Mercurial > repos > fgiacomoni > hmdb_ms_search
view lib/hmdb.pm @ 10:4eb2de7c24d1 draft
Master branch Updating - - Fxx
author | fgiacomoni |
---|---|
date | Mon, 01 Oct 2018 10:36:30 -0400 |
parents | c32280662103 |
children | 625fa968d99a |
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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 >= 700 ) { croak "Your mass list is too long : HMDB allows maximum 700 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 = LWP::UserAgent->new( keep_alive => 10 ); $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(2400) ; 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}) { ## HMDB csv output - [DEPRECATED]... # if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { # my @entry = split(/,/, $line) ; # # if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } # # $features{ENTRY_ENTRY_ID} = $entry[1] ; # $features{ENTRY_FORMULA} = $entry[2] ; # $features{ENTRY_CPD_MZ} = $entry[3] ; # $features{ENTRY_ADDUCT} = $entry[4] ; # $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; # $features{ENTRY_ADDUCT_MZ} = $entry[6] ; # $features{ENTRY_DELTA} = $entry[7] ; # # my %temp = %features ; # # push (@{$result_by_entry{$entry[0]} }, \%temp) ; # } ## NEW HMDB format V4.0 - dec2017 if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) { if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } $features{ENTRY_ENTRY_ID} = $entry[1] ; $features{ENTRY_FORMULA} = $entry[4] ; $features{ENTRY_CPD_MZ} = $entry[5] ; $features{ENTRY_ADDUCT} = $entry[6] ; $features{ENTRY_ADDUCT_TYPE} = $entry[7] ; $features{ENTRY_ADDUCT_MZ} = $entry[8] ; $features{ENTRY_DELTA} = $entry[9] ; my %temp = %features ; push (@{$result_by_entry{$entry[0]} }, \%temp) ; } else { warn "The parsed line ($line) does not match your pattern\n " ; } } else { next ; } } ## 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 =~/<table>/ ) { $catch_table = 1 ; } ## Si il existe un resultat : if($catch_table == 1) { #Id de la molecule, et creation du lien if( $line =~ /<a href=\"\/metabolites\/(\w+)\" (.*)>/ ) { $ID = $1 ; $catch_name = 0 ; next ; } #Nom de la molecule ONLY!! if ( $catch_name == 0 ) { if( $line =~ /<td>(.+)<\/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 E<lt>franck.giacomoni@clermont.inra.frE<gt> =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