# HG changeset patch # User fgiacomoni # Date 1550151412 18000 # Node ID 63ba1cb240b7d21874cbcaac083adf0ec17a7008 # Parent b5a1d5e4368528bbfc57f59a5b1325357e0f8fd5 Prod branch Updating - - Fxx diff -r b5a1d5e43685 -r 63ba1cb240b7 hmdb.tmpl --- a/hmdb.tmpl Wed Jan 23 07:49:34 2019 -0500 +++ b/hmdb.tmpl Thu Feb 14 08:36:52 2019 -0500 @@ -1,1 +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 +Galaxy HMDB queries - All results
Results of HMDB queries -

ID from inputMass (m/z)Metabolite_NameCompound_IDFormulaCompound MW (Da)AdductAdduct typeAdduct MW (Da)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
\ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 lib/hmdb.pm --- a/lib/hmdb.pm Wed Jan 23 07:49:34 2019 -0500 +++ b/lib/hmdb.pm Thu Feb 14 08:36:52 2019 -0500 @@ -144,6 +144,45 @@ } ## END of SUB + +=head2 METHOD prepareAdductListFormat + + ## Description : prepare a adduct list well formatted for https queries + ## Input : $adductString + ## Output : $formattedAdductString + ## Usage : my ( $formattedAdductString ) = prepareAdductListFormat ( $adductString ) ; + +=cut +## START of SUB +sub prepareAdductListFormat { + ## Retrieve Values + my $self = shift ; + my ( $adductString ) = @_; + my ( $formattedAdductString, $nbAdducts ) = ( undef, 0 ) ; + + ## Formatting is converting [+] in %2B, [-] as - and [,] in converted space as 'M%2BH%202M%2BH' for 'M+H,2M+2H' +# print "\t$adductString ..." ; + + if (defined $adductString) { + + ## counting selected adducts + $nbAdducts = scalar( my @adducts = ( split (/,/, $adductString) ) ) ; + + ## Converting string into http post format + $adductString =~ s/\+/%2B/g ; + $adductString =~ s/,/%20/g ; + $formattedAdductString = $adductString ; + } + else { + warn "\t[WARN]the adduct type is not defined...It will set to 'Unknown'\n" ; + } + +# print "->$formattedAdductString\n" ; + + return ($formattedAdductString, $nbAdducts) ; +} +### END of SUB + =head2 METHOD test_matches_from_hmdb_ua DEPRECATED ## Description : [DEPRECATED]test a single query with tests parameters on hmdb - get the status of the complete server infra. @@ -232,10 +271,10 @@ print "\tTesting HMDB server connexion ($top time(s) )...\n" ; $mech->post( "http://specdb.wishartlab.com/ms/search.csv", - Content => 'utf8=TRUE&mode=positive&query_masses=420.159317&tolerance=0.000001&database=HMDB&commit=Download Results As CSV' + Content => 'utf8=TRUE&mode=positive&adduct_type=M%2BH%202M%2BH&query_masses=125.0089&tolerance=0.001&database=HMDB&commit=Download Results As CSV' ); - # print Dumper $mech ; +# print Dumper $mech ; $statusPostLine = $mech->status() ; } else { @@ -243,7 +282,6 @@ } $top++ ; }## End While - return (\$statusPostLine) ; } ## END of SUB @@ -278,7 +316,10 @@ croak "Internal Server Error $$status..." ; } } - if ( $$status == 200 ) { print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ; } + if ( $$status == 200 ) { + print "\tThe HMDB server returns that your request (connexion test) was fulfilled\n" ; + print "\tAll searches should be sent successfully to HMDB...(Set verbose to \"High\" for more information!)\n" ; + } } return (1) ; @@ -342,7 +383,7 @@ =head2 METHOD getMatchesFromHmdbWithUA ## Description : HMDB querying via an user agent with parameters : mz, delta and molecular species (neutral, pos, neg) - ## Input : $mass, $delta, $mode + ## Input : $mass, $delta, $mode, adducts ## Output : $results ## Usage : my ( $results ) = getMatchesFromHmdbWithUA( $mass, $delta, $mode ) ; @@ -351,7 +392,7 @@ sub getMatchesFromHmdbWithUA { ## Retrieve Values my $self = shift ; - my ( $masses, $delta, $mode ) = @_ ; + my ( $masses, $delta, $mode, $adducts ) = @_ ; my @page = () ; @@ -381,11 +422,17 @@ $mech->add_header('Referer', 'http://www.hmdb.ca/spectra/ms/search'); $mech->add_header('Accept', 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'); } + ## adduct format is adduct_type=M%2BH%202M%2BH + if ( (!defined $adducts) or ( $adducts eq '') ) { + $adducts = 'Unknown' ; + } + my $res = $mech->post( "http://specdb.wishartlab.com/ms/search.csv", Content => 'utf8=TRUE&mode=' - .$mode.'&query_masses=' + .$mode.'&adduct_type=' + .$adducts.'&query_masses=' .$masses.'&tolerance=' .$delta.'&database=HMDB&commit=Download Results As CSV' ); @@ -473,7 +520,7 @@ foreach (@{$masses}) { if ($result_by_entry{$_}) { - ## cut all entries > $max_query + ## cut all entries > $max_query - all entries were already sorted...by hmdb my @temp_entries = @{$result_by_entry{$_}} ; my @temp_cut = () ; my $current_query = 0 ; @@ -487,12 +534,10 @@ } } push (@results, \@temp_cut) ; -# push (@results, $result_by_entry{$_}) ; } - else {push (@results, [] ) ;} ; + else { push (@results, [] ) ; } ; } - return(\@results) ; } ## END of SUB @@ -581,7 +626,7 @@ ## Description : get all unik ids from the hmdb result object ## Input : $results - ## Output : $ids + ## Output : $ids, $idsNumber ## Usage : my ( $ids ) = get_unik_ids_from_results ( $results ) ; =cut @@ -601,8 +646,8 @@ } } } - - return (\%ids) ; + my $idsNumber = keys %ids ; + return (\%ids, $idsNumber) ; } ### END of SUB @@ -636,8 +681,7 @@ if( (defined $ids) and ($ids > 0 ) ) { foreach my $id (keys %{$ids}) { - -# print "\n============== > $id **********************\n " ; + print "$id...\n" ; my $twig = undef ; if (defined $hmdb_url) { @@ -647,20 +691,21 @@ my $response = head($query) ; if (!defined $response) { + $metabocard_features{$id}{'STATUS'} = 'NOT_EXISTING' ; $metabocard_features{$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) { + } ## IF error + elsif ( $response->is_success ) { $twig = XML::Twig->nparse_ppe( twig_handlers => { # metabolite name - 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; } , + 'metabolite/name' => sub { $metabocard_features{$id}{'metabolite_name'} = $_ -> text_only ; $metabocard_features{$id}{'STATUS'} = 'EXISTING' ; } , # metabolite inchi - 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; } , + 'metabolite/inchi' => sub { $metabocard_features{$id}{'metabolite_inchi'} = $_ -> text_only ; $metabocard_features{$id}{'STATUS'} = 'EXISTING' ;} , ## metabolite logP 'metabolite/predicted_properties/property' => sub { @@ -675,6 +720,7 @@ if (defined $source ) { if ( ( $kind eq 'logp' ) and ( $source eq 'ALOGPS' ) ) { $metabocard_features{$id}{'metabolite_logp'} = $value ; + $metabocard_features{$id}{'STATUS'} = 'EXISTING' ; } ($kind, $source, $value ) = ( undef, undef, undef ) ; } @@ -689,20 +735,20 @@ # $twig->print; $twig->purge ; - if (!$@) { - - } - else { - warn $@ ; - } - } - } +# if (!$@) { +# +# } +# else { +# warn $@ ; +# } + } ## ELSIF success + } # END if defined URL else { - warn "The hmdb metabocard url is not defined\n" ; + warn "\tThe hmdb metabocard url is not defined\n" ; last; } } - } + } ## End IF defined ids else { warn "The HMDB ids list from HMDB is empty - No metabocard found\n" ; } @@ -715,7 +761,7 @@ =head2 METHOD map_suppl_data_on_hmdb_results - ## Description : map supplementary data with already collected results with hmdb search + ## Description : map supplementary data with already collected results with hmdb search - delete the entry if hmdb card doesn't exist... ## Input : $results, $features ## Output : $results ## Usage : my ( $results ) = map_suppl_data_on_hmdb_results ( $results, $features ) ; @@ -726,52 +772,64 @@ ## Retrieve Values my $self = shift ; my ( $results, $features ) = @_; - my ( @more_results ) = ( () ) ; + my ( @moreResults ) = ( () ) ; - @more_results = @{$results} ; ## Dump array ref to map - - foreach my $result (@more_results) { + foreach my $result (@{$results}) { + + my @newResult = () ; - foreach my $entries (@{$result}) { + foreach my $entry (@{$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->{"$current_id"}) { + if ( ($entry->{'ENTRY_ENTRY_ID'}) and ($entry->{'ENTRY_ENTRY_ID'} ne '' ) ) { + + my $current_id = $entry->{'ENTRY_ENTRY_ID'} ; + my $newCompletedEntry = $entry ; + + ## If the id exists in feature hash and its status is not NOT_EXISTING + if ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'EXISTING' ) ) { + ## Metabolite NAME if (defined $features->{"$current_id"}{'metabolite_name'} ) { - $entries->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'} + $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = $features->{"$current_id"}{'metabolite_name'} } else { - $entries->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ; + $newCompletedEntry->{'ENTRY_ENTRY_NAME'} = 'UNKNOWN' ; } ## Metabolite INCHI if (defined $features->{"$current_id"}{'metabolite_inchi'} ) { - $entries->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'} + $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = $features->{"$current_id"}{'metabolite_inchi'} } else { - $entries->{'ENTRY_ENTRY_INCHI'} = 'NA' ; + $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NA' ; } ## Metabolite LOGP if (defined $features->{"$current_id"}{'metabolite_logp'} ) { - $entries->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'} + $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = $features->{"$current_id"}{'metabolite_logp'} } else { - $entries->{'ENTRY_ENTRY_LOGP'} = 'NA' ; + $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NA' ; } + push (@newResult, $newCompletedEntry) ; } + elsif ( ($features->{"$current_id"} ) and ( $features->{"$current_id"}{STATUS} eq 'NOT_EXISTING' ) ) { + $newCompletedEntry = undef ; + next ; + + } + ## In cas no features are given else { -# if ($features) { -# warn "This HMDB id doesn't match any collected ids\n" ; -# } - $entries->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ; - $entries->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ; + $newCompletedEntry->{'ENTRY_ENTRY_INCHI'} = 'NONEDATA' ; + $newCompletedEntry->{'ENTRY_ENTRY_LOGP'} = 'NONEDATA' ; + push (@newResult, $newCompletedEntry) ; } } - } - } + } ## END FOREACH ENTRIES + + push (@moreResults, \@newResult) ; + + } ## END FOREACH RESULT - return (\@more_results) ; + return (\@moreResults) ; } ### END of SUB diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test01.html --- a/test-data/out_test01.html Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test01.html Thu Feb 14 08:36:52 2019 -0500 @@ -1,1 +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
\ No newline at end of file +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)Delta (ppm)InChI 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
\ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.html --- a/test-data/out_test02.html Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test02.html Thu Feb 14 08:36:52 2019 -0500 @@ -1,1 +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
BerylliumHMDB0002387Be9.012182135M+NH4-H2O+7.0203368InChI=1S/Be/q+2NA
mz_0000275.05547146
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c1-4(2)3-5/h1-2H3-0.53
AcetylhydrazineHMDB0060428C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c1-2(5)4-3/h3H2,1H3,(H,4,5)-0.78
glycinamideHMDB0062472C2H6N2O74.048012824M+H+75.0552892InChI=1S/C2H6N2O/c3-1-2(4)5/h1,3H2,(H2,4,5)-2.49
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)-1.59
Beta-Guanidinopropionic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882InChI=1S/C4H9N3O2/c5-4(6)7-2-1-3(8)9/h1-2H2,(H,8,9)(H4,5,6,7)-1.70
mz_0000375.08059797
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)NA
UNKNOWNHMDB0155221H4O7P2177.943225506M+H+2Na+75.0805990NANA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-2-3-4-5/h5H,2-4H2,1H30.84
2-Methylpropan-2-olHMDB0031456C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-4(2,3)5/h5H,1-3H30.70
IsobutanolHMDB0006006C4H10O74.073164942M+H+75.0804412InChI=1S/C4H10O/c1-4(2)3-5/h4-5H,3H2,1-2H30.60
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042InChI=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
UNKNOWNHMDB0161401C2H4NO274.024751953M+H+76.0393042NANA
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H30.42
1-deoxy-1-(N6-lysino)-D-fructoseHMDB0062186C4H7NO4133.037507709M+H+NH4+76.0393042InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)-3.52
N-acetyl-seryl-aspartateHMDB0062501C4H7NO4133.037507709M+H+NH4+76.0393042InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)-3.52
mz_0000576.07584477
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2-1.01
2-(methylamino)ethan-1-olHMDB0142449C3H9NO75.068413914M+H+76.075692InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3-1.05
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
UNKNOWNHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756892NANA
mz_0000676.07593168
3-aminopropan-1-olHMDB0140038C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c4-2-1-3-5/h5H,1-4H2-1.01
2-(methylamino)ethan-1-olHMDB0142449C3H9NO75.068413914M+H+76.075693InChI=1S/C3H9NO/c1-4-2-3-5/h4-5H,2-3H2,1H3-1.05
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3-2.01
1-Amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3-1.03
UNKNOWNHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756893NANA
\ No newline at end of file +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)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_000017.02080998
Beryllium(2+)HMDB0002387Be9.012182135M+NH4-H2O+7.0203368NONEDATANONEDATA
mz_0000275.05547146
N-NitrosodimethylamineHMDB0031419C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
AcetohydrazideHMDB0060428C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
GlycinamidHMDB0062472C2H6N2O74.048012824M+H+75.0552892NONEDATANONEDATA
CreatineHMDB0000064C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
3-Guanidinopropanoic acidHMDB0013222C4H9N3O2131.069476547M+H+NH4+75.0552882NONEDATANONEDATA
mz_0000375.08059797
PyrophosphateHMDB0000250H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
PyrophosphateHMDB0155221H4O7P2177.943225506M+H+2Na+75.0805990NONEDATANONEDATA
1-ButanolHMDB0004327C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
Tert-butanolHMDB0031456C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
IsobutanolHMDB0006006C4H10O74.073164942M+H+75.0804412NONEDATANONEDATA
mz_0000476.03942694
L-Aspartic acidHMDB0000191C4H7NO4133.037507717M+H+NH4+76.0393042NONEDATANONEDATA
GlycinateHMDB0161401C2H4NO274.024751953M+H+76.0393042NONEDATANONEDATA
Ethyl nitriteHMDB0031239C2H5NO275.032028409M+H+76.0393042NONEDATANONEDATA
Aspartic acidHMDB0062186C4H7NO4133.037507709M+H+NH4+76.0393042NONEDATANONEDATA
Aspartic acidHMDB0062501C4H7NO4133.037507709M+H+NH4+76.0393042NONEDATANONEDATA
mz_0000576.07584477
PropanolamineHMDB0140038C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
N-MethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075692NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
1-amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075692NONEDATANONEDATA
2-[ethyl(1-hydroxyethyl)amino]ethan-1-olHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756892NONEDATANONEDATA
mz_0000676.07593168
PropanolamineHMDB0140038C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
N-MethylethanolamineHMDB0142449C3H9NO75.068413914M+H+76.075693NONEDATANONEDATA
Trimethylamine N-oxideHMDB0000925C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
1-amino-propan-2-olHMDB0012136C3H9NO75.068413915M+H+76.075693NONEDATANONEDATA
2-[ethyl(1-hydroxyethyl)amino]ethan-1-olHMDB0168716C6H15NO2133.110278727M+H+NH4+76.0756893NONEDATANONEDATA
\ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.tabular --- a/test-data/out_test02.tabular Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test02.tabular Thu Feb 14 08:36:52 2019 -0500 @@ -1,7 +1,7 @@ id mz rt hmdb(delta::name::mz::formula::adduct::id) -1 7.02080998 49.38210915 68::[Beryllium]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 -2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetylhydrazine]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[glycinamide]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[Beta-Guanidinopropionic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222" -3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[UNKNOWN]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[2-Methylpropan-2-ol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006" -4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[UNKNOWN]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[1-deoxy-1-(N6-lysino)-D-fructose]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[N-acetyl-seryl-aspartate]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501" -5 76.07584477 50.51249853 "2::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" -6 76.07593168 0.149308136 "3::[3-aminopropan-1-ol]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[2-(methylamino)ethan-1-ol]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-Amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[UNKNOWN]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" +1 7.02080998 49.38210915 68::[Beryllium(2+)]::9.012182135::Be::[M+NH4-H2O]::HMDB0002387 +2 75.05547146 0.658528069 "2::[N-Nitrosodimethylamine]::74.048012824::C2H6N2O::[M+H]::HMDB0031419 | 2::[Acetohydrazide]::74.048012824::C2H6N2O::[M+H]::HMDB0060428 | 2::[Glycinamid]::74.048012824::C2H6N2O::[M+H]::HMDB0062472 | 2::[Creatine]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0000064 | 2::[3-Guanidinopropanoic acid]::131.069476547::C4H9N3O2::[M+H+NH4]::HMDB0013222" +3 75.08059797 1743.94267 "0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0000250 | 0::[Pyrophosphate]::177.943225506::H4O7P2::[M+H+2Na]::HMDB0155221 | 2::[1-Butanol]::74.073164942::C4H10O::[M+H]::HMDB0004327 | 2::[Tert-butanol]::74.073164942::C4H10O::[M+H]::HMDB0031456 | 2::[Isobutanol]::74.073164942::C4H10O::[M+H]::HMDB0006006" +4 76.03942694 51.23158899 "2::[L-Aspartic acid]::133.037507717::C4H7NO4::[M+H+NH4]::HMDB0000191 | 2::[Glycinate]::74.024751953::C2H4NO2::[M+H]::HMDB0161401 | 2::[Ethyl nitrite]::75.032028409::C2H5NO2::[M+H]::HMDB0031239 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062186 | 2::[Aspartic acid]::133.037507709::C4H7NO4::[M+H+NH4]::HMDB0062501" +5 76.07584477 50.51249853 "2::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 2::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 2::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 2::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 2::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" +6 76.07593168 0.149308136 "3::[Propanolamine]::75.068413915::C3H9NO::[M+H]::HMDB0140038 | 3::[N-Methylethanolamine]::75.068413914::C3H9NO::[M+H]::HMDB0142449 | 3::[Trimethylamine N-oxide]::75.068413915::C3H9NO::[M+H]::HMDB0000925 | 3::[1-amino-propan-2-ol]::75.068413915::C3H9NO::[M+H]::HMDB0012136 | 3::[2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol]::133.110278727::C6H15NO2::[M+H+NH4]::HMDB0168716" diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test02.txt --- a/test-data/out_test02.txt Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test02.txt Thu Feb 14 08:36:52 2019 -0500 @@ -1,27 +1,27 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 7.02080998 68 [Beryllium] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 +mz_00001 7.02080998 68 [Beryllium(2+)] 9.012182135 Be [M+NH4-H2O] 7.02033 HMDB0002387 mz_00002 75.05547146 2 [N-Nitrosodimethylamine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0031419 -mz_00002 75.05547146 2 [Acetylhydrazine] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 -mz_00002 75.05547146 2 [glycinamide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 +mz_00002 75.05547146 2 [Acetohydrazide] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0060428 +mz_00002 75.05547146 2 [Glycinamid] 74.048012824 C2H6N2O [M+H] 75.055289 HMDB0062472 mz_00002 75.05547146 2 [Creatine] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0000064 -mz_00002 75.05547146 2 [Beta-Guanidinopropionic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 +mz_00002 75.05547146 2 [3-Guanidinopropanoic acid] 131.069476547 C4H9N3O2 [M+H+NH4] 75.055288 HMDB0013222 mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0000250 -mz_00003 75.08059797 0 [UNKNOWN] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221 +mz_00003 75.08059797 0 [Pyrophosphate] 177.943225506 H4O7P2 [M+H+2Na] 75.080599 HMDB0155221 mz_00003 75.08059797 2 [1-Butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0004327 -mz_00003 75.08059797 2 [2-Methylpropan-2-ol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456 +mz_00003 75.08059797 2 [Tert-butanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0031456 mz_00003 75.08059797 2 [Isobutanol] 74.073164942 C4H10O [M+H] 75.080441 HMDB0006006 mz_00004 76.03942694 2 [L-Aspartic acid] 133.037507717 C4H7NO4 [M+H+NH4] 76.039304 HMDB0000191 -mz_00004 76.03942694 2 [UNKNOWN] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401 +mz_00004 76.03942694 2 [Glycinate] 74.024751953 C2H4NO2 [M+H] 76.039304 HMDB0161401 mz_00004 76.03942694 2 [Ethyl nitrite] 75.032028409 C2H5NO2 [M+H] 76.039304 HMDB0031239 -mz_00004 76.03942694 2 [1-deoxy-1-(N6-lysino)-D-fructose] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186 -mz_00004 76.03942694 2 [N-acetyl-seryl-aspartate] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501 -mz_00005 76.07584477 2 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00005 76.07584477 2 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062186 +mz_00004 76.03942694 2 [Aspartic acid] 133.037507709 C4H7NO4 [M+H+NH4] 76.039304 HMDB0062501 +mz_00005 76.07584477 2 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00005 76.07584477 2 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 mz_00005 76.07584477 2 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00005 76.07584477 2 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00005 76.07584477 2 [UNKNOWN] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 -mz_00006 76.07593168 3 [3-aminopropan-1-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 -mz_00006 76.07593168 3 [2-(methylamino)ethan-1-ol] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 +mz_00005 76.07584477 2 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00005 76.07584477 2 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 +mz_00006 76.07593168 3 [Propanolamine] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0140038 +mz_00006 76.07593168 3 [N-Methylethanolamine] 75.068413914 C3H9NO [M+H] 76.07569 HMDB0142449 mz_00006 76.07593168 3 [Trimethylamine N-oxide] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0000925 -mz_00006 76.07593168 3 [1-Amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 -mz_00006 76.07593168 3 [UNKNOWN] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 +mz_00006 76.07593168 3 [1-amino-propan-2-ol] 75.068413915 C3H9NO [M+H] 76.07569 HMDB0012136 +mz_00006 76.07593168 3 [2-[ethyl(1-hydroxyethyl)amino]ethan-1-ol] 133.110278727 C6H15NO2 [M+H+NH4] 76.075689 HMDB0168716 diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.html --- a/test-data/out_test03.html Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test03.html Thu Feb 14 08:36:52 2019 -0500 @@ -1,1 +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
UNKNOWNHMDB0149376C19H16O14S500.026076369M+2H+Na+175.0099490NANA
UNKNOWNHMDB0149375C19H16O14S500.026076369M+2H+Na+175.0099490NANA
UNKNOWNHMDB0149391C19H16O14S500.026076369M+2H+Na+175.0099490NANA
UNKNOWNHMDB0149392C19H16O14S500.026076369M+2H+Na+175.0099490NANA
UNKNOWNHMDB0149418C19H16O14S500.026076369M+2H+Na+175.0099490NANA
mz_00002238.19
UNKNOWNHMDB0163116C10H18O154.1357652M+IsoProp+Na+H+238.1908754NANA
UNKNOWNHMDB0187564C10H18O154.1357652M+IsoProp+Na+H+238.1908754NANA
Alpha-TerpineolHMDB0004043C10H18O154.135765198M+IsoProp+Na+H+238.1908754InChI=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-TerpineolHMDB0036086C10H18O154.135765198M+IsoProp+Na+H+238.1908754InChI=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
EucalyptolHMDB0004472C10H18O154.1357652M+IsoProp+Na+H+238.1908754InChI=1S/C10H18O/c1-9(2)8-4-6-10(3,11-9)7-5-8/h8H,4-7H2,1-3H33.36
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB0060836C17H17N3O4S359.093976737M+IsoProp+H+420.1593172InChI=1S/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-hydroxyrosiglitazoneHMDB0060838C17H17N3O4S359.093976737M+IsoProp+H+420.1593172InChI=1S/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
UNKNOWNHMDB0160148C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NANA
UNKNOWNHMDB0160149C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NANA
UNKNOWNHMDB0165020C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NANA
mz_00004780.32
UNKNOWNHMDB0162081C17H23NO8369.1423667052M+ACN+H+780.3185562NANA
Niazicinin AHMDB0031947C17H23NO8369.1423667172M+ACN+H+780.3185562InChI=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
UNKNOWNHMDB0162078C17H23NO8369.1423667052M+ACN+H+780.3185562NANA
UNKNOWNHMDB0162083C17H23NO8369.1423667052M+ACN+H+780.3185562NANA
UNKNOWNHMDB0150342C33H44O16696.262935337M+IsoProp+Na+H+780.3180453NANA
mz_00005956.25
PREHMDB0041300C44H44O24956.222252336M+NH4-H2O+956.2449525InChI=1S/C44H44O24/c45-13-21-28(51)32(55)34(57)40(67-21)43(65)36(59)23(19(49)11-5-15-1-7-17(47)8-2-15)30(53)26(38(43)61)25(42(63)64)27-31(54)24(20(50)12-6-16-3-9-18(48)10-4-16)37(60)44(66,39(27)62)41-35(58)33(56)29(52)22(14-46)68-41/h1-12,21-22,25,28-29,32-35,40-41,45-48,51-53,55-58,60-62,65-66H,13-14H2,(H,63,64)/b11-5-,12-6--0.41
UNKNOWNHMDB0168193C25H20O9464.1107322242M+2H+3H2O+956.2445846NANA
UNKNOWNHMDB0168231C25H20O9464.1107322242M+2H+3H2O+956.2445846NANA
UNKNOWNHMDB0138858C25H20O9464.1107322242M+2H+3H2O+956.2445846NANA
UNKNOWNHMDB0168237C25H20O9464.1107322242M+2H+3H2O+956.2445846NANA
mz_000061100.45
NPCHMDB0060499C28H30N4O6518.2165347122M+ACN+Na+1100.4488341InChI=1S/C28H30N4O6/c1-3-17-18-11-16(38-27(35)31-9-7-15(29)8-10-31)5-6-22(18)30-24-19(17)13-32-23(24)12-21-20(25(32)33)14-37-26(34)28(21,36)4-2/h5-6,11-12,15,36H,3-4,7-10,13-14,29H2,1-2H3/t28-/m0/s12.40
UNKNOWNHMDB0158990C24H38O10S518.2185685982M+ACN+Na+1100.4529023NANA
UNKNOWNHMDB0158993C24H38O10S518.2185685982M+ACN+Na+1100.4529023NANA
UNKNOWNHMDB0157972C24H38O10S518.2185685982M+ACN+Na+1100.4529023NANA
UNKNOWNHMDB0158992C24H38O10S518.2185685982M+ACN+Na+1100.4529023NANA
\ No newline at end of file +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)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"HMDB0149376C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"HMDB0149375C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"HMDB0149391C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"HMDB0149392C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"HMDB0149418C19H16O14S500.026076369M+2H+Na+175.0099490NONEDATANONEDATA
mz_00002238.19
"(4Z,7Z)-Deca-4,7-dien-1-ol"HMDB0163116C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
CTK8I1689HMDB0187564C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
(S)-alpha-TerpineolHMDB0004043C10H18O154.135765198M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
(S)-alpha-TerpineolHMDB0036086C10H18O154.135765198M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
EucalyptolHMDB0004472C10H18O154.1357652M+IsoProp+Na+H+238.1908754NONEDATANONEDATA
mz_00003420.16
N-Desmethyl-O-hydroxy rosiglitazoneHMDB0060836C17H17N3O4S359.093976737M+IsoProp+H+420.1593172NONEDATANONEDATA
N-Desmethyl-p-hydroxyrosiglitazoneHMDB0060838C17H17N3O4S359.093976737M+IsoProp+H+420.1593172NONEDATANONEDATA
"6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0160148C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
"6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0160149C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
"6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0165020C13H20O10336.105646844M+IsoProp+Na+H+420.1607572NONEDATANONEDATA
mz_00004780.32
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"HMDB0162081C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"HMDB0031947C17H23NO8369.1423667172M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"HMDB0162078C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"HMDB0162083C17H23NO8369.1423667052M+ACN+H+780.3185562NONEDATANONEDATA
"3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"HMDB0150342C33H44O16696.262935337M+IsoProp+Na+H+780.3180453NONEDATANONEDATA
mz_00005956.25
"2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"HMDB0041300C44H44O24956.222252336M+NH4-H2O+956.2449525NONEDATANONEDATA
"3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"HMDB0168193C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0168231C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"HMDB0138858C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
"6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"HMDB0168237C25H20O9464.1107322242M+2H+3H2O+956.2445846NONEDATANONEDATA
mz_000061100.45
NpcHMDB0060499C28H30N4O6518.2165347122M+ACN+Na+1100.4488341NONEDATANONEDATA
"4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158990C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158993C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0157972C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
"4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"HMDB0158992C24H38O10S518.2185685982M+ACN+Na+1100.4529023NONEDATANONEDATA
\ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.tabular --- a/test-data/out_test03.tabular Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test03.tabular Thu Feb 14 08:36:52 2019 -0500 @@ -1,31 +1,31 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 -mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 -mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 -mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 +mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 +mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 +mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 +mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 +mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 +mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 +mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 +mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 -mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 -mz_00004 780.32 3 [UNKNOWN] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 -mz_00005 956.25 5 [PRE] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 -mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 +mz_00003 420.16 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 +mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 +mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 +mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 +mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 +mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 +mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 +mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 +mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 +mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 +mz_00006 1100.45 1 [Npc] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 +mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test03.txt --- a/test-data/out_test03.txt Wed Jan 23 07:49:34 2019 -0500 +++ b/test-data/out_test03.txt Thu Feb 14 08:36:52 2019 -0500 @@ -1,31 +1,31 @@ ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 -mz_00001 175.01 0 [UNKNOWN] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 -mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 -mz_00002 238.19 4 [UNKNOWN] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 -mz_00002 238.19 4 [Alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 +mz_00001 175.01 0 ["2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149376 +mz_00001 175.01 0 ["2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149375 +mz_00001 175.01 0 ["2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149391 +mz_00001 175.01 0 ["2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149392 +mz_00001 175.01 0 ["2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid"] 500.026076369 C19H16O14S [M+2H+Na] 175.009949 HMDB0149418 +mz_00002 238.19 4 ["(4Z,7Z)-Deca-4,7-dien-1-ol"] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0163116 +mz_00002 238.19 4 [CTK8I1689] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0187564 +mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004043 mz_00002 238.19 4 [(S)-alpha-Terpineol] 154.135765198 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0036086 mz_00002 238.19 4 [Eucalyptol] 154.1357652 C10H18O [M+IsoProp+Na+H] 238.190875 HMDB0004472 mz_00003 420.16 2 [N-Desmethyl-O-hydroxy rosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060836 mz_00003 420.16 2 [N-Desmethyl-p-hydroxyrosiglitazone] 359.093976737 C17H17N3O4S [M+IsoProp+H] 420.159317 HMDB0060838 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 -mz_00003 420.16 2 [UNKNOWN] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 -mz_00004 780.32 2 [Niazicinin A] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 -mz_00004 780.32 2 [UNKNOWN] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 -mz_00004 780.32 3 [UNKNOWN] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 -mz_00005 956.25 5 [PRE] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 -mz_00005 956.25 6 [UNKNOWN] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 -mz_00006 1100.45 1 [NPC] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 -mz_00006 1100.45 3 [UNKNOWN] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 +mz_00003 420.16 2 ["6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160148 +mz_00003 420.16 2 ["6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0160149 +mz_00003 420.16 2 ["6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid"] 336.105646844 C13H20O10 [M+IsoProp+Na+H] 420.160757 HMDB0165020 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-5-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162081 +mz_00004 780.32 2 ["N-[(4-{[5-(acetyloxy)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}phenyl)methyl]methoxycarboximidic acid"] 369.142366717 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0031947 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-7-methyl-5H,6H,7H-cyclopenta[c]pyridin-7-yl]oxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162078 +mz_00004 780.32 2 ["3,4,5-trihydroxy-6-{[4-(methoxymethyl)-5H,6H,7H-cyclopenta[c]pyridin-7-yl]methoxy}oxane-2-carboxylic acid"] 369.142366705 C17H23NO8 [2M+ACN+H] 780.318556 HMDB0162083 +mz_00004 780.32 3 ["3,4,5-trihydroxy-6-[(9-hydroxy-16,17-dimethoxy-15-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tricyclo[12.3.1.1²,⁶]nonadeca-1(17),2,4,6(19),14(18),15-hexaen-3-yl)oxy]oxane-2-carboxylic acid"] 696.262935337 C33H44O16 [M+IsoProp+Na+H] 780.318045 HMDB0150342 +mz_00005 956.25 5 ["2-{2,3,6-trihydroxy-5-[(2Z)-3-(4-hydroxyphenyl)prop-2-enoyl]-4-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,5-dien-1-yl}-2-{2,3,4-trihydroxy-5-[3-(4-hydroxyphenyl)prop-2-enoyl]-6-oxo-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]cyclohexa-1,4-dien-1-yl}acetic acid"] 956.222252336 C44H44O24 [M+NH4-H2O] 956.244952 HMDB0041300 +mz_00005 956.25 6 ["3,4,5-trihydroxy-6-[2-(2-hydroxy-1-oxo-1H-phenalen-9-yl)phenoxy]oxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168193 +mz_00005 956.25 6 ["6-[4-(2,3-dioxo-2,3-dihydro-1H-phenalen-4-yl)phenoxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168231 +mz_00005 956.25 6 ["5-(5,7-dihydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-2-yl)-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-2,3-dihydro-1-benzofuran-3-carbaldehyde"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0138858 +mz_00005 956.25 6 ["6-[(2,3-dioxo-4-phenyl-2,3-dihydro-1H-phenalen-1-yl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid"] 464.110732224 C25H20O9 [2M+2H+3H2O] 956.244584 HMDB0168237 +mz_00006 1100.45 1 [Npc] 518.216534712 C28H30N4O6 [2M+ACN+Na] 1100.448834 HMDB0060499 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158990 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,9-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158993 +mz_00006 1100.45 3 ["4-[(2S,15R)-8,9-dihydroxy-2-(hydroxymethyl)-15-methyl-5-oxo-16-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0157972 +mz_00006 1100.45 3 ["4-[(2S,15R)-3,16-dihydroxy-15-(hydroxymethyl)-2-methyl-5-oxo-9-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid"] 518.218568598 C24H38O10S [2M+ACN+Na] 1100.452902 HMDB0158992 diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test04.html Thu Feb 14 08:36:52 2019 -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)Delta (ppm)InChI IdentifierPredicted LogP (ALOGPS)
mz_00001175.01
MercaptopurineHMDB0015167C5H4N4S152.015666838M+Na+175.00488529NONEDATANONEDATA
SCHEMBL300353HMDB0171211C4H8O4S152.014329912M+Na+175.00354837NONEDATANONEDATA
[(2Z)-but-2-en-1-yloxy]sulfonic acidHMDB0167141C4H8O4S152.014329912M+Na+175.00354837NONEDATANONEDATA
(Methylsulfanyl)(phenyl)methanoneHMDB0029694C8H8OS152.029585568M+Na+175.01880450NONEDATANONEDATA
"9H-Purine-6,8-diol"HMDB0001182C5H4N4O2152.033425392M+Na+175.02264372NONEDATANONEDATA
mz_00002238.19
[2-(Heptanoyloxy)ethyl]trimethylazaniumHMDB0013239C12H26NO2216.196354081M+Na+238.17829649NONEDATANONEDATA
FencamfaminHMDB0015508C15H21N215.167399677M+Na+238.156618140NONEDATANONEDATA
(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamineHMDB0031202C12H29N3215.236147943M+Na+238.225366148NONEDATANONEDATA
Diethylcarbamazine N-oxideHMDB0060817C10H21N3O2215.163376931M+Na+238.152595157NONEDATANONEDATA
N-NonanoylglycineHMDB0013279C11H21NO3215.152143543M+Na+238.141362204NONEDATANONEDATA
mz_00003420.16
"(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"HMDB0161604C19H27NO6S397.155908767M+Na+420.14512735NONEDATANONEDATA
"(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"HMDB0161565C19H27NO6S397.155908767M+Na+420.14512735NONEDATANONEDATA
"N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"HMDB0030435C22H23NO6397.152537473M+Na+420.14175543NONEDATANONEDATA
"6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"HMDB0165501C18H24NO9398.144557777M+Na+420.126580NONEDATANONEDATA
"3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"HMDB0158327C15H19N5O8397.123362592M+Na+420.112581113NONEDATANONEDATA
mz_00004780.32
5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acidHMDB0164422C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acidHMDB0164421C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acidHMDB0164418C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acidHMDB0164423C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acidHMDB0164424C36H51N7O11757.36465549M+Na+780.35387343NONEDATANONEDATA
mz_00005956.25
Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xylHMDB0062476C31H51NO29S933.2267458M+Na+956.21596436NONEDATANONEDATA
(3S)-3-Isopropenyl-6-oxoheptanoyl-CoAHMDB0062370C31H50N7O18P3S933.214589966M+Na+956.20380848NONEDATANONEDATA
mz_000061100.45
UNKNOWNNONEn/an/an/an/an/a0n/an/a
\ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test04.tabular Thu Feb 14 08:36:52 2019 -0500 @@ -0,0 +1,24 @@ +ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID +mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 +mz_00001 175.01 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211 +mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141 +mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 +mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 +mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 +mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 +mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 +mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 +mz_00003 420.16 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604 +mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565 +mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 +mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501 +mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327 +mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422 +mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421 +mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418 +mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423 +mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424 +mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 +mz_00005 956.25 48 [(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r b5a1d5e43685 -r 63ba1cb240b7 test-data/out_test04.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_test04.txt Thu Feb 14 08:36:52 2019 -0500 @@ -0,0 +1,24 @@ +ID Query(Da) Delta(ppm) Metabolite_Name Cpd_MW(Da) Formula Adduct Adduct_MW(Da) HMDB_ID +mz_00001 175.01 29 [Mercaptopurine] 152.015666838 C5H4N4S [M+Na] 175.004885 HMDB0015167 +mz_00001 175.01 37 [SCHEMBL300353] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0171211 +mz_00001 175.01 37 [[(2Z)-but-2-en-1-yloxy]sulfonic acid] 152.014329912 C4H8O4S [M+Na] 175.003548 HMDB0167141 +mz_00001 175.01 50 [(Methylsulfanyl)(phenyl)methanone] 152.029585568 C8H8OS [M+Na] 175.018804 HMDB0029694 +mz_00001 175.01 72 ["9H-Purine-6,8-diol"] 152.033425392 C5H4N4O2 [M+Na] 175.022643 HMDB0001182 +mz_00002 238.19 49 [[2-(Heptanoyloxy)ethyl]trimethylazanium] 216.196354081 C12H26NO2 [M+Na] 238.178296 HMDB0013239 +mz_00002 238.19 140 [Fencamfamin] 215.167399677 C15H21N [M+Na] 238.156618 HMDB0015508 +mz_00002 238.19 148 [(4-{[4-(dimethylamino)butyl]amino}butyl)dimethylamine] 215.236147943 C12H29N3 [M+Na] 238.225366 HMDB0031202 +mz_00002 238.19 157 [Diethylcarbamazine N-oxide] 215.163376931 C10H21N3O2 [M+Na] 238.152595 HMDB0060817 +mz_00002 238.19 204 [N-Nonanoylglycine] 215.152143543 C11H21NO3 [M+Na] 238.141362 HMDB0013279 +mz_00003 420.16 35 ["(2E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-2,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161604 +mz_00003 420.16 35 ["(4E,8E)-9-[4-hydroxy-3-(sulfooxy)phenyl]-N-(2-methylpropyl)nona-4,8-dienimidic acid"] 397.155908767 C19H27NO6S [M+Na] 420.145127 HMDB0161565 +mz_00003 420.16 43 ["N-[2-(2-Hydroxy-3,4-dimethoxyphenyl)-6,7-dimethoxynaphthalen-1-yl]-N-methylformamide"] 397.152537473 C22H23NO6 [M+Na] 420.141755 HMDB0030435 +mz_00003 420.16 80 ["6-[(6-carboxy-3,4-dihydroxyoxan-2-yl)oxy]-4-methoxy-6-methyl-2H,5H,6H,7H,8H-[1,3]dioxolo[4,5-g]isoquinolin-6-ium"] 398.144557777 C18H24NO9 [M+Na] 420.1265 HMDB0165501 +mz_00003 420.16 113 ["3,4,5-trihydroxy-6-[(4-hydroxy-6-propanoyl-7,8-dihydropteridin-2-yl)amino]oxane-2-carboxylic acid"] 397.123362592 C15H19N5O8 [M+Na] 420.112581 HMDB0158327 +mz_00004 780.32 43 [5-[2-(2-{[1-({1-[(carboxymethyl)-C-hydroxycarbonimidoyl]-2-(4-hydroxyphenyl)ethyl}-C-hydroxycarbonimidoyl)-2-methylpropyl]-C-hydroxycarbonimidoyl}pyrrolidine-1-carbonyl)pyrrolidin-1-yl]-4-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164422 +mz_00004 780.32 43 [1-(1-{2-[({1-[2-({2-[(2-amino-1-hydroxy-3-methylbutylidene)amino]-1-hydroxy-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl}(hydroxy)methylidene)amino]-4-carboxybutanoyl}pyrrolidine-2-carbonyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164421 +mz_00004 780.32 43 [4-({[1-(2-{[2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}acetyl)pyrrolidin-2-yl](hydroxy)methylidene}amino)-5-(2-{2-[(1-carboxy-2-methylpropyl)-C-hydroxycarbonimidoyl]pyrrolidine-1-carbonyl}pyrrolidin-1-yl)-5-oxopentanoic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164418 +mz_00004 780.32 43 [2-{[hydroxy(1-{2-[(1-hydroxy-2-{[1-hydroxy-2-({hydroxy[1-(pyrrolidine-2-carbonyl)pyrrolidin-2-yl]methylidene}amino)-3-methylbutylidene]amino}-3-(4-hydroxyphenyl)propylidene)amino]acetyl}pyrrolidin-2-yl)methylidene]amino}pentanedioic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164423 +mz_00004 780.32 43 [1-(4-carboxy-2-{[hydroxy({1-[2-({1-hydroxy-2-[(1-hydroxy-2-{[hydroxy(pyrrolidin-2-yl)methylidene]amino}-3-methylbutylidene)amino]-3-(4-hydroxyphenyl)propylidene}amino)acetyl]pyrrolidin-2-yl})methylidene]amino}butanoyl)pyrrolidine-2-carboxylic acid] 757.36465549 C36H51N7O11 [M+Na] 780.353873 HMDB0164424 +mz_00005 956.25 36 [Α-D-glcnac3S-(1→4)-β-D-glca(1→3)-β-D-gal(1→3)-β-D-gal(1→4)-D-xyl] 933.2267458 C31H51NO29S [M+Na] 956.215964 HMDB0062476 +mz_00005 956.25 48 [(3S)-3-Isopropenyl-6-oxoheptanoyl-CoA] 933.214589966 C31H50N7O18P3S [M+Na] 956.203808 HMDB0062370 +mz_00006 1100.45 0 UNKNOWN N/A N/A N/A N/A N/A diff -r b5a1d5e43685 -r 63ba1cb240b7 wsdl_hmdb.pl --- a/wsdl_hmdb.pl Wed Jan 23 07:49:34 2019 -0500 +++ b/wsdl_hmdb.pl Thu Feb 14 08:36:52 2019 -0500 @@ -27,7 +27,7 @@ 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 ) ; +my ( $adductType, $delta, $molecular_species, $out_tab, $out_html, $out_xls ) = ( undef, undef, undef, undef, undef, undef ) ; my $advancedFeatures = 0 ; my $VERBOSE = ( 3 ) ; @@ -42,13 +42,14 @@ "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 + "adduct_type:s" => \$adductType, ## A list of selected adducts "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 - "advancedFeatures:s"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. + "advancedFeatures:i"=> \$advancedFeatures, ## option : set to 1 to get advanced options or 0 to get first level only. "verbose:i" => \$VERBOSE, ## VERBOSE Of the tool ) ; @@ -84,7 +85,13 @@ my $metabocard_features = undef ; my $search_condition = "Search params : Molecular specie = $molecular_species / delta (mass-to-charge ratio) = $delta" ; -print "\t with $search_condition\n" if ($VERBOSE>1) ; +print "\twith $search_condition\n" if ($VERBOSE>1) ; + +## $adductType +if (defined $adductType ) { + print "\twith Adducts: $adductType\n" if ($VERBOSE>1) ; +} + ## --------------- retrieve input data -------------- : @@ -122,12 +129,12 @@ my $oHmdb = lib::hmdb::new() ; my $hmdb_pages = undef ; my $status = undef ; - my $hmdb_ids = undef ; + my ($hmdb_ids, $idsNumber) = (undef, 0) ; $results = [] ; # prepare arrays ref my $submasses = $oHmdb->extract_sub_mz_lists($masses, $CONF->{HMDB_LIMITS} ) ; - print "\t and ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ; + print "\tand ".scalar(@$masses)." masses are submitted as ".scalar(@$submasses)." queries to HMDB \n\n" if ($VERBOSE>1) ; ## get the hmdb server status by a test query - continuous queries or kill script. $status = $oHmdb->testMatchesFromHmdbWithUA() ; @@ -139,10 +146,11 @@ my $result = undef ; my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ; + my ($hmdb_adducts, $nb_selected_adducts) = $oHmdb->prepareAdductListFormat($adductType) ; print "\n\tSubmission of m/z cluster ".sprintf '%04s',$cluster."" if ($VERBOSE>1) ; - ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species) ; + ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdbWithUA($hmdb_masses, $delta, $molecular_species, $hmdb_adducts) ; print "...HMDB reply results with status: $status\n" if ($VERBOSE>1) ; # print Dumper $hmdb_pages ; @@ -161,15 +169,15 @@ if ($advancedFeatures > 0) { ## foreach metabolite get its own metabocard - $hmdb_ids = $oHmdb->get_unik_ids_from_results($results) ; + ($hmdb_ids, $idsNumber) = $oHmdb->get_unik_ids_from_results($results) ; - print "\tComplementary annotation: asking for ".scalar(@$results)." metabocards\n" if ($VERBOSE>1) ; + print "\tComplementary annotation: asking for $idsNumber metabocards\n" if ($VERBOSE>1) ; # $hmdb_ids->{'HMDB03125'} = 1 , $metabocard_features = $oHmdb->get_hmdb_metabocard_from_id($hmdb_ids, $CONF->{'HMDB_METABOCARD_URL'}) ; ## Try to multithread the querying - # print Dumper $results ; +# print Dumper $results ; # print Dumper $hmdb_ids ; - # print Dumper $metabocard_features ; +# print Dumper $metabocard_features ; ## Map metabocards with results (add supplementary data) if ( ( defined $results ) and ( defined $metabocard_features ) ) { $results = $oHmdb->map_suppl_data_on_hmdb_results($results, $metabocard_features) ; @@ -180,8 +188,6 @@ ## Fill with msg not asked advanced annotation $results = $oHmdb->map_suppl_data_on_hmdb_results($results, undef) ; } - - ## Uses N mz and theirs entries per page (see config file). # how many pages you need with your input mz list? @@ -327,4 +333,6 @@ version 1.6 : 23 / 01 / 2019 - Manage UA http error and advanced feature from hmdb. +version 1.6.1 : 30 / 01 / 2019 - Adding adducts and fixxing minors bugs and requirements + =cut \ No newline at end of file diff -r b5a1d5e43685 -r 63ba1cb240b7 wsdl_hmdb.xml --- a/wsdl_hmdb.xml Wed Jan 23 07:49:34 2019 -0500 +++ b/wsdl_hmdb.xml Thu Feb 14 08:36:52 2019 -0500 @@ -1,4 +1,4 @@ - + search by masses on HMDB online LCMS bank @@ -8,10 +8,11 @@ perl-html-template perl-soap-lite perl-lwp-simple - perl-libwww-perl + perl-libwww-perl perl-uri perl-text-csv perl-xml-twig + perl-www-mechanize @@ -33,7 +34,18 @@ -mass "${input_type.mass}" -output_tabular "$variableMetadata2" -output_html "$HmdbOutWeb2" -output_xls "$HmdbOutXlsx2" #end if - -delta "$delta" -mode "$mode" -maxquery "$maxquery" + + -mode "${mode_type.mode}" + + #if str($mode_type.mode) == "positive": + -adduct_type "${mode_type.data_positive_adducts}" + #elif str($mode_type.mode) == "negative": + -adduct_type "${mode_type.data_negative_adducts}" + #elif str($mode_type.mode) == "neutral": + -adduct_type "${mode_type.data_neutral_adducts}" + #end if + + -delta "$delta" -maxquery "$maxquery" -advancedFeatures "$advancedFeatures" -verbose "$verbose" @@ -64,12 +76,91 @@ - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +