00003 75.08059797 HMDB11469 C4H10O 74.073164942 0.00015697 -mz_00003 75.08059797 HMDB06006 C4H10O 74.073164942 0.00015697 -mz_00003 75.08059797 HMDB31456 C4H10O 74.073164942 0.00015697 -mz_00004 76.03942694 HMDB00191 C4H7NO4 133.037507717 0.00012294 -mz_00004 76.03942694 HMDB31239 C2H5NO2 75.032028409 0.00012294 -mz_00004 76.03942694 HMDB00123 C2H5NO2 75.032028409 0.00012294 -mz_00004 76.03942694 HMDB14691 C2H5NO2 75.032028409 0.00012294 -mz_00004 76.03942694 HMDB11753 C4H7NO4 133.037507717 0.00012294 -mz_00004 76.03942694 HMDB06483 C4H7NO4 133.037507717 0.00012294 -mz_00004 76.03942694 HMDB03125 H2O2 34.005479308 0.00012494 -mz_00004 76.03942694 HMDB01039 HO 17.002739654 0.00012494 -mz_00004 76.03942694 HMDB00201 C9H17NO4 203.115758037 0.00041606 -mz_00004 76.03942694 HMDB31603 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB40214 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31681 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31174 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB38271 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31342 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31504 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB33793 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31593 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB39819 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB30330 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB29165 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31351 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB40591 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB32460 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB38962 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB32391 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31476 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31477 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB29314 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31500 C7H12O2 128.083729628 0.00068506 -mz_00004 76.03942694 HMDB31484 C7H12O2 128.083729628 0.00068506 -mz_00005 76.07584477 HMDB12136 C3H9NO 75.068413915 0.00015477 -mz_00005 76.07584477 HMDB00925 C3H9NO 75.068413915 0.00015477 -mz_00005 76.07584477 HMDB31652 C3H6O 58.041864814 0.00015677 -mz_00005 76.07584477 HMDB62143 C3H6O 58.041864813 0.00015677 -mz_00005 76.07584477 HMDB31558 C3H6O 58.041864814 0.00015677 -mz_00005 76.07584477 HMDB03366 C3H6O 58.041864814 0.00015677 -mz_00005 76.07584477 HMDB01659 C3H6O 58.041864814 0.00015677 -mz_00005 76.07584477 HMDB62061 C9H20 128.156500644 0.00065223 -mz_00005 76.07584477 HMDB31416 C9H20 128.15650064 0.00065223 -mz_00005 76.07584477 HMDB31556 C9H20 128.15650064 0.00065223 -mz_00005 76.07584477 HMDB30301 C9H20 128.15650064 0.00065223 -mz_00005 76.07584477 HMDB29595 C9H20 128.15650064 0.00065223 -mz_00005 76.07584477 HMDB30302 C9H20 128.15650064 0.00065223 -mz_00005 76.07584477 HMDB62013 C9H20 128.156500644 0.00065223 -mz_00005 76.07584477 HMDB62017 C9H20 128.156500644 0.00065223 -mz_00006 76.07593168 HMDB12136 C3H9NO 75.068413915 0.00024168 -mz_00006 76.07593168 HMDB00925 C3H9NO 75.068413915 0.00024168 -mz_00006 76.07593168 HMDB31652 C3H6O 58.041864814 0.00024368 -mz_00006 76.07593168 HMDB62143 C3H6O 58.041864813 0.00024368 -mz_00006 76.07593168 HMDB31558 C3H6O 58.041864814 0.00024368 -mz_00006 76.07593168 HMDB03366 C3H6O 58.041864814 0.00024368 -mz_00006 76.07593168 HMDB01659 C3H6O 58.041864814 0.00024368 -mz_00006 76.07593168 HMDB62061 C9H20 128.156500644 0.00056532 -mz_00006 76.07593168 HMDB31416 C9H20 128.15650064 0.00056532 -mz_00006 76.07593168 HMDB31556 C9H20 128.15650064 0.00056532 -mz_00006 76.07593168 HMDB30301 C9H20 128.15650064 0.00056532 -mz_00006 76.07593168 HMDB29595 C9H20 128.15650064 0.00056532 -mz_00006 76.07593168 HMDB30302 C9H20 128.15650064 0.00056532 -mz_00006 76.07593168 HMDB62013 C9H20 128.156500644 0.00056532 -mz_00006 76.07593168 HMDB62017 C9H20 128.156500644 0.00056532 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test02.html --- a/hmdb/test_data/out_test02.html Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Compound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)Delta
mz_000017.02080998
No_result_found_on_HMDBn/an/an/an/an/a0
mz_0000275.05547146
HMDB31419C2H6N2O74.048012824M+H+75.0552890.00018246
HMDB60428C2H6N2O74.048012824M+H+75.0552890.00018246
HMDB00064C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346
HMDB13222C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346
HMDB32439H3NO33.021463723M+ACN+H+75.0552870.00018446
HMDB03338H3NO33.021463723M+ACN+H+75.0552870.00018446
HMDB13162C11H22NO2200.165053953M+2H+Na+75.0562750.00080354
mz_0000375.08059797
HMDB04327C4H10O74.073164942M+H+75.0804410.00015697
HMDB62103C4H10O74.073164942M+H+75.0804410.00015697
HMDB11469C4H10O74.073164942M+H+75.0804410.00015697
HMDB06006C4H10O74.073164942M+H+75.0804410.00015697
HMDB31456C4H10O74.073164942M+H+75.0804410.00015697
mz_0000476.03942694
HMDB00191C4H7NO4133.037507717M+H+NH4+76.0393040.00012294
HMDB31239C2H5NO275.032028409M+H+76.0393040.00012294
HMDB00123C2H5NO275.032028409M+H+76.0393040.00012294
HMDB14691C2H5NO275.032028409M+H+76.0393040.00012294
HMDB11753C4H7NO4133.037507717M+H+NH4+76.0393040.00012294
HMDB06483C4H7NO4133.037507717M+H+NH4+76.0393040.00012294
HMDB03125H2O234.005479308M+ACN+H+76.0393020.00012494
HMDB01039HO17.0027396542M+ACN+H+76.0393020.00012494
HMDB00201C9H17NO4203.115758037M+2H+Na+76.0398430.00041606
HMDB31603C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB40214C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31681C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31174C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB38271C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31342C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31504C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB33793C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31593C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB39819C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB30330C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB29165C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31351C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB40591C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB32460C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB38962C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB32391C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31476C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31477C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB29314C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31500C7H12O2128.083729628M+H+Na+76.0401120.00068506
HMDB31484C7H12O2128.083729628M+H+Na+76.0401120.00068506
mz_0000576.07584477
HMDB12136C3H9NO75.068413915M+H+76.075690.00015477
HMDB00925C3H9NO75.068413915M+H+76.075690.00015477
HMDB31652C3H6O58.041864814M+NH4+76.0756880.00015677
HMDB62143C3H6O58.041864813M+NH4+76.0756880.00015677
HMDB31558C3H6O58.041864814M+NH4+76.0756880.00015677
HMDB03366C3H6O58.041864814M+NH4+76.0756880.00015677
HMDB01659C3H6O58.041864814M+NH4+76.0756880.00015677
HMDB62061C9H20128.156500644M+H+Na+76.0764970.00065223
HMDB31416C9H20128.15650064M+H+Na+76.0764970.00065223
HMDB31556C9H20128.15650064M+H+Na+76.0764970.00065223
HMDB30301C9H20128.15650064M+H+Na+76.0764970.00065223
HMDB29595C9H20128.15650064M+H+Na+76.0764970.00065223
HMDB30302C9H20128.15650064M+H+Na+76.0764970.00065223
HMDB62013C9H20128.156500644M+H+Na+76.0764970.00065223
HMDB62017C9H20128.156500644M+H+Na+76.0764970.00065223
mz_0000676.07593168
HMDB12136C3H9NO75.068413915M+H+76.075690.00024168
HMDB00925C3H9NO75.068413915M+H+76.075690.00024168
HMDB31652C3H6O58.041864814M+NH4+76.0756880.00024368
HMDB62143C3H6O58.041864813M+NH4+76.0756880.00024368
HMDB31558C3H6O58.041864814M+NH4+76.0756880.00024368
HMDB03366C3H6O58.041864814M+NH4+76.0756880.00024368
HMDB01659C3H6O58.041864814M+NH4+76.0756880.00024368
HMDB62061C9H20128.156500644M+H+Na+76.0764970.00056532
HMDB31416C9H20128.15650064M+H+Na+76.0764970.00056532
HMDB31556C9H20128.15650064M+H+Na+76.0764970.00056532
HMDB30301C9H20128.15650064M+H+Na+76.0764970.00056532
HMDB29595C9H20128.15650064M+H+Na+76.0764970.00056532
HMDB30302C9H20128.15650064M+H+Na+76.0764970.00056532
HMDB62013C9H20128.156500644M+H+Na+76.0764970.00056532
HMDB62017C9H20128.156500644M+H+Na+76.0764970.00056532

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test02.tsv --- a/hmdb/test_data/out_test02.tsv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -id mz rt hmdb -1 7.02080998 49.38210915 No_result_found_on_HMDB -2 75.05547146 0.658528069 HMDB31419|HMDB60428|HMDB00064|HMDB13222|HMDB32439|HMDB03338|HMDB13162 -3 75.08059797 1743.94267 HMDB04327|HMDB62103|HMDB11469|HMDB06006|HMDB31456 -4 76.03942694 51.23158899 HMDB00191|HMDB31239|HMDB00123|HMDB14691|HMDB11753|HMDB06483|HMDB03125|HMDB01039|HMDB00201|HMDB31603|HMDB40214|HMDB31681|HMDB31174|HMDB38271|HMDB31342|HMDB31504|HMDB33793|HMDB31593|HMDB39819|HMDB30330|HMDB29165|HMDB31351|HMDB40591|HMDB32460|HMDB38962|HMDB32391|HMDB31476|HMDB31477|HMDB29314|HMDB31500|HMDB31484 -5 76.07584477 50.51249853 HMDB12136|HMDB00925|HMDB31652|HMDB62143|HMDB31558|HMDB03366|HMDB01659|HMDB62061|HMDB31416|HMDB31556|HMDB30301|HMDB29595|HMDB30302|HMDB62013|HMDB62017 -6 76.07593168 0.149308136 HMDB12136|HMDB00925|HMDB31652|HMDB62143|HMDB31558|HMDB03366|HMDB01659|HMDB62061|HMDB31416|HMDB31556|HMDB30301|HMDB29595|HMDB30302|HMDB62013|HMDB62017 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test03.csv --- a/hmdb/test_data/out_test03.csv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1116 +0,0 @@ -ID MASS_SUBMIT HMDB_ID CPD_FORMULA CPD_MW DELTA -mz_00001 175.01 HMDB60293 H2O3S2 113.94453531 0.000125 -mz_00001 175.01 HMDB03745 C2H6O3S2 141.975835438 0.000676 -mz_00001 175.01 HMDB31436 H4O4Si 95.987885149 0.000895 -mz_00001 175.01 HMDB33657 C17H10O6 310.047738052 0.000914 -mz_00001 175.01 HMDB35230 C17H10O6 310.047738052 0.000914 -mz_00001 175.01 HMDB34155 CH4N2S 76.009518828 0.001744 -mz_00001 175.01 HMDB01570 C10H13N2O7P 304.046037292 0.002237 -mz_00001 175.01 HMDB01270 C3H8O10P2 265.9592695 0.003458 -mz_00001 175.01 HMDB01294 C3H8O10P2 265.9592695 0.003458 -mz_00001 175.01 HMDB60394 C9H12FN2O8P 326.031530087 0.004012 -mz_00001 175.01 HMDB60015 C6H6O4S 173.99867937 0.004045 -mz_00001 175.01 HMDB00021 C9H10INO3 306.970536611 0.004182 -mz_00001 175.01 HMDB15167 C5H4N4S 152.015666838 0.005115 -mz_00001 175.01 HMDB40364 C3H7MnO6P 224.936074104 0.005134 -mz_00001 175.01 HMDB62056 C6H7O4P 174.008195703 0.005472 -mz_00001 175.01 HMDB41485 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB00209 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB06853 C4H4O 68.02621475 0.005588 -mz_00001 175.01 HMDB03767 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB40733 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB38176 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33968 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB29635 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33128 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33766 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB40638 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32568 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB29686 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32603 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32400 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB31459 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB13785 C4H4O 68.02621475 0.005588 -mz_00001 175.01 HMDB02340 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB14912 C8H8F3N3O4S2 330.990831754 0.005966 -mz_00001 175.01 HMDB60764 C16H11ClN4O 310.062138701 0.006286 -mz_00001 175.01 HMDB40238 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB31370 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB37493 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB37787 C5H10N2 98.08439833 0.006562 -mz_00001 175.01 HMDB61807 C10H9Cl3O2 265.966812653 0.007229 -mz_00001 175.01 HMDB59985 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB59987 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB60020 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB14581 C5H4N4O 136.03851077 0.008331 -mz_00001 175.01 HMDB00157 C5H4N4O 136.03851077 0.008331 -mz_00001 175.01 HMDB40631 C15H12O7 304.058302738 0.008369 -mz_00001 175.01 HMDB31778 C14H9ClF2N2O2 310.032061659 0.008752 -mz_00001 175.01 HMDB31160 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB33053 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB33054 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB29694 C8H8OS 152.029585568 0.008804 -mz_00001 175.01 HMDB29783 C14H14O8 310.068867424 0.009651 -mz_00001 175.01 HMDB00613 C4H8O5 136.037173366 0.009669 -mz_00001 175.01 HMDB00943 C4H8O5 136.037173366 0.009669 -mz_00001 175.01 HMDB00115 C2H4O3 76.016043994 0.011306 -mz_00001 175.01 HMDB31608 C2H4O3 76.016043994 0.011306 -mz_00001 175.01 HMDB41797 C8H6Cl2O3 219.969399472 0.011761 -mz_00001 175.01 HMDB15413 C12H14N4O4S 310.073575646 0.012005 -mz_00001 175.01 HMDB15621 C12H14N4O4S 310.073575646 0.012005 -mz_00001 175.01 HMDB31825 C8H8S 136.034670946 0.012171 -mz_00001 175.01 HMDB31781 C14H15O2PS2 310.025107616 0.012229 -mz_00001 175.01 HMDB00634 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 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420.16 HMDB31025 C41H62O15 794.408871314 0.033654 -mz_00003 420.16 HMDB01162 C49H58FeN4O5 838.375663119 0.035108 -mz_00003 420.16 HMDB32382 C19H23N3O3 341.173941617 0.035162 -mz_00003 420.16 HMDB05026 C18H21N3O3S 359.130362243 0.035702 -mz_00003 420.16 HMDB30394 C16H25NO9 375.152931403 0.035909 -mz_00003 420.16 HMDB15107 C22H24ClN3O 381.160790112 0.036052 -mz_00003 420.16 HMDB14717 C17H18N2O6S 378.088557008 0.03762 -mz_00003 420.16 HMDB38228 C13H23NO9 337.137281339 0.037651 -mz_00003 420.16 HMDB12286 C8H15NO2S 189.082349419 0.038522 -mz_00003 420.16 HMDB61100 C14H19N5O5 337.138618743 0.038989 -mz_00003 420.16 HMDB01117 C12H23N2O9PS 402.086187546 0.039989 -mz_00003 420.16 HMDB41986 C19H24N4O3 356.184840654 0.040606 -mz_00003 420.16 HMDB61220 C19H24N4O3 356.184840654 0.040606 -mz_00003 420.16 HMDB61221 C19H24N4O3 356.184840654 0.040606 -mz_00003 420.16 HMDB59631 C14H12O 196.088815006 0.04075 -mz_00003 420.16 HMDB00715 C10H7NO3 189.042593095 0.040991 -mz_00003 420.16 HMDB60331 C10H7NO3 189.042593095 0.040991 -mz_00003 420.16 HMDB60332 C10H7NO3 189.042593095 0.040991 -mz_00003 420.16 HMDB14411 C19H12O6 336.063388116 0.041502 -mz_00003 420.16 HMDB34129 C19H12O6 336.063388116 0.041502 -mz_00003 420.16 HMDB34039 C19H12O6 336.063388116 0.041502 -mz_00003 420.16 HMDB34049 C19H12O6 336.063388116 0.041502 -mz_00003 420.16 HMDB37373 C39H32O16 756.169034976 0.04166 -mz_00003 420.16 HMDB41231 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB36900 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB41349 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB35053 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB41002 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB34474 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB30657 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB29542 C22H26O7 402.167853186 0.041676 -mz_00003 420.16 HMDB36694 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB36945 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB34016 C22H26O7 402.167853186 0.041676 -mz_00003 420.16 HMDB36897 C20H26O7 378.167853186 0.041676 -mz_00003 420.16 HMDB60871 C44H55NO14 821.362255473 0.041678 -mz_00003 420.16 HMDB60870 C44H55NO14 821.362255473 0.041678 -mz_00003 420.16 HMDB33356 C21H26NO4 356.186183325 0.041948 -mz_00003 420.16 HMDB41519 C20H20N2O3 336.147392516 0.042503 -mz_00003 420.16 HMDB01132 C11H16NO9P 337.056267627 0.043362 -mz_00003 420.16 HMDB14739 C16H20FN3O4 337.143784348 0.044154 -mz_00003 420.16 HMDB59612 C11H17N5O8P 378.081474057 0.044703 -mz_00003 420.16 HMDB31833 C17H14ClN3O2S 359.049525104 0.045135 -mz_00003 420.16 HMDB13929 C16H16ClNO3S 337.05394178 0.045688 -mz_00003 420.16 HMDB29684 C7H6N4O2 178.049075456 0.046084 -mz_00003 420.16 HMDB39318 C42H62O17 838.398700558 0.046626 -mz_00003 420.16 HMDB31714 C7H14OS2 178.04860645 0.047022 -mz_00003 420.16 HMDB60667 C24H25NO 343.193614427 0.047346 -mz_00003 420.16 HMDB61086 C24H25NO 343.193614427 0.047346 -mz_00003 420.16 HMDB40241 C11H16OS 196.092185824 0.047492 -mz_00003 420.16 HMDB41088 C26H27NO7 465.178752223 0.047592 -mz_00003 420.16 HMDB01956 C40H40N4O14 800.254102008 0.047732 -mz_00003 420.16 HMDB60775 C16H13ClFNO4 337.051713821 0.047916 -mz_00003 420.16 HMDB61718 C21H28N2OS 356.192234218 0.047999 -mz_00003 420.16 HMDB14645 C21H23ClFNO2 375.140134897 0.048705 -mz_00003 420.16 HMDB00150 C6H10O6 178.047738052 0.048759 -mz_00003 420.16 HMDB01353 C6H10O6 178.047738052 0.048759 -mz_00003 420.16 HMDB01385 C6H10O6 178.047738052 0.048759 -mz_00003 420.16 HMDB02541 C6H10O6 178.047738052 0.048759 -mz_00003 420.16 HMDB03466 C6H10O6 178.047738052 0.048759 -mz_00003 420.16 HMDB39724 C12H20O12 356.095476104 0.048759 -mz_00003 420.16 HMDB39726 C12H20O12 356.095476104 0.048759 -mz_00003 420.16 HMDB29938 C12H20O12 356.095476104 0.048759 -mz_00003 420.16 HMDB39722 C12H20O12 356.095476104 0.048759 -mz_00003 420.16 HMDB29932 C6H10O6 178.047738052 0.048759 -mz_00004 780.32 HMDB31947 C17H23NO8 369.142366717 0.001444 -mz_00004 780.32 HMDB35940 C44H44O9 716.298533006 0.005702 -mz_00004 780.32 HMDB33906 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB39032 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB32731 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB39575 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB32105 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB35108 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB30081 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB36780 C20H24O7 376.152203122 0.007526 -mz_00004 780.32 HMDB15535 C16H26N2O5S 358.156242642 0.00825 -mz_00004 780.32 HMDB33715 C68H112O37 1520.688244598 0.009339 -mz_00004 780.32 HMDB14038 C21H20FNO4 369.137636338 0.010904 -mz_00004 780.32 HMDB38999 C17H26O6S 358.145009254 0.014216 -mz_00004 780.32 HMDB00244 C17H20N4O6 376.138284392 0.020311 -mz_00004 780.32 HMDB35698 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB35467 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB38113 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB41276 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB30573 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB30709 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB35789 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB36837 C20H22O6 358.141638436 0.020958 -mz_00004 780.32 HMDB40600 C16H24O10 376.136946988 0.022986 -mz_00004 780.32 HMDB33300 C16H24O10 376.136946988 0.022986 -mz_00004 780.32 HMDB33301 C16H24O10 376.136946988 0.022986 -mz_00004 780.32 HMDB06676 C54H89N3O41 1435.497149365 0.024328 -mz_00004 780.32 HMDB01069 C16H18N6O4 358.138953094 0.026329 -mz_00004 780.32 HMDB33084 C21H23NO5 369.157622851 0.029069 -mz_00004 780.32 HMDB36765 C21H23NO5 369.157622851 0.029069 -mz_00004 780.32 HMDB61331 C21H23NO5 369.157622851 0.029069 -mz_00004 780.32 HMDB38971 C19H24N2O6 376.16343651 0.029993 -mz_00004 780.32 HMDB00768 C14H23NO11 381.127110583 0.031956 -mz_00004 780.32 HMDB33932 C23H20O5 376.13107375 0.034732 -mz_00004 780.32 HMDB38229 C37H40N4O11 716.269358142 0.034877 -mz_00004 780.32 HMDB15107 C22H24ClN3O 381.160790112 0.035403 -mz_00004 780.32 HMDB29788 C24H24O4 376.167459256 0.038039 -mz_00004 780.32 HMDB29299 C32H40O17 696.226549854 0.03834 -mz_00004 780.32 HMDB61254 C38H41N3O11S 747.246179859 0.040331 -mz_00004 780.32 HMDB61256 C38H41N3O11S 747.246179859 0.040331 -mz_00004 780.32 HMDB33965 C15H27NO10 381.163496089 0.040815 -mz_00004 780.32 HMDB12364 C36H66NO10P 703.442433849 0.041474 -mz_00004 780.32 HMDB12344 C36H66NO10P 703.442433849 0.041474 -mz_00004 780.32 HMDB06606 C29H49NO23 779.269536879 0.043187 -mz_00004 780.32 HMDB13001 C54H92O46 1476.485975556 0.043189 -mz_00004 780.32 HMDB12201 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB41369 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB12202 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB12203 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB32000 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB29401 C20H19NO6 369.121237345 0.043702 -mz_00004 780.32 HMDB33522 C21H19NO6 381.121237345 0.043702 -mz_00004 780.32 HMDB29360 C20H19NO6 369.121237345 0.043702 -mz_00005 956.25 HMDB35451 C43H49O23 933.266462874 0.005681 -mz_00005 956.25 HMDB38095 C43H49O23 933.266462874 0.005681 -mz_00005 956.25 HMDB40803 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB02219 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB38821 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB40511 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB34149 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB33990 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB35931 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB29617 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB36630 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB41455 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB60157 C30H52N7O18P3S 923.230238121 0.013727 -mz_00005 956.25 HMDB33021 C43H49O22 917.271548252 0.015294 -mz_00005 956.25 HMDB41153 C40H41O22 873.208947996 0.019318 -mz_00005 956.25 HMDB60375 C35H54N7O19P3S 1001.240802807 0.019643 -mz_00005 956.25 HMDB35163 C40H42O26 938.196431516 0.019745 -mz_00005 956.25 HMDB29794 C40H42O26 938.196431516 0.019745 -mz_00005 956.25 HMDB04047 C27H44N7O19P3S 895.162552487 0.022108 -mz_00005 956.25 HMDB40378 C45H38O21 914.190558278 0.025619 -mz_00005 956.25 HMDB14756 C21H21ClN2O8 464.098643365 0.029593 -mz_00005 956.25 HMDB12207 C28H42N7O17P3S 873.157073179 0.032557 -mz_00005 956.25 HMDB35883 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB37932 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB34725 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB33132 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB40478 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB34360 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB37362 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB30775 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB30747 C22H24O11 464.13186161 0.036843 -mz_00005 956.25 HMDB37535 C22H24O11 464.13186161 0.036843 -mz_00005 956.25 HMDB14927 C28H54GdN5O20 938.260314726 0.044138 -mz_00006 1100.45 HMDB60499 C28H30N4O6 518.216534712 0.001166 -mz_00006 1100.45 HMDB32198 C30H34Cl2N4O 536.210967144 0.004946 -mz_00006 1100.45 HMDB06568 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB02060 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB06582 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB10345 C27H36O11 536.225761994 0.024644 -mz_00006 1100.45 HMDB36888 C27H36O11 536.225761994 0.024644 -mz_00006 1100.45 HMDB39422 C48H64N11O18 1082.443079299 0.026902 -mz_00006 1100.45 HMDB35520 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB38923 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB29773 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB15455 C53H67N9O10S 1021.473160099 0.04438 -mz_00006 1100.45 HMDB40723 C30H30O8 518.194067936 0.046099 -mz_00006 1100.45 HMDB01980 C46H65N13O12S2 1055.431705989 0.047134 -mz_00006 1100.45 HMDB33282 C26H32O12 536.189376488 0.048127 -mz_00006 1100.45 HMDB33281 C26H32O12 536.189376488 0.048127 -mz_00006 1100.45 HMDB15595 C28H22F3N7O 529.183792976 0.048591 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test03.html --- a/hmdb/test_data/out_test03.html Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Compound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)Delta
mz_00001175.01
HMDB60293H2O3S2113.94453531M+IsoProp+H+175.0098750.000125
HMDB03745C2H6O3S2141.975835438M+CH3OH+H+175.0093240.000676
HMDB31436H4O4Si95.987885149M+DMSO+H+175.0091050.000895
HMDB33657C17H10O6310.047738052M+H+K+175.0090860.000914
HMDB35230C17H10O6310.047738052M+H+K+175.0090860.000914
HMDB34155CH4N2S76.0095188282M+Na+175.0082560.001744
HMDB01570C10H13N2O7P304.046037292M+2Na+175.0122370.002237
HMDB01270C3H8O10P2265.9592695M+2ACN+2H+175.0134580.003458
HMDB01294C3H8O10P2265.9592695M+2ACN+2H+175.0134580.003458
HMDB60394C9H12FN2O8P326.031530087M+H+Na+175.0140120.004012
HMDB60015C6H6O4S173.99867937M+H+175.0059550.004045
HMDB00021C9H10INO3306.970536611M+ACN+2H+175.0058180.004182
HMDB15167C5H4N4S152.015666838M+Na+175.0048850.005115
HMDB40364C3H7MnO6P224.936074104M+3ACN+2H+175.0151340.005134
HMDB62056C6H7O4P174.008195703M+H+175.0154720.005472
HMDB41485C8H8O2136.0524295M+K+175.0155880.005588
HMDB00209C8H8O2136.0524295M+K+175.0155880.005588
HMDB06853C4H4O68.026214752M+K+175.0155880.005588
HMDB03767C8H8O2136.0524295M+K+175.0155880.005588
HMDB40733C8H8O2136.0524295M+K+175.0155880.005588
HMDB38176C8H8O2136.0524295M+K+175.0155880.005588
HMDB33968C8H8O2136.0524295M+K+175.0155880.005588
HMDB29635C8H8O2136.0524295M+K+175.0155880.005588
HMDB33128C8H8O2136.0524295M+K+175.0155880.005588
HMDB33766C8H8O2136.0524295M+K+175.0155880.005588
HMDB40638C8H8O2136.0524295M+K+175.0155880.005588
HMDB32568C8H8O2136.0524295M+K+175.0155880.005588
HMDB29686C8H8O2136.0524295M+K+175.0155880.005588
HMDB32603C8H8O2136.0524295M+K+175.0155880.005588
HMDB32400C8H8O2136.0524295M+K+175.0155880.005588
HMDB31459C8H8O2136.0524295M+K+175.0155880.005588
HMDB13785C4H4O68.026214752M+K+175.0155880.005588
HMDB02340C8H8O2136.0524295M+K+175.0155880.005588
HMDB14912C8H8F3N3O4S2330.990831754M+H+NH4+175.0159660.005966
HMDB60764C16H11ClN4O310.062138701M+H+K+175.0162860.006286
HMDB40238C6H10OS130.045235632M+2Na-H+175.0163960.006396
HMDB31370C6H10OS130.045235632M+2Na-H+175.0163960.006396
HMDB37493C6H10OS130.045235632M+2Na-H+175.0163960.006396
HMDB37787C5H10N298.08439833M+2K+H+175.0034380.006562
HMDB61807C10H9Cl3O2265.966812653M+2ACN+2H+175.0172290.007229
HMDB59985C11H12O8S304.02528805M+2Na+175.0018620.008138
HMDB59987C11H12O8S304.02528805M+2Na+175.0018620.008138
HMDB60020C11H12O8S304.02528805M+2Na+175.0018620.008138
HMDB14581C5H4N4O136.03851077M+K+175.0016690.008331
HMDB00157C5H4N4O136.03851077M+K+175.0016690.008331
HMDB40631C15H12O7304.058302738M+2Na+175.0183690.008369
HMDB31778C14H9ClF2N2O2310.032061659M+H+K+175.0012480.008752
HMDB31160C5H12S2136.038041764M+K+175.00120.0088
HMDB33053C5H12S2136.038041764M+K+175.00120.0088
HMDB33054C5H12S2136.038041764M+K+175.00120.0088
HMDB29694C8H8OS152.029585568M+Na+175.0188040.008804
HMDB29783C14H14O8310.068867424M+H+K+175.0196510.009651
HMDB00613C4H8O5136.037173366M+K+175.0003310.009669
HMDB00943C4H8O5136.037173366M+K+175.0003310.009669
HMDB00115C2H4O376.0160439942M+Na+175.0213060.011306
HMDB31608C2H4O376.0160439942M+Na+175.0213060.011306
HMDB41797C8H6Cl2O3219.969399472M+2Na+H+174.9982390.011761
HMDB15413C12H14N4O4S310.073575646M+H+K+175.0220050.012005
HMDB15621C12H14N4O4S310.073575646M+H+K+175.0220050.012005
HMDB31825C8H8S136.034670946M+K+174.9978290.012171
HMDB31781C14H15O2PS2310.025107616M+H+K+174.9977710.012229
HMDB00634C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB00620C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB61185C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB00749C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB02092C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB33809C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB13233C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB59743C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB60365C5H6O4130.02660868M+2Na-H+174.9977690.012231
HMDB60689C4H11Cl2N2O2P219.993519532M+2Na+H+175.022360.01236
HMDB60691C4H11Cl2N2O2P219.993519532M+2Na+H+175.022360.01236
HMDB00292C5H4N4O2152.033425392M+Na+175.0226430.012643
HMDB00786C5H4N4O2152.033425392M+Na+175.0226430.012643
HMDB01182C5H4N4O2152.033425392M+Na+175.0226430.012643
HMDB00072C6H6O6174.016437924M+H+175.0237140.013714
HMDB00958C6H6O6174.016437924M+H+175.0237140.013714
HMDB01264C6H6O6174.016437924M+H+175.0237140.013714
HMDB61101C11H10BrN5O307.006872614M+ACN+2H+175.0239860.013986
HMDB01520C17H21N4O9P456.104614802M+3Na+175.024090.01409
HMDB37945C23H20O10456.10564686M+3Na+175.0244340.014434
HMDB39328C23H20O10456.10564686M+3Na+175.0244340.014434
HMDB40200C7H10OS2174.017306322M+H+175.0245820.014582
HMDB29614C13H21O2PS2304.072057808M+2Na+175.0252470.015247
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HMDB40600C16H24O10376.1369469882M+3H2O+2H+780.2970140.022986
HMDB33300C16H24O10376.1369469882M+3H2O+2H+780.2970140.022986
HMDB33301C16H24O10376.1369469882M+3H2O+2H+780.2970140.022986
HMDB06676C54H89N3O411435.497149365M+3ACN+2H+780.2956720.024328
HMDB01069C16H18N6O4358.1389530942M+ACN+Na+780.2936710.026329
HMDB33084C21H23NO5369.1576228512M+ACN+H+780.3490690.029069
HMDB36765C21H23NO5369.1576228512M+ACN+H+780.3490690.029069
HMDB61331C21H23NO5369.1576228512M+ACN+H+780.3490690.029069
HMDB38971C19H24N2O6376.163436512M+3H2O+2H+780.3499930.029993
HMDB00768C14H23NO11381.1271105832M+NH4+780.2880440.031956
HMDB33932C23H20O5376.131073752M+3H2O+2H+780.2852680.034732
HMDB38229C37H40N4O11716.269358142M+ACN+Na+780.2851230.034877
HMDB15107C22H24ClN3O381.1607901122M+NH4+780.3554030.035403
HMDB29788C24H24O4376.1674592562M+3H2O+2H+780.3580390.038039
HMDB29299C32H40O17696.226549854M+IsoProp+Na+H+780.281660.03834
HMDB61254C38H41N3O11S747.246179859M+CH3OH+H+780.2796690.040331
HMDB61256C38H41N3O11S747.246179859M+CH3OH+H+780.2796690.040331
HMDB33965C15H27NO10381.1634960892M+NH4+780.3608150.040815
HMDB12364C36H66NO10P703.442433849M+2K+H+780.3614740.041474
HMDB12344C36H66NO10P703.442433849M+2K+H+780.3614740.041474
HMDB06606C29H49NO23779.269536879M+H+780.2768130.043187
HMDB13001C54H92O461476.485975556M+2ACN+2H+780.2768110.043189
HMDB12201C16H23N5O6381.1648334932M+NH4+780.363490.04349
HMDB41369C16H23N5O6381.1648334932M+NH4+780.363490.04349
HMDB12202C16H23N5O6381.1648334932M+NH4+780.363490.04349
HMDB12203C16H23N5O6381.1648334932M+NH4+780.363490.04349
HMDB32000C16H23N5O6381.1648334932M+NH4+780.363490.04349
HMDB29401C20H19NO6369.1212373452M+ACN+H+780.2762980.043702
HMDB33522C21H19NO6381.1212373452M+NH4+780.2762980.043702
HMDB29360C20H19NO6369.1212373452M+ACN+H+780.2762980.043702
mz_00005956.25
HMDB35451C43H49O23933.266462874M+Na+956.2556810.005681
HMDB38095C43H49O23933.266462874M+Na+956.2556810.005681
HMDB40803C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB02219C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB38821C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB40511C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB34149C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB33990C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB35931C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB29617C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB36630C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB41455C22H22O10446.1212969242M+ACN+Na+956.2583590.008359
HMDB60157C30H52N7O18P3S923.230238121M+CH3OH+H+956.2637270.013727
HMDB33021C43H49O22917.271548252M+K+956.2347060.015294
HMDB41153C40H41O22873.208947996M+2ACN+H+956.2693180.019318
HMDB60375C35H54N7O19P3S1001.240802807M+2Na+H+956.2696430.019643
HMDB35163C40H42O26938.196431516M+NH4+956.2302550.019745
HMDB29794C40H42O26938.196431516M+NH4+956.2302550.019745
HMDB04047C27H44N7O19P3S895.162552487M+IsoProp+H+956.2278920.022108
HMDB40378C45H38O21914.190558278M+ACN+H+956.2243810.025619
HMDB14756C21H21ClN2O8464.0986433652M+3H2O+2H+956.2204070.029593
HMDB12207C28H42N7O17P3S873.157073179M+2ACN+H+956.2174430.032557
HMDB35883C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB37932C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB34725C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB33132C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB40478C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB34360C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB37362C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB30775C21H20O12464.0954761042M+3H2O+2H+956.2140720.035928
HMDB30747C22H24O11464.131861612M+3H2O+2H+956.2868430.036843
HMDB37535C22H24O11464.131861612M+3H2O+2H+956.2868430.036843
HMDB14927C28H54GdN5O20938.260314726M+NH4+956.2941380.044138
mz_000061100.45
HMDB60499C28H30N4O6518.2165347122M+ACN+Na+1100.4488340.001166
HMDB32198C30H34Cl2N4O536.2109671442M+3H2O+2H+1100.4450540.004946
HMDB06568C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838
HMDB02060C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838
HMDB06582C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838
HMDB10345C27H36O11536.2257619942M+3H2O+2H+1100.4746440.024644
HMDB36888C27H36O11536.2257619942M+3H2O+2H+1100.4746440.024644
HMDB39422C48H64N11O181082.443079299M+NH4+1100.4769020.026902
HMDB35520C24H38O12518.236326682M+ACN+Na+1100.4884180.038418
HMDB38923C24H38O12518.236326682M+ACN+Na+1100.4884180.038418
HMDB29773C24H38O12518.236326682M+ACN+Na+1100.4884180.038418
HMDB15455C53H67N9O10S1021.473160099M+DMSO+H+1100.494380.04438
HMDB40723C30H30O8518.1940679362M+ACN+Na+1100.4039010.046099
HMDB01980C46H65N13O12S21055.431705989M+2Na-H+1100.4028660.047134
HMDB33282C26H32O12536.1893764882M+3H2O+2H+1100.4018730.048127
HMDB33281C26H32O12536.1893764882M+3H2O+2H+1100.4018730.048127
HMDB15595C28H22F3N7O529.1837929762M+ACN+H+1100.4014090.048591

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/test_data/out_test03.tsv --- a/hmdb/test_data/out_test03.tsv Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1116 +0,0 @@ -ID MASS_SUBMIT HMDB_ID CPD_FORMULA CPD_MW DELTA -mz_00001 175.01 HMDB60293 H2O3S2 113.94453531 0.000125 -mz_00001 175.01 HMDB03745 C2H6O3S2 141.975835438 0.000676 -mz_00001 175.01 HMDB31436 H4O4Si 95.987885149 0.000895 -mz_00001 175.01 HMDB33657 C17H10O6 310.047738052 0.000914 -mz_00001 175.01 HMDB35230 C17H10O6 310.047738052 0.000914 -mz_00001 175.01 HMDB34155 CH4N2S 76.009518828 0.001744 -mz_00001 175.01 HMDB01570 C10H13N2O7P 304.046037292 0.002237 -mz_00001 175.01 HMDB01270 C3H8O10P2 265.9592695 0.003458 -mz_00001 175.01 HMDB01294 C3H8O10P2 265.9592695 0.003458 -mz_00001 175.01 HMDB60394 C9H12FN2O8P 326.031530087 0.004012 -mz_00001 175.01 HMDB60015 C6H6O4S 173.99867937 0.004045 -mz_00001 175.01 HMDB00021 C9H10INO3 306.970536611 0.004182 -mz_00001 175.01 HMDB15167 C5H4N4S 152.015666838 0.005115 -mz_00001 175.01 HMDB40364 C3H7MnO6P 224.936074104 0.005134 -mz_00001 175.01 HMDB62056 C6H7O4P 174.008195703 0.005472 -mz_00001 175.01 HMDB41485 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB00209 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB06853 C4H4O 68.02621475 0.005588 -mz_00001 175.01 HMDB03767 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB40733 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB38176 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33968 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB29635 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33128 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB33766 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB40638 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32568 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB29686 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32603 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB32400 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB31459 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB13785 C4H4O 68.02621475 0.005588 -mz_00001 175.01 HMDB02340 C8H8O2 136.0524295 0.005588 -mz_00001 175.01 HMDB14912 C8H8F3N3O4S2 330.990831754 0.005966 -mz_00001 175.01 HMDB60764 C16H11ClN4O 310.062138701 0.006286 -mz_00001 175.01 HMDB40238 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB31370 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB37493 C6H10OS 130.045235632 0.006396 -mz_00001 175.01 HMDB37787 C5H10N2 98.08439833 0.006562 -mz_00001 175.01 HMDB61807 C10H9Cl3O2 265.966812653 0.007229 -mz_00001 175.01 HMDB59985 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB59987 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB60020 C11H12O8S 304.02528805 0.008138 -mz_00001 175.01 HMDB14581 C5H4N4O 136.03851077 0.008331 -mz_00001 175.01 HMDB00157 C5H4N4O 136.03851077 0.008331 -mz_00001 175.01 HMDB40631 C15H12O7 304.058302738 0.008369 -mz_00001 175.01 HMDB31778 C14H9ClF2N2O2 310.032061659 0.008752 -mz_00001 175.01 HMDB31160 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB33053 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB33054 C5H12S2 136.038041764 0.0088 -mz_00001 175.01 HMDB29694 C8H8OS 152.029585568 0.008804 -mz_00001 175.01 HMDB29783 C14H14O8 310.068867424 0.009651 -mz_00001 175.01 HMDB00613 C4H8O5 136.037173366 0.009669 -mz_00001 175.01 HMDB00943 C4H8O5 136.037173366 0.009669 -mz_00001 175.01 HMDB00115 C2H4O3 76.016043994 0.011306 -mz_00001 175.01 HMDB31608 C2H4O3 76.016043994 0.011306 -mz_00001 175.01 HMDB41797 C8H6Cl2O3 219.969399472 0.011761 -mz_00001 175.01 HMDB15413 C12H14N4O4S 310.073575646 0.012005 -mz_00001 175.01 HMDB15621 C12H14N4O4S 310.073575646 0.012005 -mz_00001 175.01 HMDB31825 C8H8S 136.034670946 0.012171 -mz_00001 175.01 HMDB31781 C14H15O2PS2 310.025107616 0.012229 -mz_00001 175.01 HMDB00634 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB00620 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB61185 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB00749 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB02092 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB33809 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB13233 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB59743 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB60365 C5H6O4 130.02660868 0.012231 -mz_00001 175.01 HMDB60689 C4H11Cl2N2O2P 219.993519532 0.01236 -mz_00001 175.01 HMDB60691 C4H11Cl2N2O2P 219.993519532 0.01236 -mz_00001 175.01 HMDB00292 C5H4N4O2 152.033425392 0.012643 -mz_00001 175.01 HMDB00786 C5H4N4O2 152.033425392 0.012643 -mz_00001 175.01 HMDB01182 C5H4N4O2 152.033425392 0.012643 -mz_00001 175.01 HMDB00072 C6H6O6 174.016437924 0.013714 -mz_00001 175.01 HMDB00958 C6H6O6 174.016437924 0.013714 -mz_00001 175.01 HMDB01264 C6H6O6 174.016437924 0.013714 -mz_00001 175.01 HMDB61101 C11H10BrN5O 307.006872614 0.013986 -mz_00001 175.01 HMDB01520 C17H21N4O9P 456.104614802 0.01409 -mz_00001 175.01 HMDB37945 C23H20O10 456.10564686 0.014434 -mz_00001 175.01 HMDB39328 C23H20O10 456.10564686 0.014434 -mz_00001 175.01 HMDB40200 C7H10OS2 174.017306322 0.014582 -mz_00001 175.01 HMDB29614 C13H21O2PS2 304.072057808 0.015247 -mz_00001 175.01 HMDB32909 C19H12O4 304.073558872 0.015997 -mz_00001 175.01 HMDB38322 C19H12O4 304.073558872 0.015997 -mz_00001 175.01 HMDB41450 C19H12O4 304.073558872 0.015997 -mz_00001 175.01 HMDB15176 C13H18Cl2N2O2 304.074533244 0.016485 -mz_00001 175.01 HMDB03152 C7H8N2O 136.063662888 0.016821 -mz_00001 175.01 HMDB33947 C7H8N2O 136.063662888 0.016821 -mz_00001 175.01 HMDB37819 C7H8N2O 136.063662888 0.016821 -mz_00001 175.01 HMDB30001 C7H8N2O 136.063662888 0.016821 -mz_00001 175.01 HMDB59711 C7H8N2O 136.063662888 0.016821 -mz_00001 175.01 HMDB40357 C18H14O5 310.084123558 0.017279 -mz_00001 175.01 HMDB03315 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31563 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB30332 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31564 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB33714 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB33549 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31498 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31497 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31196 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB31496 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB35239 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB40264 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB40271 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB62031 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB62127 C6H10O 98.073164942 0.017795 -mz_00001 175.01 HMDB62136 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB61783 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB61892 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB61893 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB61895 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB61894 C7H14 98.109550448 0.01859 -mz_00001 175.01 HMDB15679 C13H8Cl2N2O4 325.986112168 0.018697 -mz_00001 175.01 HMDB61135 C16H17ClN2S 304.080096951 0.019266 -mz_00001 175.01 HMDB29199 C14H14O9 326.063782046 0.020138 -mz_00001 175.01 HMDB12152 C9H17O12P 348.04576252 0.020157 -mz_00001 175.01 HMDB00175 C10H13N4O8P 348.047099924 0.020826 -mz_00001 175.01 HMDB11681 C10H13N4O8P 348.047099924 0.020826 -mz_00001 175.01 HMDB14684 C4H3FN2O2 130.017855555 0.020984 -mz_00001 175.01 HMDB39638 C9H6N2S 174.025168892 0.022445 -mz_00001 175.01 HMDB60086 C18H24N4O8S 456.131484454 0.023046 -mz_00001 175.01 HMDB14649 C12H9N3O5S 307.026291103 0.023696 -mz_00001 175.01 HMDB00695 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB00408 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB00491 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB01864 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB06024 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB10717 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB33302 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB33286 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB31216 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB31218 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB33698 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB31214 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB59876 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB12882 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB61881 C6H10O3 130.062994186 0.024154 -mz_00001 175.01 HMDB59664 C4H8O2S2 151.99657088 0.024211 -mz_00001 175.01 HMDB31188 C2H4OS 75.99828544 0.024211 -mz_00001 175.01 HMDB35716 C4H8O2S2 151.99657088 0.024211 -mz_00001 175.01 HMDB33670 C4H8O2S2 151.99657088 0.024211 -mz_00001 175.01 HMDB01067 C11H16N2O8 304.090665498 0.024551 -mz_00001 175.01 HMDB02818 C4H2N2O4 142.001456562 0.024946 -mz_00001 175.01 HMDB38442 C4H7NS2 133.001990609 0.025814 -mz_00001 175.01 HMDB00703 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB01101 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB00020 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB00440 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB00669 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB02390 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB03791 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB04815 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB12308 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB30662 C16H16O6 304.094688244 0.026562 -mz_00001 175.01 HMDB41507 C16H16O6 304.094688244 0.026562 -mz_00001 175.01 HMDB36907 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB32919 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB41283 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB29657 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB32606 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB34172 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB30745 C16H16O6 304.094688244 0.026562 -mz_00001 175.01 HMDB32604 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB29661 C8H8O3 152.047344122 0.026562 -mz_00001 175.01 HMDB29662 C8H8O3 152.047344122 0.026562 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0.038039 -mz_00004 780.32 HMDB29299 C32H40O17 696.226549854 0.03834 -mz_00004 780.32 HMDB61254 C38H41N3O11S 747.246179859 0.040331 -mz_00004 780.32 HMDB61256 C38H41N3O11S 747.246179859 0.040331 -mz_00004 780.32 HMDB33965 C15H27NO10 381.163496089 0.040815 -mz_00004 780.32 HMDB12364 C36H66NO10P 703.442433849 0.041474 -mz_00004 780.32 HMDB12344 C36H66NO10P 703.442433849 0.041474 -mz_00004 780.32 HMDB06606 C29H49NO23 779.269536879 0.043187 -mz_00004 780.32 HMDB13001 C54H92O46 1476.485975556 0.043189 -mz_00004 780.32 HMDB12201 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB41369 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB12202 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB12203 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB32000 C16H23N5O6 381.164833493 0.04349 -mz_00004 780.32 HMDB29401 C20H19NO6 369.121237345 0.043702 -mz_00004 780.32 HMDB33522 C21H19NO6 381.121237345 0.043702 -mz_00004 780.32 HMDB29360 C20H19NO6 369.121237345 0.043702 -mz_00005 956.25 HMDB35451 C43H49O23 933.266462874 0.005681 -mz_00005 956.25 HMDB38095 C43H49O23 933.266462874 0.005681 -mz_00005 956.25 HMDB40803 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB02219 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB38821 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB40511 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB34149 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB33990 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB35931 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB29617 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB36630 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB41455 C22H22O10 446.121296924 0.008359 -mz_00005 956.25 HMDB60157 C30H52N7O18P3S 923.230238121 0.013727 -mz_00005 956.25 HMDB33021 C43H49O22 917.271548252 0.015294 -mz_00005 956.25 HMDB41153 C40H41O22 873.208947996 0.019318 -mz_00005 956.25 HMDB60375 C35H54N7O19P3S 1001.240802807 0.019643 -mz_00005 956.25 HMDB35163 C40H42O26 938.196431516 0.019745 -mz_00005 956.25 HMDB29794 C40H42O26 938.196431516 0.019745 -mz_00005 956.25 HMDB04047 C27H44N7O19P3S 895.162552487 0.022108 -mz_00005 956.25 HMDB40378 C45H38O21 914.190558278 0.025619 -mz_00005 956.25 HMDB14756 C21H21ClN2O8 464.098643365 0.029593 -mz_00005 956.25 HMDB12207 C28H42N7O17P3S 873.157073179 0.032557 -mz_00005 956.25 HMDB35883 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB37932 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB34725 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB33132 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB40478 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB34360 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB37362 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB30775 C21H20O12 464.095476104 0.035928 -mz_00005 956.25 HMDB30747 C22H24O11 464.13186161 0.036843 -mz_00005 956.25 HMDB37535 C22H24O11 464.13186161 0.036843 -mz_00005 956.25 HMDB14927 C28H54GdN5O20 938.260314726 0.044138 -mz_00006 1100.45 HMDB60499 C28H30N4O6 518.216534712 0.001166 -mz_00006 1100.45 HMDB32198 C30H34Cl2N4O 536.210967144 0.004946 -mz_00006 1100.45 HMDB06568 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB02060 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB06582 C20H35NO15 529.200669455 0.014838 -mz_00006 1100.45 HMDB10345 C27H36O11 536.225761994 0.024644 -mz_00006 1100.45 HMDB36888 C27H36O11 536.225761994 0.024644 -mz_00006 1100.45 HMDB39422 C48H64N11O18 1082.443079299 0.026902 -mz_00006 1100.45 HMDB35520 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB38923 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB29773 C24H38O12 518.23632668 0.038418 -mz_00006 1100.45 HMDB15455 C53H67N9O10S 1021.473160099 0.04438 -mz_00006 1100.45 HMDB40723 C30H30O8 518.194067936 0.046099 -mz_00006 1100.45 HMDB01980 C46H65N13O12S2 1055.431705989 0.047134 -mz_00006 1100.45 HMDB33282 C26H32O12 536.189376488 0.048127 -mz_00006 1100.45 HMDB33281 C26H32O12 536.189376488 0.048127 -mz_00006 1100.45 HMDB15595 C28H22F3N7O 529.183792976 0.048591 diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/wsdl_hmdb.pl --- a/hmdb/wsdl_hmdb.pl Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,265 +0,0 @@ -#!perl - -## script : wsdl_hmdb.pl -#============================================================================= -# Included modules and versions -#============================================================================= -## Perl modules -use strict ; -use warnings ; -use Carp qw (cluck croak carp) ; - -use Data::Dumper ; -use Getopt::Long ; -use Text::CSV ; -use POSIX ; -use FindBin ; ## Permet de localisez le repertoire du script perl d'origine - -## Specific Modules (Home made...) -use lib $FindBin::Bin ; -my $binPath = $FindBin::Bin ; -use lib::hmdb qw( :ALL ) ; -## PFEM Perl Modules -use lib::conf qw( :ALL ) ; -use lib::csv qw( :ALL ) ; - -## Initialized values -my ( $help ) = undef ; -my ( $mass ) = undef ; -my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ; -my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ; - - -#============================================================================= -# Manage EXCEPTIONS -#============================================================================= - -&GetOptions ( "h" => \$help, # HELP - "mass:s" => \$mass, ## option : one masse - "masses:s" => \$masses_file, ## option : path to the input - "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file - "nblineheader:i" => \$nbline_header, ## numbre of header line present in file - "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file - "delta:f" => \$delta, - "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral) - "output|o:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) - "view|v:s" => \$out_html, ## option : path to the results view (output2) - "outputxls:s" => \$out_xls, ## option : path to the xls-like format output - ) ; - -#============================================================================= -# EXCEPTIONS -#============================================================================= -$help and &help ; - -#============================================================================= -# MAIN SCRIPT -#============================================================================= - - -## -------------- Conf file ------------------------ : -my ( $CONF ) = ( undef ) ; -foreach my $conf ( <$binPath/*.cfg> ) { - my $oConf = lib::conf::new() ; - $CONF = $oConf->as_conf($conf) ; -} - -## -------------- HTML template file ------------------------ : -foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; } - - -## --------------- Global parameters ---------------- : -my ( $ids, $masses, $results ) = ( undef, undef, undef ) ; -my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ; -my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ; - -## --------------- retrieve input data -------------- : - -## manage only one mass -if ( ( defined $mass ) and ( $mass ne '' ) ) { - my @masses = split(" ", $mass); - $masses = \@masses ; - for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } -} ## END IF -## manage csv file containing list of masses -elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) { - ## parse all csv for later : output csv build - my $ocsv_input = lib::csv->new() ; - my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ; - $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ; - - ## parse masses and set ids - my $ocsv = lib::csv->new() ; - my $csv = $ocsv->get_csv_object( "\t" ) ; - if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; } - $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv - my $nbmz = @$masses ; - for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } -} -else { - warn "[warning] Input data are missing : none mass or file of masses\n" ; - &help ; -} - -## ---------------- launch queries -------------------- : - -if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) { - ## prepare masses list and execute query - my $oHmdb = lib::hmdb::new() ; - my $hmdb_pages = undef ; - - $results = [] ; # prepare arrays ref - my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; - - ## get the hmdb server status by a test query - continuous queries or kill script. - my $status = $oHmdb->test_matches_from_hmdb_ua() ; - $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution - - foreach my $mzs ( @{$submasses} ) { - - my $result = undef ; - my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; - $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; - $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result - - $results = [ @$results, @$result ] ; - } - - ## Uses N mz and theirs entries per page (see config file). - # how many pages you need with your input mz list? - $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ; - -# print Dumper $results ; -} -else { - croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ; -} ## end ELSE - -## -------------- Produce HTML/CSV output ------------------ : - -if ( ( defined $out_html ) and ( defined $results ) ) { - my $oHtml = lib::hmdb::new() ; - my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; - ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ; - ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ; - my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; - -} ## END IF -else { - warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ; -} - -if ( ( defined $out_tab ) and ( defined $results ) ) { - # produce a csv based on METLIN format - my $ocsv = lib::hmdb::new() ; - if (defined $masses_file) { - my $lm_matrix = undef ; - if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) { -# $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ; - $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ; - $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ; - } - elsif ( ( $header_choice eq 'no' ) ) { -# $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ; - $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ; - $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ; - } - $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ; - } - elsif (defined $mass) { - $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ; - } -} ## END IF -else { - warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ; -} - -## Write XLS like format -if ( ( defined $out_xls ) and ( defined $results ) ) { - my $ocsv = lib::hmdb::new() ; - $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ; -} - - -#==================================================================================== -# Help subroutine called with -h option -# number of arguments : 0 -# Argument(s) : -# Return : 1 -#==================================================================================== -sub help { - print STDERR " -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 -# Author : Franck Giacomoni and Marion Landi -# Email : fgiacomoni\@clermont.inra.fr -# Version : 1.4 -# Created : 08/07/2012 -# Updated : 21/01/2016 -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] - - or - wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] - -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] - - or - wsdl_hmdb.pl -h for help - - "; - exit(1); -} - -## END of script - F Giacomoni - -__END__ - -=head1 NAME - - wsdl_hmdb.pl -- script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. - -=head1 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] - - or - wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] - -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] - -=head1 SYNOPSIS - -This script manages batch queries on HMDB server. - -=head1 DESCRIPTION - -This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. - -=over 4 - -=item B - -=item B - -=back - -=head1 AUTHOR - -Franck Giacomoni Efranck.giacomoni@clermont.inra.frE - -=head1 LICENSE - -This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. - -=head1 VERSION - -version 1.0 : 06 / 06 / 2013 - -version 1.2 : 27 / 01 / 2014 - -version 1.3 : 19 / 11 / 2014 - -version 1.4 : 21 / 01 / 2016 - a clean version for community - -=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a hmdb/wsdl_hmdb.xml --- a/hmdb/wsdl_hmdb.xml Thu Jan 28 10:52:26 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,239 +0,0 @@ - - - search by masses on HMDB online bank - - - wsdl_hmdb.pl - #if str($input_type.choice) == "YES": - -masses "${input_type.masses}" - -header_choice "${input_type.header.header_choice}" - #if str($input_type.header.header_choice) == "yes": - -nblineheader "${$input_type.header.nbHeader}" - #end if - -colfactor "${input_type.colfactor}" - #else: - -mass "${input_type.mass}" - #end if - -delta "$delta" -mode "$mode" - -output "$variableMetadata" -view "$HmdbResView" -outputxls "$HmdbResXls" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: infomark - -**Authors** Marion Landi and Franck Giacomoni - ---------------------------------------------------- - -.. class:: infomark - -**Please cite** If you use this tool, please cite - | `Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al., HMDB 3.0—The Human Metabolome Database in 2013. Nucleic Acids Res. 2013. <http://www.ncbi.nlm.nih.gov/pubmed/23161693>`_ - - ---------------------------------------------------- - -============== -HMDB MS search -============== - ------------ -Description ------------ - - | Search informations (like : HMDB id, Name, Adduct, delta mass) on HMDB online bank - | with one or more mass(es) in a file or entered manually - - ------------------ -Workflow position ------------------ - - -.. image:: ./static/images/metabolomics/hmdb.png - :width: 800 - - ------------ -Input files ------------ - - -+-------------------------+-----------+ -| Parameter : num + label | Format | -+=========================+===========+ -| 1 : File of masses | tabular | -+-------------------------+-----------+ - -File of masses (Generally variable metadata file) must have at least the following column : - * Masses : column with all the masses in the tsv input file - ----------- -Parameters ----------- - -Would you use a file - | Choose whether the masses are in a file or entered manually - | YES (default) : parameters **File of masses ; Do you have a header ; Column of masses** are visible - | NO : parameter **Mass to submit** is visible - | - - -If 'use file'='YES' - -File of masses - | see "Input files" section above - | Tabular file format, Generally variable metadata file - | - -Do you have a header - | YES (default) : parameter **Number of header lines** is visible - | NO : all lines are considered to contain masses - | - -If 'have a header'='YES' - -Number of header lines - | Number of lines not containing masses values, these lines will be ignored - | - -In all header cases : - -Column of masses - | Specify the column number for the mass in the tsv input file - | - - -If 'use file'='NO' - -Mass to submit - | Specify a list of mass to request - | one or more mass(es) entered manually - | For a masses list, writes : m1 m2 m3 - | You must separate yours values with space - | dot (.) is for float number - | - -In all cases : - -Mass-to-charge ratio - | Specify a delta (mass-to-charge ratio) to apply on mass - This value is a float, between 0.0000000000000001 and 10. - | - -Molecular Species - | Type of ionization of the molecule : *positif, negatif, neutral* - | - - ------------- -Output files ------------- - -Two types of files - | wsdl_hmdb_VIEW.HTML : for viewing result via HTML. - | - | wsdl_hmdb_TSV.tabular : for linking with others modules. - | - | an excel-like output will be available. - | - ---------------------------------------------------- - - ---------------- -Working example ---------------- - - -.. class:: warningmark - -Refer to the corresponding `"W4M HowTo" <http://workflow4metabolomics.org/howto>`_ page: - | Format Data For Postprocessing - | Perform LCMS Annotations - -.. class:: warningmark - -And their "W4M courses 2015": - | Using Galaxy4Metabolomics - W4M table format for Galaxy - | Annotation Banks - Annotation - - - - \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a lib/conf.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/conf.pm Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,259 @@ +package lib::conf ; + +use strict; +use warnings ; +use Exporter ; +use Carp ; +use Data::Dumper ; + +use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); + +our $VERSION = "1.0" ; +our @ISA = qw(Exporter) ; +our @EXPORT = qw( as_conf get_value_from_conf check_path_and_file ) ; +our %EXPORT_TAGS = ( ALL => [qw( as_conf get_value_from_conf )] ) ; + +=head1 NAME + +conf - A module for manage pfem conf file + +=head1 SYNOPSIS + + use conf ; + my $object = conf->new() ; + +=head1 DESCRIPTION + +This module does manage conf file (extract all or selected fields) + +=head1 METHODS + +Methods are : + +=head2 METHOD new + + ## Description : new + ## Input : $self + ## Ouput : bless $self ; + ## Usage : new() ; + +=cut +## START of SUB +sub new { + ## Variables + my $self={}; + bless($self) ; + return $self ; +} +### END of SUB + +=head2 METHOD as_conf + + ## Description : permet de creer l'object conf a partir d'un fichier de conf de type KEY=VALUE + ## Input : $file + ## Ouput : $oConf (a hash) + ## Usage : my ( $oConf ) = as_conf( $file ) ; + +=cut +## START of SUB +sub as_conf { + ## Retrieve Values + my $self = shift ; + my ( $file, $separator ) = @_ ; + +# if (!defined $separator) { $separator = ';' } ## set separator to ; + + if ( !defined $file ) { croak "Can't create object with an none defined file\n" ; } + + my %Conf = () ; ## Hash devant contenir l'ensemble des parametres locaux + + if (-e $file) { + open (CFG, "<$file") or die "Can't open $file\n" ; + while () { + chomp $_ ; + if ( $_ =~ /^#(.*)/) { next ; } + elsif ($_ =~/^(\w+?)=(.*)/) { ## ALPHANUMERIC OR UNDERSCORE ONLY FOR THE KEY AND ANYTHING ELSE FOR VALUE + + my ($key, $value) = ($1, $2) ; + + if (defined $separator) { + if ( $value=~/$separator/ ) { ## is a list to split + my @tmp = split(/$separator/ , $value) ; + $Conf{$key} = \@tmp ; + } + } + else { + $Conf{$key} = $value ; + } + } + } + close(CFG) ; + } + else { + croak "Can't create object with an none existing file\n" ; + } + + return ( \%Conf ) ; +} +## END of SUB + +=head2 METHOD as_conf_list + + ## Description : permet de charger une liste txt en array + ## Input : $file + ## Output : elements + ## Usage : my ( elements ) = as_conf_list( $conf_file ) ; + +=cut +## START of SUB +sub as_conf_list { + ## Retrieve Values + my $self = shift ; + my ( $file ) = @_ ; + + my @elements = () ; + if ( !defined $file ) { croak "Can't create object with an none defined file\n" ; } + + if (-e $file) { + open (CFG, "<$file") or die "Can't open $file\n" ; + while () { + chomp $_ ; + if ( $_ =~ /^#(.*)/) { next ; } + elsif ($_ =~/^(.*)/) { if (defined $1) { push (@elements, $1) ; } } + } + } + else { + croak "Can't create object with an none existing file\n" ; + } + return(\@elements) ; +} +## END of SUB + +=head2 METHOD get_value_from_conf + + ## Description : permet de retourner une valeur du hash de conf a partir d'une key + ## Input : $oConf, $Key + ## Ouput : $Value + ## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ; + +=cut +## START of SUB +sub get_value_from_conf { + ## Retrieve Values + my $self = shift ; + my ( $oConf, $Key ) = @_ ; + + my $Value = undef ; + + if ( defined $oConf ) { + if ( defined $oConf->{$Key} ) { + $Value = $oConf->{$Key} ; + } + } + else { + croak "Can't manage value with undefined object\n" ; + } + return($Value) ; +} +## END of SUB + +=head2 METHOD get_value_from_conf + + ## Description : permet de retourner une valeur du hash de conf a partir d'une key + ## Input : $oConf, $Key + ## Ouput : $Value + ## Usage : my ( $Value ) = get_value_from_conf( $oConf, $Key ) ; + +=cut +## START of SUB +sub split_value_from_conf { + ## Retrieve Values + my $self = shift ; + my ( $oConf, $Key, $sep ) = @_ ; + + my $value = undef ; + my @values = () ; + + if ( defined $oConf ) { + if ( defined $oConf->{$Key} ) { + $value = $oConf->{$Key} ; + @values = split ( /$sep/, $value) ; + } + } + else { + croak "Can't manage value with undefined object\n" ; + } + return(\@values) ; +} +## END of SUB + + +=head2 METHOD check_path_and_file + + ## Description : permet de verifier les path et la presence des exe decrits dans le file conf. Bloque le script en cas de probleme + ## Input : $oConfs + ## Ouput : NA + ## Usage : &get_value_from_conf( $oConf ) ; + +=cut +## START of SUB +sub check_path_and_file { + + my $self = shift ; + my ( $oConfs ) = @_ ; + + foreach my $conf ( keys %{ $oConfs } ) { + if ( $conf =~ /^FILE/ ) { + if ( -e $oConfs->{$conf} ) { + if ( -s $oConfs->{$conf} ) { next ; } + else { carp "[Warning] : The size of file $oConfs->{$conf} is null\n" ; } + } + else { + carp "[Warning] : The file $oConfs->{$conf} doesn't exist\n" ; + } + } + elsif ( $conf =~ /^PATH/ ) { + if ( -d $oConfs->{$conf} ) { next ; } + else { carp "[Warning] : The dir $oConfs->{$conf} doesn't exist\n" ; } + } + else { next ; } + } + return ; +} +## END of SUB + +1 ; + + +__END__ + +=head1 SUPPORT + +You can find documentation for this module with the perldoc command. + + perldoc conf.pm + + +=head1 Exports + +=over 4 + +=item :ALL is as_conf get_value_from_conf + +=back + +=head1 AUTHOR + +Franck Giacomoni Efranck.giacomoni@clermont.inra.frE + +=head1 LICENSE + +This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. + +=head1 VERSION + +version 1 : 10 / 02 / 2013 + +version 2 : ?? + +=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a lib/csv.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/csv.pm Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,240 @@ +package lib::csv ; + +use strict; +use warnings ; +use Exporter ; +use Carp ; + +use Text::CSV ; + +use Data::Dumper ; + +use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); + +our $VERSION = "1.0"; +our @ISA = qw(Exporter); +our @EXPORT = qw( get_csv_object get_value_from_csv_multi_header ); +our %EXPORT_TAGS = ( ALL => [qw( get_csv_object get_value_from_csv_multi_header )] ); + +=head1 NAME + +My::Module - An example module + +=head1 SYNOPSIS + + use My::Module; + my $object = My::Module->new(); + print $object->as_string; + +=head1 DESCRIPTION + +This module does not really exist, it +was made for the sole purpose of +demonstrating how POD works. + +=head1 METHODS + +Methods are : + +=head2 METHOD new + + ## Description : new + ## Input : $self + ## Ouput : bless $self ; + ## Usage : new() ; + +=cut + +sub new { + ## Variables + my $self={}; + bless($self) ; + return $self ; +} +### END of SUB + +=head2 METHOD get_csv_object + + ## Description : builds a csv object and etablishes format + ## Input : $separator + ## Output : $csv + ## Usage : my ( $csv ) = get_csv_object( $separator ) ; + +=cut +## START of SUB +sub get_csv_object { + ## Retrieve Values + my $self = shift ; + my ( $separator ) = @_ ; + +# my $csv = Text::CSV->new({'sep_char' => "$separator"}); + my $csv = Text::CSV->new ( {'sep_char' => "$separator", binary => 1 } ) # should set binary attribute. + or die "Cannot use CSV: ".Text::CSV->error_diag (); + + return($csv) ; +} +## END of SUB + +=head2 METHOD get_value_from_csv_multi_header + + ## Description : extract a targeted column in a csv file + ## Input : $csv, $file, $column, $is_header, $nb_header + ## Output : $value + ## Usage : my ( $value ) = get_value_from_csv_multi_header( $csv, $file, $column, $is_header, $nb_header ) ; + +=cut +## START of SUB +sub get_value_from_csv_multi_header { + ## Retrieve Values + my $self = shift ; + my ( $csv, $file, $column, $is_header, $nb_header ) = @_ ; + + my @value = () ; + + ## Adapte the number of the colunm : (nb of column to position in array) + $column = $column - 1 ; + + open (CSV, "<", $file) or die $! ; + + my $line = 0 ; + + while () { + $line++ ; + chomp $_ ; + # file has a header + if ( defined $is_header and $is_header eq 'yes') { if ($line <= $nb_header) { next ; } } + # parsing the targeted column + if ( $csv->parse($_) ) { + my @columns = $csv->fields(); + push ( @value, $columns[$column] ) ; + } + else { + my $err = $csv->error_input; + die "Failed to parse line: $err"; + } + } + close CSV; + return(\@value) ; +} +## END of SUB + +=head2 METHOD parse_csv_object + + ## Description : parse_all csv object and return a array of rows + ## Input : $csv, $file + ## Output : $csv_matrix + ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file ) ; + +=cut +## START of SUB +sub parse_csv_object { + ## Retrieve Values + my $self = shift ; + my ( $csv, $file ) = @_ ; + + my @csv_matrix = () ; + + open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; + + while ( my $row = $csv->getline( $fh ) ) { + push @csv_matrix, $row; + } + $csv->eof or $csv->error_diag(); + close $fh; + + return(\@csv_matrix) ; +} +## END of SUB + +=head2 METHOD parse_allcsv_object + + ## Description : parse_all csv object and return a array of rows with or without header + ## Input : $csv, $file, $keep_header + ## Output : $csv_matrix + ## Usage : my ( $csv_matrix ) = parse_csv_object( $csv, $file, $keep_header ) ; + +=cut +## START of SUB +sub parse_allcsv_object { + ## Retrieve Values + my $self = shift ; + my ( $csv, $file, $keep_header ) = @_ ; + + my @csv_matrix = () ; + my $line = 1 ; + + open my $fh, "<:encoding(utf8)", $$file or die "Can't open csv file $$file: $!"; + + while ( my $row = $csv->getline( $fh ) ) { + if ( ( $keep_header eq 'n' ) and ($line == 1) ) { } + else { push @csv_matrix, $row; } + $line ++ ; + } + my $status = $csv->eof or $csv->error_diag(); + close $fh; + + return(\@csv_matrix, $status) ; +} +## END of SUB + + +=head2 METHOD write_csv_from_arrays + + ## Description : write a csv file from list of rows + ## Input : $csv, $file_name, $rows + ## Output : $csv_file + ## Usage : my ( $csv_file ) = write_csv_from_arrays( $csv, $file_name, $rows ) ; + +=cut +## START of SUB +sub write_csv_from_arrays { + ## Retrieve Values + my $self = shift ; + my ( $csv, $file_name, $rows ) = @_ ; + + my $fh = undef ; + $csv->eol ("\n"); ## end-of-line string to add to rows + $csv->quote_char(undef) ; + open $fh, ">:encoding(utf8)", "$file_name" or die "$file_name: $!"; + + my $status = $csv->print ($fh, $_) for @{$rows}; + close $fh or die "$file_name: $!"; + + return(\$file_name) ; +} +## END of SUB + +1 ; + + +__END__ + +=head1 SUPPORT + +You can find documentation for this module with the perldoc command. + + perldoc csv.pm + +=head1 Exports + +=over 4 + +=item :ALL is get_csv_object, get_value_from_csv_multi_header + +=back + +=head1 AUTHOR + +Franck Giacomoni Efranck.giacomoni@clermont.inra.frE + +=head1 LICENSE + +This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. + +=head1 VERSION + +version 1 : 23 / 10 / 2013 + +version 2 : ?? + +=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a lib/hmdb.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/hmdb.pm Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,1144 @@ +package lib::hmdb ; + +use strict; +use warnings ; +use Exporter ; +use Carp ; + +use LWP::Simple; +use LWP::UserAgent; +use URI::URL; +use SOAP::Lite; +use Encode; +use HTML::Template ; +use XML::Twig ; +use Text::CSV ; + +use Data::Dumper ; + +use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS); + +our $VERSION = "1.0"; +our @ISA = qw(Exporter); +our @EXPORT = qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass ); +our %EXPORT_TAGS = ( ALL => [qw( map_suppl_data_on_hmdb_results get_unik_ids_from_results get_hmdb_metabocard_from_id extract_sub_mz_lists test_matches_from_hmdb_ua prepare_multi_masses_query get_matches_from_hmdb_ua parse_hmdb_csv_results set_html_tbody_object add_mz_to_tbody_object add_entries_to_tbody_object write_html_skel set_lm_matrix_object set_hmdb_matrix_object_with_ids add_lm_matrix_to_input_matrix write_csv_skel write_csv_one_mass )] ); + +=head1 NAME + +My::Module - An example module + +=head1 SYNOPSIS + + use My::Module; + my $object = My::Module->new(); + print $object->as_string; + +=head1 DESCRIPTION + +This module does not really exist, it +was made for the sole purpose of +demonstrating how POD works. + +=head1 METHODS + +Methods are : + +=head2 METHOD new + + ## Description : new + ## Input : $self + ## Ouput : bless $self ; + ## Usage : new() ; + +=cut + +sub new { + ## Variables + my $self={}; + bless($self) ; + return $self ; +} +### END of SUB + + +=head2 METHOD extract_sub_mz_lists + + ## Description : extract a couples of sublist from a long mz list (more than $HMDB_LIMITS) + ## Input : $HMDB_LIMITS, $masses + ## Output : $sublists + ## Usage : my ( $sublists ) = extract_sub_mz_lists( $HMDB_LIMITS, $masses ) ; + +=cut +## START of SUB +sub extract_sub_mz_lists { + ## Retrieve Values + my $self = shift ; + my ( $masses, $HMDB_LIMITS ) = @_ ; + + my ( @sublists, @sublist ) = ( (), () ) ; + my $nb_mz = 0 ; + my $nb_total_mzs = scalar(@{$masses}) ; + + if ($nb_total_mzs == 0) { + die "The provided mzs list is empty" ; + } + + for ( my $current_pos = 0 ; $current_pos < $nb_total_mzs ; $current_pos++ ) { + + if ( $nb_mz < $HMDB_LIMITS ) { + if ( $masses->[$current_pos] ) { push (@sublist, $masses->[$current_pos]) ; $nb_mz++ ; } # build sub list + } + elsif ( $nb_mz == $HMDB_LIMITS ) { + my @tmp = @sublist ; push (@sublists, \@tmp) ; @sublist = () ; $nb_mz = 0 ; + $current_pos-- ; + } + if ($current_pos == $nb_total_mzs-1) { my @tmp = @sublist ; push (@sublists, \@tmp) ; } + } + return(\@sublists) ; +} +## END of SUB + +=head2 METHOD prepare_multi_masses_query + + ## Description : Generate the adapted format of the mz list for HMDB + ## Input : $masses + ## Output : $hmdb_masses + ## Usage : my ( $hmdb_masses ) = prepare_multi_masses_query( $masses ) ; + +=cut +## START of SUB +sub prepare_multi_masses_query { + ## Retrieve Values + my $self = shift ; + my ( $masses ) = @_ ; + + my $hmdb_masses = undef ; + my $sep = '%0D%0A' ; ## retour chariot encode + my ($nb_masses, $i) = (0, 0) ; + + if ( defined $masses ) { + my @masses = @{$masses} ; + my $nb_masses = scalar ( @masses ) ; + if ( $nb_masses == 0 ) { croak "The input method parameter mass list is empty" ; } + elsif ( $nb_masses >= 150 ) { croak "Your mass list is too long : HMDB allows maximum 150 query masses per request \n" ; } ## Del it --- temporary patch + + foreach my $mass (@masses) { + + if ($i < $nb_masses) { + $hmdb_masses .= $mass.$sep ; + } + elsif ( $i == $nb_masses ) { + $hmdb_masses .= $mass ; + } + else { + last ; + } + $i ++ ; + } + } + else { + croak "No mass list found \n" ; + } + return($hmdb_masses, $nb_masses) ; +} +## END of SUB + +=head2 METHOD test_matches_from_hmdb_ua + + ## Description : test a single query with tests parameters on hmdb - get the status of the complete server infra. + ## Input : none + ## Output : $status_line + ## Usage : my ( $status_line ) = test_matches_from_hmdb_ua( ) ; + +=cut +## START of SUB +sub test_matches_from_hmdb_ua { + ## Retrieve Values + my $self = shift ; + + my @page = () ; + + my $ua = new LWP::UserAgent; + $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); + + my $req = HTTP::Request->new( + POST => 'http://specdb.wishartlab.com/ms/search.csv'); + + $req->content_type('application/x-www-form-urlencoded'); + $req->content('utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV'); + + my $res = $ua->request($req); +# print $res->as_string; + my $status_line = $res->status_line ; + ($status_line) = ($status_line =~ /(\d+)/); + + + return (\$status_line) ; +} +## END of SUB + +=head2 METHOD check_state_from_hmdb_ua + + ## Description : check the thhp status of hmdb and kill correctly the script if necessary. + ## Input : $status + ## Output : none + ## Usage : check_state_from_hmdb_ua($status) ; + +=cut +## START of SUB +sub check_state_from_hmdb_ua { + ## Retrieve Values + my $self = shift ; + my ($status) = @_ ; + + if (!defined $$status) { + croak "No http status is defined for the distant server" ; + } + else { + unless ( $$status == 200 ) { + if ( $$status == 504 ) { croak "Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server" ; } + else { + ## None supported http code error ## + } + } + } + + return (1) ; +} +## END of SUB + +=head2 METHOD get_matches_from_hmdb_ua + + ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg) + ## Input : $mass, $delta, $mode + ## Output : $results + ## Usage : my ( $results ) = get_matches_from_hmdb( $mass, $delta, $mode ) ; + +=cut +## START of SUB +sub get_matches_from_hmdb_ua { + ## Retrieve Values + my $self = shift ; + my ( $masses, $delta, $mode ) = @_ ; + + my @page = () ; + + my $ua = new LWP::UserAgent; + $ua->agent("Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36"); + $ua->timeout(500); + + my $req = HTTP::Request->new( + POST => 'http://specdb.wishartlab.com/ms/search.csv'); + + $req->content_type('application/x-www-form-urlencoded'); + $req->content('utf8=TRUE&mode='.$mode.'&query_masses='.$masses.'&tolerance='.$delta.'&database=HMDB&commit=Download Results As CSV'); + + my $res = $ua->request($req); +# print $res->as_string; + if ($res->is_success) { + @page = split ( /\n/, $res->decoded_content ) ; + } else { + my $status_line = $res->status_line ; + ($status_line) = ($status_line =~ /(\d+)/); + croak "HMDB service none available !! Status of the HMDB server is : $status_line\n" ; + } + + + return (\@page) ; +} +## END of SUB + +=head2 METHOD parse_hmdb_csv_results + + ## Description : parse the csv results and get data + ## Input : $csv + ## Output : $results + ## Usage : my ( $results ) = parse_hmdb_csv_results( $csv ) ; + +=cut +## START of SUB +sub parse_hmdb_csv_results { + ## Retrieve Values + my $self = shift ; + my ( $csv, $masses, $max_query ) = @_ ; + + my $test = 0 ; + my ($query_mass,$compound_id,$formula,$compound_mass,$adduct,$adduct_type,$adduct_mass,$delta) = (0, undef, undef, undef, undef, undef, undef, undef) ; + + my %result_by_entry = () ; + my %features = () ; + +# 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]} = [] ; } + + $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) ; + } + else { + next ; + } + } ## end foreach + + ## manage per query_mzs (keep query masses order by array) + my @results = () ; + foreach (@{$masses}) { + if ($result_by_entry{$_}) { + + ## cut all entries > $max_query + my @temp_entries = @{$result_by_entry{$_}} ; + my @temp_cut = () ; + my $current_query = 0 ; + foreach (@temp_entries) { + $current_query ++ ; + if ($current_query > $max_query) { + last ; + } + else { + push (@temp_cut, $_) ; + } + } + push (@results, \@temp_cut) ; +# push (@results, $result_by_entry{$_}) ; + } + else {push (@results, [] ) ;} ; + + } + return(\@results) ; +} +## END of SUB + +=head2 METHOD parse_hmdb_page_results + + ## Description : [DEPRECATED] old HMDB html page parser + ## Input : $page + ## Output : $results + ## Usage : my ( $results ) = parse_hmdb_page_result( $pages ) ; + +=cut +## START of SUB +sub parse_hmdb_page_results { + ## Retrieve Values + my $self = shift ; + my ( $page ) = @_ ; + + my @results = () ; + my ($catch_table, $catch_name) = (0, 0) ; + my ($name, $adduct, $adduct_mw, $cpd_mw, $delta) = (undef, undef, undef, undef, undef) ; + + if ( defined $page ) { + + my @page = @{$page} ; + my $ID = undef ; + my @result_by_mz = () ; + my %result_by_entry = () ; + + foreach my $line (@page) { + + #Section de la page contenant les resultat + if( $line =~// ) { $catch_table = 1 ; } + + ## Si il existe un resultat : + if($catch_table == 1) { + + #Id de la molecule, et creation du lien + if( $line =~ // ) { + $ID = $1 ; + $catch_name = 0 ; + next ; + } + #Nom de la molecule ONLY!! + if ( $catch_name == 0 ) { + + if( $line =~ /
(.+)<\/td>/ ) { + + if ( !defined $name ) { + $name = $1 ; + $result_by_entry{'ENTRY_ENTRY_ID'} = $ID ; + $result_by_entry{'ENTRY_NAME'} = $name ; + next ; + } + if ( !defined $adduct ) { $adduct = $1 ; $result_by_entry{'ENTRY_ADDUCT'} = $adduct ; next ; } + if ( !defined $adduct_mw ) { $adduct_mw = $1 ; $result_by_entry{'ENTRY_ADDUCT_MZ'} = $adduct_mw ; next ; } + if ( !defined $cpd_mw ) { $cpd_mw = $1 ; $result_by_entry{'ENTRY_CPD_MZ'} = $cpd_mw ; next ; } + if ( !defined $delta ) { + $delta = $1 ; + $result_by_entry{'ENTRY_DELTA'} = $delta ; + $catch_name = 1 ; + my %tmp = %result_by_entry ; + push (@result_by_mz, \%tmp) ; + %result_by_entry = () ; + ( $name, $cpd_mw, $delta, $adduct, $adduct_mw ) = ( undef, undef, undef, undef, undef ) ; + next ; + } + } + } + } + #Fin de la section contenant les resultats + if( $line =~ /<\/table>/ ) { + $catch_table = 0 ; + my @Tmp = @result_by_mz ; + push(@results, \@Tmp) ; + @result_by_mz = () ; + } + } + } + return(\@results) ; +} +## END of SUB + + +=head2 METHOD get_unik_ids_from_results + + ## Description : get all unik ids from the hmdb result object + ## Input : $results + ## Output : $ids + ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ; + +=cut +## START of SUB +sub get_unik_ids_from_results { + ## Retrieve Values + my $self = shift ; + my ( $results ) = @_; + my ( %ids ) = ( () ) ; + + foreach my $result (@{$results}) { + + foreach my $entries (@{$result}) { + + if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) { + $ids{$entries->{'ENTRY_ENTRY_ID'}} = 1 ; + } + } + } + + return (\%ids) ; +} +### END of SUB + + + +=head2 METHOD get_hmdb_metabocard_from_id + + ## Description : get a metabocard (xml format from an ID on HMDB) + ## Input : $ids + ## Output : $metabocard_features + ## Usage : my ( $metabocard_features ) = get_hmdb_metabocard_from_id ( $ids ) ; + +=cut +## START of SUB +sub get_hmdb_metabocard_from_id { + ## Retrieve Values + my $self = shift ; + my ( $ids, $hmdb_url ) = @_; + my ( %metabocard_features ) = ( () ) ; + my $query = undef ; + + ## structure %metabocard_features + # metabolite_id = ( + # 'metabolite_name' => '__name__', + # 'metabolite_inchi' => '__inchi__', + # 'metabolite_logp' => '__logp-ALOGPS__', + # + # ) + + + if( (defined $ids) and ($ids > 0 ) ) { + + foreach my $id (keys %{$ids}) { + +# print "\n============== > $id **********************\n " ; + my $twig = undef ; + + if (defined $hmdb_url) { + $query = $hmdb_url.$id.'.xml' ; + + ## test the header if exists + my $response = head($query) ; + + if (!defined $response) { + $metabocard_features{$id}{'metabolite_name'} = undef ; + $metabocard_features{$id}{'metabolite_inchi'} = undef ; + $metabocard_features{$id}{'metabolite_logp'} = undef ; + ## Need to be improve to manage http 404 or other response diff than 200 + } + elsif ($response->is_success) { + + $twig = XML::Twig->nparse_ppe( + + twig_handlers => { + # metabolite name + 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; } , + # metabolite inchi + 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; } , + ## metabolite logP + 'metabolite/predicted_properties/property' => sub { + + my ($kind, $source, $value ) = ( undef, undef, undef ) ; + + if (defined $_->children ) { + foreach my $field ($_->children) { + if ( $field->name eq 'kind') { $kind = $field->text ; } + elsif ( $field->name eq 'source') { $source = $field->text ; } + elsif ( $field->name eq 'value') { $value = $field->text ; } + + if (defined $source ) { + if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) { + $metabocard_features{$id}{'metabolite_logp'} = $value ; + } + ($kind, $source, $value ) = ( undef, undef, undef ) ; + } + } + } + } + }, + pretty_print => 'indented', + error_context => 1, $query + ); + +# $twig->print; + $twig->purge ; + + if (!$@) { + + } + else { + warn $@ ; + } + } + } + else { + warn "The hmdb metabocard url is not defined\n" ; + last; + } + } + } + else { + warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ; + } + +# print Dumper %metabocard_features ; + return (\%metabocard_features) ; +} +### END of SUB + + +=head2 METHOD map_suppl_data_on_hmdb_results + + ## Description : map supplementary data with already collected results with hmdb search + ## Input : $results, $features + ## Output : $results + ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ; + +=cut +## START of SUB +sub map_suppl_data_on_hmdb_results { + ## Retrieve Values + my $self = shift ; + my ( $results, $features ) = @_; + my ( @more_results ) = ( () ) ; + + @more_results = @{$results} ; ## Dump array ref to map + + foreach my $result (@more_results) { + + foreach my $entries (@{$result}) { + + if ( ($entries->{'ENTRY_ENTRY_ID'}) and ($entries->{'ENTRY_ENTRY_ID'} ne '' ) ) { + ## check that we have a ID for mapping + my $current_id = $entries->{'ENTRY_ENTRY_ID'} ; + if ($features->{"$current_id"}) { + ## Metabolite NAME + if (defined $features->{"$current_id"}{'metabolite_name'} ) { + $entries->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'} + } + else { + $entries->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ; + } + ## Metabolite INCHI + if (defined $features->{"$current_id"}{'metabolite_inchi'} ) { + $entries->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'} + } + else { + $entries->{'ENTRY_ENTRY_INCHI'} = 'NA' ; + } + ## Metabolite LOGP + if (defined $features->{"$current_id"}{'metabolite_logp'} ) { + $entries->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'} + } + else { + $entries->{'ENTRY_ENTRY_LOGP'} = 'NA' ; + } + } + else { + warn "This HMDB id doesn't match any collected ids\n" ; + } + } + } + } + + return (\@more_results) ; +} +### END of SUB + + +=head2 METHOD set_html_tbody_object + + ## Description : initializes and build the tbody object (perl array) needed to html template + ## Input : $nb_pages, $nb_items_per_page + ## Output : $tbody_object + ## Usage : my ( $tbody_object ) = set_html_tbody_object($nb_pages, $nb_items_per_page) ; + +=cut +## START of SUB +sub set_html_tbody_object { + my $self = shift ; + my ( $nb_pages, $nb_items_per_page ) = @_ ; + + my ( @tbody_object ) = ( ) ; + + for ( my $i = 1 ; $i <= $nb_pages ; $i++ ) { + + my %pages = ( + # tbody feature + PAGE_NB => $i, + MASSES => [], ## end MASSES + ) ; ## end TBODY N + push (@tbody_object, \%pages) ; + } + return(\@tbody_object) ; +} +## END of SUB + +=head2 METHOD add_mz_to_tbody_object + + ## Description : initializes and build the mz object (perl array) needed to html template + ## Input : $tbody_object, $nb_items_per_page, $mz_list + ## Output : $tbody_object + ## Usage : my ( $tbody_object ) = add_mz_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list ) ; + +=cut +## START of SUB +sub add_mz_to_tbody_object { + my $self = shift ; + my ( $tbody_object, $nb_items_per_page, $mz_list, $ids_list ) = @_ ; + + my ( $current_page, $mz_index ) = ( 0, 0 ) ; + + foreach my $page ( @{$tbody_object} ) { + + my @colors = ('white', 'green') ; + my ( $current_index, , $icolor ) = ( 0, 0 ) ; + + for ( my $i = 1 ; $i <= $nb_items_per_page ; $i++ ) { + # + if ( $current_index > $nb_items_per_page ) { ## manage exact mz per html page + $current_index = 0 ; + last ; ## + } + else { + $current_index++ ; + if ( $icolor > 1 ) { $icolor = 0 ; } + + if ( exists $mz_list->[$mz_index] ) { + + my %mz = ( + # mass feature + MASSES_ID_QUERY => $ids_list->[$mz_index], + MASSES_MZ_QUERY => $mz_list->[$mz_index], + MZ_COLOR => $colors[$icolor], + MASSES_NB => $mz_index+1, + ENTRIES => [] , + ) ; + push ( @{ $tbody_object->[$current_page]{MASSES} }, \%mz ) ; + # Html attr for mass + $icolor++ ; + } + } + $mz_index++ ; + } ## foreach mz + + $current_page++ ; + } + return($tbody_object) ; +} +## END of SUB + +=head2 METHOD add_entries_to_tbody_object + + ## Description : initializes and build the entries object (perl array) needed to html template + ## Input : $tbody_object, $nb_items_per_page, $mz_list, $entries + ## Output : $tbody_object + ## Usage : my ( $tbody_object ) = add_entries_to_tbody_object( $tbody_object, $nb_items_per_page, $mz_list, $entries ) ; + +=cut +## START of SUB +sub add_entries_to_tbody_object { + ## Retrieve Values + my $self = shift ; + my ( $tbody_object, $nb_items_per_page, $mz_list, $entries ) = @_ ; + + my $index_page = 0 ; + my $index_mz_continous = 0 ; + + foreach my $page (@{$tbody_object}) { + + my $index_mz = 0 ; + + foreach my $mz (@{ $tbody_object->[$index_page]{MASSES} }) { + + my $index_entry = 0 ; + + my @anti_redondant = ('N/A') ; + my $check_rebond = 0 ; + my $check_noentry = 0 ; + + foreach my $entry (@{ $entries->[$index_mz_continous] }) { + $check_noentry ++ ; + ## dispo anti doublons des entries + foreach my $rebond (@anti_redondant) { + if ( $rebond eq $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } + } + + if ( $check_rebond == 0 ) { + + push ( @anti_redondant, $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID} ) ; + + my %entry = ( + ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR}, + ENTRY_ENTRY_NAME => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_NAME}, + ENTRY_ENTRY_ID => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID}, + ENTRY_ENTRY_ID2 => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_ID}, + ENTRY_FORMULA => $entries->[$index_mz_continous][$index_entry]{ENTRY_FORMULA}, + ENTRY_CPD_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_CPD_MZ}, + ENTRY_ADDUCT => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT}, + ENTRY_ADDUCT_TYPE => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_TYPE}, + ENTRY_ADDUCT_MZ => $entries->[$index_mz_continous][$index_entry]{ENTRY_ADDUCT_MZ}, + ENTRY_DELTA => $entries->[$index_mz_continous][$index_entry]{ENTRY_DELTA}, + ENTRY_ENTRY_INCHI => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_INCHI}, + ENTRY_ENTRY_LOGP => $entries->[$index_mz_continous][$index_entry]{ENTRY_ENTRY_LOGP}, + ) ; + + push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ; + } + $check_rebond = 0 ; ## reinit double control + $index_entry++ ; + } ## end foreach + if ($check_noentry == 0 ) { + my %entry = ( + ENTRY_COLOR => $tbody_object->[$index_page]{MASSES}[$index_mz]{MZ_COLOR}, + ENTRY_ENTRY_NAME => 'UNKNOWN', + ENTRY_ENTRY_ID => 'NONE', + ENTRY_ENTRY_ID2 => '', + ENTRY_FORMULA => 'n/a', + ENTRY_CPD_MZ => 'n/a', + ENTRY_ADDUCT => 'n/a', + ENTRY_ADDUCT_TYPE => 'n/a', + ENTRY_ADDUCT_MZ => 'n/a', + ENTRY_DELTA => 0, + ENTRY_ENTRY_INCHI => 'n/a', + ENTRY_ENTRY_LOGP => 'n/a', + ) ; + push ( @{ $tbody_object->[$index_page]{MASSES}[$index_mz]{ENTRIES} }, \%entry) ; + } + $index_mz ++ ; + $index_mz_continous ++ ; + } + $index_page++ ; + } + return($tbody_object) ; +} +## END of SUB + +=head2 METHOD write_html_skel + + ## Description : prepare and write the html output file + ## Input : $html_file_name, $html_object, $html_template + ## Output : $html_file_name + ## Usage : my ( $html_file_name ) = write_html_skel( $html_file_name, $html_object ) ; + +=cut +## START of SUB +sub write_html_skel { + ## Retrieve Values + my $self = shift ; + my ( $html_file_name, $html_object, $pages , $search_condition, $html_template, $js_path, $css_path ) = @_ ; + + my $html_file = $$html_file_name ; + + if ( defined $html_file ) { + open ( HTML, ">$html_file" ) or die "Can't create the output file $html_file " ; + + if (-e $html_template) { + my $ohtml = HTML::Template->new(filename => $html_template); + $ohtml->param( JS_GALAXY_PATH => $js_path, CSS_GALAXY_PATH => $css_path ) ; + $ohtml->param( CONDITIONS => $search_condition ) ; + $ohtml->param( PAGES_NB => $pages ) ; + $ohtml->param( PAGES => $html_object ) ; + print HTML $ohtml->output ; + } + else { + croak "Can't fill any html output : No template available ($html_template)\n" ; + } + + close (HTML) ; + } + else { + croak "No output file name available to write HTML file\n" ; + } + return(\$html_file) ; +} +## END of SUB + +=head2 METHOD set_lm_matrix_object + + ## Description : build the hmdb_row under its ref form + ## Input : $header, $init_mzs, $entries + ## Output : $hmdb_matrix + ## Usage : my ( $hmdb_matrix ) = set_lm_matrix_object( $header, $init_mzs, $entries ) ; + +=cut +## START of SUB +sub set_lm_matrix_object { + ## Retrieve Values + my $self = shift ; + my ( $header, $init_mzs, $entries ) = @_ ; + + my @hmdb_matrix = () ; + + if ( defined $header ) { + my @headers = () ; + push @headers, $header ; + push @hmdb_matrix, \@headers ; + } + + my $index_mz = 0 ; + + foreach my $mz ( @{$init_mzs} ) { + + my $index_entries = 0 ; + my @clusters = () ; + my $cluster_col = undef ; + + my @anti_redondant = ('N/A') ; + my $check_rebond = 0 ; + + my $nb_entries = scalar (@{ $entries->[$index_mz] }) ; + + foreach my $entry (@{ $entries->[$index_mz] }) { + + ## dispo anti doublons des entries + foreach my $rebond (@anti_redondant) { + if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } + } + + if ( $check_rebond == 0 ) { + + push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ; + + my $delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ; + my $formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ; + my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; + + ## METLIN data display model + ## entry1=VAR1::VAR2::VAR3::VAR4|entry2=VAR1::VAR2::VAR3::VAR4|... + # manage final pipe + if ($index_entries < $nb_entries-1 ) { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id.'|' ; } + else { $cluster_col .= $delta.'::('.$formula.')::'.$hmdb_id ; } + + } + $check_rebond = 0 ; ## reinit double control + $index_entries++ ; + } ## end foreach + if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; } + push (@clusters, $cluster_col) ; + push (@hmdb_matrix, \@clusters) ; + $index_mz++ ; + } + return(\@hmdb_matrix) ; +} +## END of SUB + +=head2 METHOD set_hmdb_matrix_object_with_ids + + ## Description : build the hmdb_row under its ref form (IDS only) + ## Input : $header, $init_mzs, $entries + ## Output : $hmdb_matrix + ## Usage : my ( $hmdb_matrix ) = set_hmdb_matrix_object_with_ids( $header, $init_mzs, $entries ) ; + +=cut +## START of SUB +sub set_hmdb_matrix_object_with_ids { + ## Retrieve Values + my $self = shift ; + my ( $header, $init_mzs, $entries ) = @_ ; + + my @hmdb_matrix = () ; + + if ( defined $header ) { + my @headers = () ; + + ## redefined the header hmdb(delta::name::mz::formula::adduct::id) + $header = 'hmdb(delta::name::mz::formula::adduct::id)' ; + push @headers, $header ; + push @hmdb_matrix, \@headers ; + } + + my $index_mz = 0 ; + + foreach my $mz ( @{$init_mzs} ) { + + my $index_entries = 0 ; + my @clusters = () ; + my $cluster_col = undef ; + + my @anti_redondant = ('N/A') ; + my $check_rebond = 0 ; + + my $nb_entries = scalar (@{ $entries->[$index_mz] }) ; + + foreach my $entry (@{ $entries->[$index_mz] }) { + + ## dispo anti doublons des entries + foreach my $rebond (@anti_redondant) { + if ( $rebond eq $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } + } + + if ( $check_rebond == 0 ) { + + push ( @anti_redondant, $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ) ; + ## + my $hmdb_name = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_NAME} ; + my $hmdb_id = $entries->[$index_mz][$index_entries]{ENTRY_ENTRY_ID} ; + my $hmdb_formula = $entries->[$index_mz][$index_entries]{ENTRY_FORMULA} ; + my $hmdb_cpd_mz = $entries->[$index_mz][$index_entries]{ENTRY_CPD_MZ} ; + my $hmdb_adduct = $entries->[$index_mz][$index_entries]{ENTRY_ADDUCT} ; + my $hmdb_delta = $entries->[$index_mz][$index_entries]{ENTRY_DELTA} ; + + ## METLIN data display model + ## entry1= ENTRY_DELTA::ENTRY_ENTRY_NAME::ENTRY_CPD_MZ::ENTRY_FORMULA::ENTRY_ADDUCT::ENTRY_ENTRY_ID | entry2=VAR1::VAR2::VAR3::VAR4|... + my $entry = $hmdb_delta.'::['."$hmdb_name".']::'.$hmdb_cpd_mz.'::'.$hmdb_formula.'::['.$hmdb_adduct.']::'.$hmdb_id ; + + # manage final pipe + if ($index_entries < $nb_entries-1 ) { $cluster_col .= $entry.' | ' ; } + else { $cluster_col .= $entry ; } + + } + $check_rebond = 0 ; ## reinit double control + $index_entries++ ; + } ## end foreach + if ( !defined $cluster_col ) { $cluster_col = 'NONE' ; } + push (@clusters, $cluster_col) ; + push (@hmdb_matrix, \@clusters) ; + $index_mz++ ; + } + return(\@hmdb_matrix) ; +} +## END of SUB + +=head2 METHOD add_lm_matrix_to_input_matrix + + ## Description : build a full matrix (input + lm column) + ## Input : $input_matrix_object, $lm_matrix_object, $nb_header + ## Output : $output_matrix_object + ## Usage : my ( $output_matrix_object ) = add_lm_matrix_to_input_matrix( $input_matrix_object, $lm_matrix_object, $nb_header ) ; + +=cut +## START of SUB +sub add_lm_matrix_to_input_matrix { + ## Retrieve Values + my $self = shift ; + my ( $input_matrix_object, $lm_matrix_object, $nb_header ) = @_ ; + + my @output_matrix_object = () ; + my $index_row = 0 ; + my $line = 0 ; + + foreach my $row ( @{$input_matrix_object} ) { + my @init_row = @{$row} ; + $line++; + + if ( ( defined $nb_header ) and ( $line <= $nb_header) ) { + push (@output_matrix_object, \@init_row) ; + next ; + } + + if ( $lm_matrix_object->[$index_row] ) { + my $dim = scalar(@{$lm_matrix_object->[$index_row]}) ; + + if ($dim > 1) { warn "the add method can't manage more than one column\n" ;} + my $lm_col = $lm_matrix_object->[$index_row][$dim-1] ; + + push (@init_row, $lm_col) ; + $index_row++ ; + } + push (@output_matrix_object, \@init_row) ; + } + return(\@output_matrix_object) ; +} +## END of SUB + +=head2 METHOD write_csv_skel + + ## Description : prepare and write csv output file + ## Input : $csv_file, $rows + ## Output : $csv_file + ## Usage : my ( $csv_file ) = write_csv_skel( $csv_file, $rows ) ; + +=cut +## START of SUB +sub write_csv_skel { + ## Retrieve Values + my $self = shift ; + my ( $csv_file, $rows ) = @_ ; + + my $ocsv = lib::csv::new( {is_binary => 1 , quote_binary => 0, quote_char => undef }) ; + my $csv = $ocsv->get_csv_object("\t") ; + $ocsv->write_csv_from_arrays($csv, $$csv_file, $rows) ; + + return($csv_file) ; +} +## END of SUB + +=head2 METHOD write_csv_one_mass + + ## Description : print a cvs file + ## Input : $masses, $ids, $results, $file + ## Output : N/A + ## Usage : write_csv_one_mass( $ids, $results, $file ) ; + +=cut +## START of SUB +sub write_csv_one_mass { + ## Retrieve Values + my $self = shift ; + my ( $masses, $ids, $results, $file, ) = @_ ; + + open(CSV, '>:utf8', "$file") or die "Cant' create the file $file\n" ; + print CSV "ID\tQuery(Da)\tDelta\tMetabolite_Name\tCpd_MW(Da)\tFormula\tAdduct\tAdduct_MW(Da)\tHMDB_ID\n" ; + + my $i = 0 ; + + foreach my $id (@{$ids}) { + my $mass = undef ; + if ( $masses->[$i] ) { $mass = $masses->[$i] ; } + else { last ; } + + if ( $results->[$i] ) { ## an requested id has a result in the list of hashes $results. + + my @anti_redondant = ('N/A') ; + my $check_rebond = 0 ; + my $check_noentry = 0 ; + + foreach my $entry (@{$results->[$i]}) { + $check_noentry ++ ; + ## dispo anti doublons des entries + foreach my $rebond (@anti_redondant) { + if ( $rebond eq $entry->{ENTRY_ENTRY_ID} ) { $check_rebond = 1 ; last ; } + } +# print "\n-----------------------" ; +# print Dumper $entry->{ENTRY_ENTRY_ID} ; +# print "-------------------------$check_rebond\n" ; +# print Dumper @anti_redondant ; + if ( $check_rebond == 0 ) { + + push ( @anti_redondant, $entry->{ENTRY_ENTRY_ID} ) ; + + print CSV "$id\t$mass\t" ; + + ## print delta + if ( $entry->{ENTRY_DELTA} ) { print CSV "$entry->{ENTRY_DELTA}\t" ; } + else { print CSV "0\t" ; } + + ## print cpd name + if ( $entry->{ENTRY_ENTRY_NAME} ) { print CSV "[$entry->{ENTRY_ENTRY_NAME}]\t" ; } + else { print CSV "UNKNOWN\t" ; } + + ## print cpd mz + if ( $entry->{ENTRY_CPD_MZ} ) { print CSV "$entry->{ENTRY_CPD_MZ}\t" ; } + else { print CSV "N/A\t" ; } + + ## print cpd formula + if ( $entry->{ENTRY_FORMULA} ) { print CSV "$entry->{ENTRY_FORMULA}\t" ; } + else { print CSV "N/A\t" ; } + + ## print adduct + if ( $entry->{ENTRY_ADDUCT} ) { print CSV "[$entry->{ENTRY_ADDUCT}]\t" ; } + else { print CSV "N/A\t" ; } + + ## print adduct mz + if ( $entry->{ENTRY_ADDUCT_MZ} ) { print CSV "$entry->{ENTRY_ADDUCT_MZ}\t" ; } + else { print CSV "N/A\t" ; } + + ## print cpd id + if ( $entry->{ENTRY_ENTRY_ID} ) { print CSV "$entry->{ENTRY_ENTRY_ID}\n" ; } + else { print CSV "N/A\n" ; } + } + $check_rebond = 0 ; ## reinit double control + } ## end foreach + if ($check_noentry == 0 ) { + print CSV "$id\t$mass\t0\tUNKNOWN\tN/A\tN/A\tN/A\tN/A\tN/A\n" ; + } + } + $i++ ; + } + close(CSV) ; + return() ; +} +## END of SUB + +1 ; + + +__END__ + +=head1 SUPPORT + +You can find documentation for this module with the perldoc command. + + perldoc hmdb.pm + +=head1 Exports + +=over 4 + +=item :ALL is ... + +=back + +=head1 AUTHOR + +Franck Giacomoni Efranck.giacomoni@clermont.inra.frE + +=head1 LICENSE + +This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. + +=head1 VERSION + +version 1 : 06 / 06 / 2013 + +version 2 : 27 / 01 / 2014 + +version 3 : 19 / 11 / 2014 + +version 4 : 28 / 01 / 2016 + +version 5 : 02 / 11 /2016 + +=cut diff -r 9583f9772198 -r 6d0a0f8f672a static/images/hmdb.png Binary file static/images/hmdb.png has changed diff -r 9583f9772198 -r 6d0a0f8f672a t/hmdb_managerTest.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/t/hmdb_managerTest.pl Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,134 @@ +#! perl +use diagnostics; +use warnings; +no warnings qw/void/; +use strict; +no strict "refs" ; +use Test::More qw( no_plan ); +use Test::Exception; +use FindBin ; +use Carp ; + +## Specific Modules +use lib $FindBin::Bin ; +my $binPath = $FindBin::Bin ; +use lib::hmdbTest qw( :ALL ) ; + + +## To launch the right sequence : API, MAPPER, THREADER, ... +#my $sequence = 'MAPPER' ; +my $sequence = 'MAIN' ; +my $current_test = 1 ; + +if ($sequence eq "MAIN") { + print "\n\t\t\t\t * * * * * * \n" ; + print "\t * * * - - - Test HMDB Main script - - - * * * \n\n" ; + + + print "\n** Test $current_test extract_sub_mz_lists with an empty list of mzs **\n" ; $current_test++; + + throws_ok{ extract_sub_mz_listsTest([], 3)} '/The provided mzs list is empty/', 'Method \'extract_sub_mz_lists\' detects empty argument and died correctly' ; + + print "\n** Test $current_test extract_sub_mz_lists with a list of mzs and a limit of 3 **\n" ; $current_test++; + is_deeply( extract_sub_mz_listsTest( + ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ], 3), + [ [ '175.01', '238.19', '420.16' ], [ '780.32', '956.25', '1100.45' ] ], + 'Method \'extract_sub_mz_lists\' works with a list and return a well formated list of sublist of mzs'); + + print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; + throws_ok{ prepare_multi_masses_queryTest([])} '/The input method parameter mass list is empty/', 'Method \'prepare_multi_masses_query\' detects empty argument and died correctly' ; + + print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++; + is_deeply( prepare_multi_masses_queryTest( + ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ), + '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', + 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying'); + + print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++; + is_deeply( get_matches_from_hmdb_uaTest( + '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'), + [ + 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', + '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', + '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', + '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', + '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', + '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', + '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', + '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + ], + 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb'); + + print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++; + is_deeply (test_matches_from_hmdb_uaTest (), + \'200', + 'The HMDB server is available: returns successful HTTP requests' ) ; + + print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++; + is_deeply (check_state_from_hmdb_uaTest (\'200'), + 1, + 'The status 200 returns no error/warn' ) ; + + print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; + throws_ok{ check_state_from_hmdb_uaTest(\'504')} + '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/', + 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ; + + print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; + is_deeply ( parse_hmdb_csv_resultsTest ( + [ + 'query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta', + '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', + '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', + '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', + '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', + '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', + '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', + '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' + ], + ['175.01', '238.19', '420.16'] + ), + [ + [ + { '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' }, + { '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' }, + { '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' }, + { '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' }, + { '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' } + ], + [], + [ + { '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' }, + { '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' } + ] + ], + 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; + + print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++; + is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ), + [ [], [], [] ], + 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ; + + print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++; + is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), + [], + 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; +} + + + + + + + + + + + + + + + + + +## END of the script \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a t/lib/hmdbTest.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/t/lib/hmdbTest.pm Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,83 @@ +package lib::hmdbTest ; + +use diagnostics; # this gives you more debugging information +use warnings; # this warns you of bad practices +use strict; # this prevents silly errors +use Exporter ; +use Carp ; + +our $VERSION = "1.0"; +our @ISA = qw(Exporter); +our @EXPORT = qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest); +our %EXPORT_TAGS = ( ALL => [qw( parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] ); + +use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ; +use lib::hmdb qw( :ALL ) ; + +use Data::Dumper ; + +## sub +sub extract_sub_mz_listsTest { + + my ($masses, $hmdb_limits, ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my $submasses = $oHmdb->extract_sub_mz_lists($masses, $hmdb_limits ) ; + + return ($submasses) ; +} + +## sub +sub prepare_multi_masses_queryTest { + + my ($mzs ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; + + return ($hmdb_masses) ; +} + +## sub +sub get_matches_from_hmdb_uaTest { + + my ( $hmdb_masses, $delta, $molecular_species ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; + return ($hmdb_pages) ; +} + + +## sub +sub test_matches_from_hmdb_uaTest { + + my $oHmdb = lib::hmdb->new() ; + my $status = $oHmdb->test_matches_from_hmdb_ua() ; + return ($status) ; +} + + +## sub +sub check_state_from_hmdb_uaTest { + my ($status ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my $res = $oHmdb->check_state_from_hmdb_ua($status) ; + return($res) ; +} + + + +## sub +sub parse_hmdb_csv_resultsTest { + my ($hmdb_pages, $mzs ) = @_ ; + + my $oHmdb = lib::hmdb->new() ; + my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs) ; ## hash format result + + return($result) ; +} + + +1 ; \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/input_test01_fake-mzrt-input-with-id.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_test01_fake-mzrt-input-with-id.tabular Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,7 @@ +id mz rt +1 7.02080998 49.38210915 +2 75.05547146 0.658528069 +3 75.08059797 1743.94267 +4 76.03942694 51.23158899 +5 76.07584477 50.51249853 +6 76.07593168 0.149308136 \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/input_test02_mzrt-input-with-id.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_test02_mzrt-input-with-id.tabular Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,7 @@ +id mz rt +1 7.02080998 49.38210915 +2 75.05547146 0.658528069 +3 75.08059797 1743.94267 +4 76.03942694 51.23158899 +5 76.07584477 50.51249853 +6 76.07593168 0.149308136 \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test01.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test01.html Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,1 @@ +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = neutral / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000275.05547146
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000375.08059797
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000476.03942694
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000576.07584477
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000676.07593168
UNKNOWNNONEn/an/an/an/an/a0n/an/a

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test01.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test01.tabular Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,7 @@ +id mz rt hmdb(delta::name::mz::formula::adduct::id) +1 7.02080998 49.38210915 NONE +2 75.05547146 0.658528069 NONE +3 75.08059797 1743.94267 NONE +4 76.03942694 51.23158899 NONE +5 76.07584477 50.51249853 NONE +6 76.07593168 0.149308136 NONE diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test01.xlsx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test01.xlsx Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,7 @@ +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 UNKNOWN N/A N/A N/A N/A N/A +mz_00003 75.08059797 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00004 76.03942694 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00005 76.07584477 0 UNKNOWN N/A N/A N/A N/A N/A +mz_00006 76.07593168 0 UNKNOWN N/A N/A N/A N/A N/A diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test02.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test02.html Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,1 @@ +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.001

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
UNKNOWNNONEn/an/an/an/an/a0n/an/a
mz_0000275.05547146
N-NitrosodimethylamineHMDB31419C2H6N2O74.048012824M+H+75.0552890.00018246InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3-0.53
AcetylhydrazineHMDB60428C2H6N2O74.048012824M+H+75.0552890.00018246InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)-0.78
CreatineHMDB00064C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)-1.59
Beta-Guanidinopropionic acidHMDB13222C4H9N3O2131.069476547M+H+NH4+75.0552880.00018346InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)-1.70
Nitrogen oxidesHMDB32439H3NO33.021463723M+ACN+H+75.0552870.00018446InChI=1S/H3NO/c1-2/h1H3NA
mz_0000375.08059797
1-ButanolHMDB04327C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H30.84
UNKNOWNHMDB62103C4H10O74.073164942M+H+75.0804410.00015697NANA
2-ButanolHMDB11469C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H30.66
IsobutanolHMDB06006C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H30.60
2-Methylpropan-2-olHMDB31456C4H10O74.073164942M+H+75.0804410.00015697InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H30.70
mz_0000476.03942694
L-Aspartic acidHMDB00191C4H7NO4133.037507717M+H+NH4+76.0393040.00012294InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1-3.52
Ethyl nitriteHMDB31239C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H30.42
GlycineHMDB00123C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)-3.34
Acetohydroxamic AcidHMDB14691C2H5NO275.032028409M+H+76.0393040.00012294InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)-1.46
Iminodiacetic acidHMDB11753C4H7NO4133.037507717M+H+NH4+76.0393040.00012294InChI=1S/C4H7NO4/c6-3(7)1-5-2-4(8)9/h5H,1-2H2,(H,6,7)(H,8,9)-2.50
mz_0000576.07584477
1-Amino-propan-2-olHMDB12136C3H9NO75.068413915M+H+76.075690.00015477InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
Trimethylamine N-oxideHMDB00925C3H9NO75.068413915M+H+76.075690.00015477InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB31652C3H6O58.041864814M+NH4+76.0756880.00015677InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
UNKNOWNHMDB62143C3H6O58.041864813M+NH4+76.0756880.00015677NANA
MethyloxiraneHMDB31558C3H6O58.041864814M+NH4+76.0756880.00015677InChI=1/C3H6O/c1-3-2-4-3/h3H,2H2,1H30.04
mz_0000676.07593168
1-Amino-propan-2-olHMDB12136C3H9NO75.068413915M+H+76.075690.00024168InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
Trimethylamine N-oxideHMDB00925C3H9NO75.068413915M+H+76.075690.00024168InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
Allyl alcoholHMDB31652C3H6O58.041864814M+NH4+76.0756880.00024368InChI=1S/C3H6O/c1-2-3-4/h2,4H,1,3H2-0.03
UNKNOWNHMDB62143C3H6O58.041864813M+NH4+76.0756880.00024368NANA
MethyloxiraneHMDB31558C3H6O58.041864814M+NH4+76.0756880.00024368InChI=1/C3H6O/c1-3-2-4-3/h3H,2H2,1H30.04

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test02.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test02.tabular Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +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 diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test02.xlsx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test02.xlsx Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +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 diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test03.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test03.html Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,1 @@ +Galaxy HMDB queries - All results
Results of HMDB queries - Search params : Molecular specie = positive / delta (mass-to-charge ratio) = 0.05

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct_TypeAdduct MW (Da)DeltaInChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
HydroxidodioxidosulfidosulfateHMDB60293H2O3S2113.94453531M+IsoProp+H+175.0098750.000125InChI=1S/H2O3S2/c1-5(2,3)4/h(H2,1,2,3,4)NA
MesnaHMDB03745C2H6O3S2141.975835438M+CH3OH+H+175.0093240.000676InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)-1.53
Silicic acidHMDB31436H4O4Si95.987885149M+DMSO+H+175.0091050.000895InChI=1S/H4O4Si/c1-5(2,3)4/h1-4HNA
De-O-methylsterigmatocystinHMDB33657C17H10O6310.047738052M+H+K+175.0090860.000914InChI=1/C17H10O6/c18-8-2-1-3-10-13(8)15(20)14-9(19)6-11-12(16(14)22-10)7-4-5-21-17(7)23-11/h1-7,17-19H2.72
Aurantricholide BHMDB35230C17H10O6310.047738052M+H+K+175.0090860.000914InChI=1S/C17H10O6/c18-10-3-1-8(2-4-10)15-16-14(23-17(15)21)6-9-5-11(19)12(20)7-13(9)22-16/h1-7,18-20H3.05
mz_00002238.19
Alpha-TerpineolHMDB04043C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m0/s13.17
(S)-alpha-TerpineolHMDB36086C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-8-4-6-9(7-5-8)10(2,3)11/h4,9,11H,5-7H2,1-3H3/t9-/m1/s13.17
EucalyptolHMDB04472C10H18O154.1357652M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-9(2)8-4-6-10(3,11-9)7-5-8/h8H,4-7H2,1-3H33.36
GeraniolHMDB05812C10H18O154.1357652M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-9(2)5-4-6-10(3)7-8-11/h5,7,11H,4,6,8H2,1-3H3/b10-7-2.89
trans-(-)-p-Menth-1-en-3-olHMDB35861C10H18O154.135765198M+IsoProp+Na+H+238.1908750.000875InChI=1S/C10H18O/c1-7(2)9-5-4-8(3)6-10(9)11/h6-7,9-11H,4-5H2,1-3H3/t9-,10+/m0/s12.64
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB60836C17H17N3O4S359.093976737M+IsoProp+H+420.1593170.000683InChI=1/C17H17N3O4S/c21-13-2-1-7-18-15(13)19-8-9-24-12-5-3-11(4-6-12)10-14-16(22)20-17(23)25-14/h1-7,14,21H,8-10H2,(H,18,19)(H,20,22,23)2.33
N-Desmethyl-p-hydroxyrosiglitazoneHMDB60838C17H17N3O4S359.093976737M+IsoProp+H+420.1593170.000683InChI=1/C17H17N3O4S/c21-12-3-6-15(19-10-12)18-7-8-24-13-4-1-11(2-5-13)9-14-16(22)20-17(23)25-14/h1-6,10,14,21H,7-9H2,(H,18,19)(H,20,22,23)2.31
Benzyl glycinate 4-methylbenzenesulfonate saltHMDB33374C16H19NO5S337.098393413M+2ACN+H+420.1587630.001237InChI=1S/C9H11NO2.C7H8O3S/c10-6-9(11)12-7-8-4-2-1-3-5-8;1-6-2-4-7(5-3-6)11(8,9)10/h1-5H,6-7,10H2;2-5H,1H3,(H,8,9,10)NA
GlutarylglycineHMDB00590C7H11NO5189.0637224672M+ACN+H+420.1612680.001268InChI=1S/C7H11NO5/c9-5(8-4-7(12)13)2-1-3-6(10)11/h1-4H2,(H,8,9)(H,10,11)(H,12,13)-0.82
N-Acetylglutamic acidHMDB01138C7H11NO5189.0637224672M+ACN+H+420.1612680.001268InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)-0.67
mz_00004780.32
Niazicinin AHMDB31947C17H23NO8369.1423667172M+ACN+H+780.3185560.001444InChI=1S/C17H23NO8/c1-9-15(25-10(2)19)13(20)14(21)16(24-9)26-12-6-4-11(5-7-12)8-18-17(22)23-3/h4-7,9,13-16,20-21H,8H2,1-3H3,(H,18,22)0.57
Mulberrofuran THMDB35940C44H44O9716.298533006M+ACN+Na+780.3142980.005702InChI=1/C44H44O9/c1-22(2)6-10-29-34(46)15-13-31(42(29)51)43(52)40-32(28-12-9-27(45)21-36(28)48)16-24(5)17-33(40)41-37(49)18-26(19-38(41)50)39-20-25-8-14-35(47)30(44(25)53-39)11-7-23(3)4/h6-9,12-15,17-21,32-33,40,45-51H,10-11,16H2,1-5H35.95
2'-Hydroxy-3',4',5',7,8-pentamethoxyflavanHMDB33906C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-22-14-9-7-11-6-8-13(27-17(11)18(14)24-3)12-10-15(23-2)19(25-4)20(26-5)16(12)21/h7,9-10,13,21H,6,8H2,1-5H32.58
trans-Grandmarin isovalerateHMDB39032C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-10(2)8-15(22)26-19-17(23)16-13(27-20(19,3)4)9-12(24-5)11-6-7-14(21)25-18(11)16/h6-7,9-10,17,19,23H,8H2,1-5H32.89
(1E,4Z,6a,8b,10a)-8-Angeloyloxy-10,15-dihydroxy-3-oxo-1,4,11(13)-germacratrien-12,6-olideHMDB32731C20H24O7376.1522031222M+3H2O+2H+780.3275260.007526InChI=1/C20H24O7/c1-5-11(2)18(23)27-16-9-20(4,25)7-6-14(22)13(10-21)8-15-17(16)12(3)19(24)26-15/h5-8,15-17,21,25H,3,9-10H2,1-2,4H3/b7-6-,11-5+,13-8-0.83
mz_00005956.25
Pelargonidin 3-O-[b-D-Glucopyranosyl-(1->2)-[4-hydroxy-3-methoxy-(E)-cinnamoyl-(->6)]-b-D-glucopyranoside] 5-O-b-D-glucopyranosideHMDB35451C43H49O23933.266462874M+Na+956.2556810.005681InChI=1/C43H48O23/c1-58-25-10-17(2-8-22(25)48)3-9-30(49)59-16-29-33(52)36(55)40(66-42-38(57)35(54)32(51)28(15-45)64-42)43(65-29)62-26-13-21-23(60-39(26)18-4-6-19(46)7-5-18)11-20(47)12-24(21)61-41-37(56)34(53)31(50)27(14-44)63-41/h2-13,27-29,31-38,40-45,50-57H,14-16H2,1H3,(H2-,46,47,48,49)/p+11.22
PetaninHMDB38095C43H49O23933.266462874M+Na+956.2556810.005681InChI=1/C43H48O23/c1-16-39(66-29(48)8-5-17-3-6-19(45)7-4-17)35(54)38(57)41(60-16)59-15-28-32(51)34(53)37(56)43(65-28)63-26-13-21-23(61-40(26)18-9-22(47)30(49)25(10-18)58-2)11-20(46)12-24(21)62-42-36(55)33(52)31(50)27(14-44)64-42/h3-13,16,27-28,31-39,41-44,50-57H,14-15H2,1-2H3,(H3-,45,46,47,48,49)/p+11.58
Kaempferide 3-rhamnosideHMDB40803C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1/C22H22O10/c1-9-16(25)18(27)19(28)22(30-9)32-21-17(26)15-13(24)7-11(23)8-14(15)31-20(21)10-3-5-12(29-2)6-4-10/h3-9,16,18-19,22-25,27-28H,1-2H31.45
GlycitinHMDB02219C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1S/C22H22O10/c1-29-15-6-12-14(30-9-13(18(12)25)10-2-4-11(24)5-3-10)7-16(15)31-22-21(28)20(27)19(26)17(8-23)32-22/h2-7,9,17,19-24,26-28H,8H2,1H30.83
Calycosin 7-galactosideHMDB38821C22H22O10446.1212969242M+ACN+Na+956.2583590.008359InChI=1/C22H22O10/c1-29-15-5-2-10(6-14(15)24)13-9-30-16-7-11(3-4-12(16)18(13)25)31-22-21(28)20(27)19(26)17(8-23)32-22/h2-7,9,17,19-24,26-28H,8H2,1H30.80
mz_000061100.45
NPCHMDB60499C28H30N4O6518.2165347122M+ACN+Na+1100.4488340.001166InChI=1/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-/s22.40
Cellulose triacetateHMDB32198C30H34Cl2N4O536.2109671442M+3H2O+2H+1100.4450540.004946InChI=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)7.37
Lewis X trisaccharideHMDB06568C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=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/s1-2.26
O-6-deoxy-a-L-galactopyranosyl-(1->2)-O-b-D-galactopyranosyl-(1->3)-2-(acetylamino)-2-deoxy-D-GalactoseHMDB02060C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=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/s1-2.25
Lewis a trisaccharideHMDB06582C20H35NO15529.2006694552M+ACN+H+1100.4351620.014838InChI=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/s1-2.27

Copyright © INRA, N Paulhe, F Giacomoni 2014

\ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test03.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test03.tabular Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +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 diff -r 9583f9772198 -r 6d0a0f8f672a test-data/out_test03.xlsx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test03.xlsx Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +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 diff -r 9583f9772198 -r 6d0a0f8f672a wsdl_hmdb.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wsdl_hmdb.pl Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,287 @@ +#!perl + +## script : wsdl_hmdb.pl +#============================================================================= +# Included modules and versions +#============================================================================= +## Perl modules +use strict ; +use warnings ; +use Carp qw (cluck croak carp) ; + +use Data::Dumper ; +use Getopt::Long ; +use POSIX ; +use FindBin ; ## Permet de localisez le repertoire du script perl d'origine + +## Specific Modules (Home made...) +use lib $FindBin::Bin ; +my $binPath = $FindBin::Bin ; +use lib::hmdb qw( :ALL ) ; +## PFEM Perl Modules +use lib::conf qw( :ALL ) ; +use lib::csv qw( :ALL ) ; + +## Initialized values +my ( $help ) = undef ; +my ( $mass ) = undef ; +my ( $masses_file, $col_id, $col_mass, $header_choice, $nbline_header ) = ( undef, undef, undef, undef, undef ) ; +my $max_query = undef ; +my ( $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef ) ; + + +#============================================================================= +# Manage EXCEPTIONS +#============================================================================= + +&GetOptions ( "h" => \$help, # HELP + "mass:s" => \$mass, ## option : one masse + "masses:s" => \$masses_file, ## option : path to the input + "header_choice:s" => \$header_choice, ## Presence or not of header in tabular file + "nblineheader:i" => \$nbline_header, ## numbre of header line present in file + "colfactor:i" => \$col_mass, ## Column id for retrieve formula list in tabular file + "delta:f" => \$delta, + "mode:s" => \$molecular_species, ## Molecular species (positive/negative/neutral) + "maxquery:i" => \$max_query, ## Maximum query return (default is 20 entries by query // min 1 & max 50 ) + "output_tabular:s" => \$out_tab, ## option : path to the ouput (tabular : input+results ) + "output_html|v:s" => \$out_html, ## option : path to the results view (output2) + "output_xlsx:s" => \$out_xls, ## option : path to the xls-like format output + ) ; + +#============================================================================= +# EXCEPTIONS +#============================================================================= +$help and &help ; + +#============================================================================= +# MAIN SCRIPT +#============================================================================= + + +## -------------- Conf file ------------------------ : +my ( $CONF ) = ( undef ) ; +foreach my $conf ( <$binPath/*.cfg> ) { + my $oConf = lib::conf::new() ; + $CONF = $oConf->as_conf($conf) ; +} + +## -------------- HTML template file ------------------------ : +foreach my $html_template ( <$binPath/*.tmpl> ) { $CONF->{'HTML_TEMPLATE'} = $html_template ; } + +if (!defined $max_query) { + $max_query = $CONF->{'HMDB_MAX_QUERY'} ; +} + + +## --------------- Global parameters ---------------- : +my ( $ids, $masses, $results ) = ( undef, undef, undef ) ; +my ( $complete_rows, $nb_pages_for_html_out ) = ( undef, 1 ) ; +my $metabocard_features = undef ; +my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ; + +## --------------- retrieve input data -------------- : + +## manage only one mass +if ( ( defined $mass ) and ( $mass ne '' ) ) { + my @masses = split(" ", $mass); + $masses = \@masses ; + for (my $i=1 ; $i<=$#masses+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } +} ## END IF +## manage csv file containing list of masses +elsif ( ( defined $masses_file ) and ( $masses_file ne "" ) and ( -e $masses_file ) ) { + ## parse all csv for later : output csv build + my $ocsv_input = lib::csv->new() ; + my $complete_csv = $ocsv_input->get_csv_object( "\t" ) ; + $complete_rows = $ocsv_input->parse_csv_object($complete_csv, \$masses_file) ; + + ## parse masses and set ids + my $ocsv = lib::csv->new() ; + my $csv = $ocsv->get_csv_object( "\t" ) ; + if ( ( !defined $nbline_header ) or ( $nbline_header < 0 ) ) { $nbline_header = 0 ; } + $masses = $ocsv->get_value_from_csv_multi_header( $csv, $masses_file, $col_mass, $header_choice, $nbline_header ) ; ## retrieve mz values on csv + my $nbmz = @$masses ; + for (my $i=1 ; $i<=$nbmz+1 ; $i++){ push (@$ids,"mz_0".sprintf("%04s", $i ) ); } +} +else { + warn "[warning] Input data are missing : none mass or file of masses\n" ; + &help ; +} +#print Dumper $masses ; +## ---------------- launch queries -------------------- : + +if ( ( defined $delta ) and ( $delta > 0 ) and ( defined $molecular_species ) and ( $molecular_species ne '' ) ) { + ## prepare masses list and execute query + my $oHmdb = lib::hmdb::new() ; + my $hmdb_pages = undef ; + my $hmdb_ids = undef ; + + $results = [] ; # prepare arrays ref + my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; + + ## get the hmdb server status by a test query - continuous queries or kill script. + my $status = $oHmdb->test_matches_from_hmdb_ua() ; + $oHmdb->check_state_from_hmdb_ua($status) ; ## can kill the script execution + + foreach my $mzs ( @{$submasses} ) { + + my $result = undef ; + my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; + $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ; + ($result) = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max_query) ; ## hash format result + ## This previous step return results with cutoff on the number of entries returned ! + $results = [ @$results, @$result ] ; + } + + ## foreach metabolite get its own metabocard + $hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ; +# $hmdb_ids->{'HMDB03125'} = 1 , + $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying + + ## Map metabocards with results (add supplementary data) + +# print Dumper $results ; +# print Dumper $hmdb_ids ; +# print Dumper $metabocard_features ; + + if ( ( defined $results ) and ( defined $metabocard_features ) ) { + $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ; + } + + ## Uses N mz and theirs entries per page (see config file). + # how many pages you need with your input mz list? + $nb_pages_for_html_out = ceil( scalar(@{$masses} ) / $CONF->{HTML_ENTRIES_PER_PAGE} ) ; + +# print Dumper $results ; +} +else { + croak "Can't work with HMDB : missing paramaters (list of masses, delta or molecular species)\n" ; +} ## end ELSE + +## -------------- Produce HTML/CSV output ------------------ : + +if ( ( defined $out_html ) and ( defined $results ) ) { + my $oHtml = lib::hmdb::new() ; + my ($tbody_object) = $oHtml->set_html_tbody_object( $nb_pages_for_html_out, $CONF->{HTML_ENTRIES_PER_PAGE} ) ; + ($tbody_object) = $oHtml->add_mz_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $ids) ; + ($tbody_object) = $oHtml->add_entries_to_tbody_object($tbody_object, $CONF->{HTML_ENTRIES_PER_PAGE}, $masses, $results) ; + my $output_html = $oHtml->write_html_skel(\$out_html, $tbody_object, $nb_pages_for_html_out, $search_condition, $CONF->{'HTML_TEMPLATE'}, $CONF->{'JS_GALAXY_PATH'}, $CONF->{'CSS_GALAXY_PATH'}) ; + +} ## END IF +else { + warn "Can't create a HTML output for HMDB : no result found or your output file is not defined\n" ; +} + +if ( ( defined $out_tab ) and ( defined $results ) ) { + # produce a csv based on METLIN format + my $ocsv = lib::hmdb::new() ; + if (defined $masses_file) { + my $lm_matrix = undef ; + if ( ( defined $nbline_header ) and ( $header_choice eq 'yes' ) ) { +# $lm_matrix = $ocsv->set_lm_matrix_object('hmdb', $masses, $results ) ; + $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids('hmdb', $masses, $results ) ; + $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, $nbline_header-1) ; + } + elsif ( ( $header_choice eq 'no' ) ) { +# $lm_matrix = $ocsv->set_lm_matrix_object(undef, $masses, $results ) ; + $lm_matrix = $ocsv->set_hmdb_matrix_object_with_ids(undef, $masses, $results ) ; + $lm_matrix = $ocsv->add_lm_matrix_to_input_matrix($complete_rows, $lm_matrix, 0) ; + } + $ocsv->write_csv_skel(\$out_tab, $lm_matrix) ; + } + elsif (defined $mass) { + $ocsv->write_csv_one_mass($masses, $ids, $results, $out_tab) ; + } +} ## END IF +else { + warn "Can't create a tabular output for HMDB : no result found or your output file is not defined\n" ; +} + +## Write XLS like format +if ( ( defined $out_xls ) and ( defined $results ) ) { + my $ocsv = lib::hmdb::new() ; + $ocsv->write_csv_one_mass($masses, $ids, $results, $out_xls) ; +} + + +#==================================================================================== +# Help subroutine called with -h option +# number of arguments : 0 +# Argument(s) : +# Return : 1 +#==================================================================================== +sub help { + print STDERR " +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 +# Author : Franck Giacomoni and Marion Landi +# Email : fgiacomoni\@clermont.inra.fr +# Version : 1.4 +# Created : 08/07/2012 +# Updated : 21/01/2016 +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] + + or + wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] + -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + + or + wsdl_hmdb.pl -h for help + + "; + exit(1); +} + +## END of script - F Giacomoni + +__END__ + +=head1 NAME + + wsdl_hmdb.pl -- script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. + +=head1 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] + + or + wsdl_hmdb.pl -masses [an input file of mzs] -colfactor [col of mz] -header_choice [yes|no] -nblineheader [nb of lines containing file header : 0-n] + -delta [mz delta] -mode [molecular species: positive|negative|neutral] -output [output tabular file] -view [output html file] + +=head1 SYNOPSIS + +This script manages batch queries on HMDB server. + +=head1 DESCRIPTION + +This main program is a script to query HMDB website using mz and return a list of candidates sent by HMDB based on the ms search tool. + +=over 4 + +=item B + +=item B + +=back + +=head1 AUTHOR + +Franck Giacomoni Efranck.giacomoni@clermont.inra.frE + +=head1 LICENSE + +This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. + +=head1 VERSION + +version 1.0 : 06 / 06 / 2013 + +version 1.2 : 27 / 01 / 2014 + +version 1.3 : 19 / 11 / 2014 + +version 1.4 : 21 / 01 / 2016 - a clean version for community + +=cut \ No newline at end of file diff -r 9583f9772198 -r 6d0a0f8f672a wsdl_hmdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wsdl_hmdb.xml Wed Nov 23 09:31:50 2016 -0500 @@ -0,0 +1,279 @@ + + + search by masses on HMDB online bank + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + input_type['choice'] == "YES" + + + input_type['choice'] == "YES" + + + input_type['choice'] == "YES" + + + input_type['choice'] == "NO" + + + input_type['choice'] == "NO" + + + input_type['choice'] == "NO" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file