Mercurial > repos > fgiacomoni > hmdb_ms_search
diff t/hmdb_managerTest.pl @ 23:2d8a310e86ce draft
Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
| author | fgiacomoni |
|---|---|
| date | Thu, 19 May 2022 13:43:09 +0000 |
| parents | 4eb2de7c24d1 |
| children |
line wrap: on
line diff
--- a/t/hmdb_managerTest.pl Fri Nov 20 17:29:18 2020 +0000 +++ b/t/hmdb_managerTest.pl Thu May 19 13:43:09 2022 +0000 @@ -43,68 +43,36 @@ ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ), '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying'); - + print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++; - is_deeply( get_matches_from_hmdb_uaTest( + is_deeply( getMatchesFromHmdb5WithUATest( '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'), [ - 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', -# '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', -# '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', -# '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', -# '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', -# '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', -# '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', -# '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' - ## Update format - 2018-01-19... HMDB V04 -# '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', -# '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', -# '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', -# '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', -# '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5', -# '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', -# '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', - ## Update results - 2018-09-20... HMDBv4 - #'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', - '175.01,HMDB0149376,"2-{[5,6-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0149375,"2-({5,6-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0149419,"2-{[5,8-dihydroxy-3-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0149418,"2-({5,8-dihydroxy-4-oxo-3-[4-(sulfooxy)phenyl]-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)-3-hydroxybutanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0149392,"2-{[3-(3,4-dihydroxyphenyl)-5-hydroxy-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3-(sulfooxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0149391,"2-hydroxy-3-({5-hydroxy-3-[4-hydroxy-3-(sulfooxy)phenyl]-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl}oxy)butanedioic acid",n/a,C19H16O14S,500.026076369,M+2H+Na,+,175.009949,0', - '175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', - '175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', - '175.01,HMDB0141391,{4-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3', - '175.01,HMDB0141389,{3-[(1E)-3-oxo-3-phenylprop-1-en-1-yl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3', - '175.01,HMDB0135622,{4-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3', - '175.01,HMDB0135448,{3-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3', - '175.01,HMDB0240280,Methanesulfonic acid,C11145,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4', - '175.01,HMDB0003745,Coenzyme m,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', - '175.01,HMDB0142159,[2-hydroxy-2-(2-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142160,[2-hydroxy-1-(2-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142162,"[3-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142166,"[4-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142164,[2-hydroxy-1-(3-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142163,[2-hydroxy-2-(3-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142167,[2-hydroxy-2-(4-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0142168,[2-hydroxy-1-(4-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0129951,"{3-[2-(3,5-dihydroxyphenyl)ethyl]phenyl}oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4', - '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', - '175.01,HMDB0033657,"11,15-Dihydroxy-6,8,20-trioxapentacyclo[10.8.0.0²,⁹.0³,⁷.0¹⁴,¹⁹]icosa-1(12),2(9),4,10,14,16,18-heptaen-13-one",C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', - '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)-2H-furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5', - '175.01,HMDB0155176,5-Hydroxy-6-hydrouracil,n/a,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6', - '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', - '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', - '420.16,HMDB0160148,"6-[(5-carboxy-3-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2', - '420.16,HMDB0160149,"6-[(5-carboxy-4-methylpentanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2', - '420.16,HMDB0165020,"6-{[2-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2', - '420.16,HMDB0175397,"6-{[3-(acetyloxy)-3-methylbutanoyl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2', - '420.16,HMDB0184353,"6-[(4-carboxy-3,3-dimethylbutanoyl)oxy]-3,4,5-trihydroxyoxane-2-carboxylic acid",n/a,C13H20O10,336.105646844,M+IsoProp+Na+H,+,420.160757,2' + 'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value', + '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,', + '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,', + '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,', + '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,', + '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,', + '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,', + '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,', + '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,', + '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,', + '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,', + '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,', + '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,', + '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,', + '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,', + '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,', + '420.16,HMDB0245742,"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea",C19H18F2N4O,356.144867542,M+ACN+Na,+,420.160633,2,', + '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,', + '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,', + '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,' ], - 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb'); + 'Method \'getMatchesFromHmdb5WithUA\' works again (API v5.0 compatible) with a well-formated string of mzs and return a complete csv from hmdb'); print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++; - is_deeply (test_matches_from_hmdb_uaTest (), + is_deeply (testMatchesFromHmdb5WithUATest (), \'200', 'The HMDB server is available: returns successful HTTP requests' ) ; @@ -113,147 +81,144 @@ 1, 'The status 200 returns no error/warn' ) ; - print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; + print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++; throws_ok{ check_state_from_hmdb_uaTest(\'504')} - '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/', + qr/Gateway Timeout \(504\): The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server\. The Hmdb tool is stopped with error\./, 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ; - print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( + + print "\n** Test $current_test parseHmdb5CSVResults (version 5.0) with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; + is_deeply ( parseHmdb5CSVResultsTest ( [ - 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', -# '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', -# '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', -# '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', -# '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', -# '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', -# '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', -# '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' - ## Update format - 2018-01-19... HMDB V04 - '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', - '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', - '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', - '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', - '175.01,HMDB0035230,"6,7-Dihydroxy-3-(4-hydroxyphenyl)furo[3,2-b]chromen-2-one",n/a,C17H10O6,310.047738052,M+H+K,+,175.009086,5', - '420.16,HMDB0060838,"4-hydroxy-5-[(4-{2-[(5-hydroxy-1,2-dihydropyridin-2-ylidene)amino]ethoxy}phenyl)methyl]-2,5-dihydro-1,3-thiazol-2-one",n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', - '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', + 'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value', + '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,', + '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,', + '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,', + '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,', + '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,', + '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,', + '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,', + '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,', + '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,', + '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,', + '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,', + '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,', + '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,', + '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,', + '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,', + '420.16,HMDB0245742,"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea",C19H18F2N4O,356.144867542,M+ACN+Na,+,420.160633,2,', + '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,', + '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,', + '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,' ], ['175.01', '238.19', '420.16'], 10 ), [ [ - { 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_ENTRY_ID' => 'HMDB0060293', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT_MZ' => '175.009875', 'ENTRY_DELTA' => '1', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT' => 'M+IsoProp+H' }, - {'ENTRY_DELTA' => '4','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+CH3OH+H','ENTRY_CPD_MZ' => '141.975835438','ENTRY_ENTRY_ID' => 'HMDB0003745','ENTRY_FORMULA' => 'C2H6O3S2','ENTRY_ADDUCT_MZ' => '175.009324'}, - {'ENTRY_ENTRY_ID' => 'HMDB0031436','ENTRY_CPD_MZ' => '95.987885149','ENTRY_ADDUCT_MZ' => '175.009105','ENTRY_FORMULA' => 'H4O4Si','ENTRY_DELTA' => '5','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+DMSO+H'}, - {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0033657','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT' => 'M+H+K','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '5'}, - {'ENTRY_ADDUCT_MZ' => '175.009086','ENTRY_FORMULA' => 'C17H10O6','ENTRY_ENTRY_ID' => 'HMDB0035230','ENTRY_CPD_MZ' => '310.047738052','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+H+K','ENTRY_DELTA' => '5'} + { 'ENTRY_CPD_MZ' => '310.04795597', 'ENTRY_DELTA' => '5', 'ENTRY_FORMULA' => 'C10H18N2O3S3', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_NAME' => '"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine"', 'ENTRY_ENTRY_ID' => 'HMDB0259477', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009195' }, + { 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.00949', 'ENTRY_ENTRY_ID' => 'HMDB0258038', 'ENTRY_ENTRY_NAME' => '9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid', 'ENTRY_FORMULA' => 'C15H12O5S', 'ENTRY_ADDUCT' => 'M+2Na', 'ENTRY_DELTA' => '3', 'ENTRY_CPD_MZ' => '304.04054466' }, + { 'ENTRY_FORMULA' => 'C14H14O6S', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_NAME' => 'Dihydroresveratrol 4\'-sulfate', 'ENTRY_CPD_MZ' => '310.051109345', 'ENTRY_DELTA' => '4', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.010772', 'ENTRY_ENTRY_ID' => 'HMDB0240502' }, + { 'ENTRY_ADDUCT_MZ' => '175.010772', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0240500', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_FORMULA' => 'C14H14O6S', 'ENTRY_ENTRY_NAME' => 'Dihydroresveratrol 3-sulfate', 'ENTRY_CPD_MZ' => '310.051109345', 'ENTRY_DELTA' => '4' }, + { 'ENTRY_ENTRY_ID' => 'HMDB0246744', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.010662', 'ENTRY_CPD_MZ' => '132.976839457', 'ENTRY_DELTA' => '4', 'ENTRY_ENTRY_NAME' => '"5-Amino-1,3,4-thiadiazole-2-thiol"', 'ENTRY_FORMULA' => 'C2H3N3S2', 'ENTRY_ADDUCT' => 'M+ACN+H' }, + { 'ENTRY_ENTRY_ID' => 'HMDB0252977', 'ENTRY_ADDUCT_MZ' => '175.009491', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_CPD_MZ' => '522.006645625', 'ENTRY_DELTA' => '3', 'ENTRY_ADDUCT' => 'M+3H', 'ENTRY_FORMULA' => 'C10H17N6O13P3', 'ENTRY_ENTRY_NAME' => 'Phosphoaminophosphonic acid-guanylate ester' }, + { 'ENTRY_ENTRY_ID' => 'HMDB0258677', 'ENTRY_ADDUCT_MZ' => '175.010699', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_CPD_MZ' => '306.980298509', 'ENTRY_DELTA' => '4', 'ENTRY_ADDUCT' => 'M+ACN+2H', 'ENTRY_FORMULA' => 'C14H7Cl2NO3', 'ENTRY_ENTRY_NAME' => 'Tafamidis' }, + { 'ENTRY_ENTRY_ID' => 'HMDB0240280', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009335', 'ENTRY_DELTA' => '4', 'ENTRY_CPD_MZ' => '95.988114684', 'ENTRY_FORMULA' => 'CH4O3S', 'ENTRY_ADDUCT' => 'M+DMSO+H', 'ENTRY_ENTRY_NAME' => 'Mesylate' }, + { 'ENTRY_DELTA' => '1', 'ENTRY_CPD_MZ' => '113.94453531', 'ENTRY_FORMULA' => 'H2O3S2', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_ENTRY_NAME' => 'Thiosulfate', 'ENTRY_ENTRY_ID' => 'HMDB0000257', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009875' }, + { 'ENTRY_DELTA' => '5', 'ENTRY_CPD_MZ' => '310.047738052', 'ENTRY_ENTRY_NAME' => 'Aurantricholide B', 'ENTRY_FORMULA' => 'C17H10O6', 'ENTRY_ADDUCT' => 'M+H+K', 'ENTRY_ENTRY_ID' => 'HMDB0035230', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '175.009086' } ], [], [ - {'ENTRY_FORMULA' => 'C17H17N3O4S','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ENTRY_ID' => 'HMDB0060838','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ADDUCT_TYPE' => '+','ENTRY_DELTA' => '2'}, - {'ENTRY_DELTA' => '2','ENTRY_ADDUCT_TYPE' => '+','ENTRY_ADDUCT' => 'M+IsoProp+H','ENTRY_ENTRY_ID' => 'HMDB0060836','ENTRY_CPD_MZ' => '359.093976737','ENTRY_ADDUCT_MZ' => '420.159317','ENTRY_FORMULA' => 'C17H17N3O4S'} + { 'ENTRY_ADDUCT_MZ' => '420.160599', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0250452', 'ENTRY_ADDUCT' => 'M+2ACN+2H', 'ENTRY_FORMULA' => 'C27H48O24', 'ENTRY_ENTRY_NAME' => 'Core oligosaccharide', 'ENTRY_CPD_MZ' => '756.253552426', 'ENTRY_DELTA' => '1' }, + { 'ENTRY_CPD_MZ' => '356.144867542', 'ENTRY_DELTA' => '2', 'ENTRY_ENTRY_NAME' => '"N-(6,8-Difluoro-2-methyl-4-quinolinyl)-N\'-[4-(dimethylamino)phenyl]urea"', 'ENTRY_FORMULA' => 'C19H18F2N4O', 'ENTRY_ADDUCT' => 'M+ACN+Na', 'ENTRY_ENTRY_ID' => 'HMDB0245742', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ADDUCT_MZ' => '420.160633' }, + { 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0060838', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_NAME' => 'N-Desmethyl-p-hydroxyrosiglitazone', 'ENTRY_CPD_MZ' => '359.093976737', 'ENTRY_DELTA' => '2' }, + { 'ENTRY_ADDUCT_MZ' => '420.159317', 'ENTRY_ADDUCT_TYPE' => '+', 'ENTRY_ENTRY_ID' => 'HMDB0060836', 'ENTRY_ADDUCT' => 'M+IsoProp+H', 'ENTRY_FORMULA' => 'C17H17N3O4S', 'ENTRY_ENTRY_NAME' => 'N-Desmethyl-O-hydroxy rosiglitazone', 'ENTRY_DELTA' => '2', 'ENTRY_CPD_MZ' => '359.093976737' } ] ], - 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; - - print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ), - [ [], [], [] ], - 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ; - - print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), - [], - 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; - - ## Other example... from mz 265.0567515 - print "\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; - is_deeply ( parse_hmdb_csv_resultsTest ( - [ - 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', - '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2', - '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', - '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', - '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', - '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', - '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3', - '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', - '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', - '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', - '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4', - ], - ['265.0567515'], - 5 - ), - [ - [ - { - 'ENTRY_DELTA' => '2', - 'ENTRY_FORMULA' => 'C5H8O2S', - 'ENTRY_ENTRY_ID' => 'HMDB0059667', - 'ENTRY_ADDUCT_MZ' => '265.056276', - 'ENTRY_ADDUCT_TYPE' => '+', - 'ENTRY_CPD_MZ' => '132.02450019', - 'ENTRY_ADDUCT' => '2M+H' - }, - { - 'ENTRY_ADDUCT_MZ' => '265.056128', - 'ENTRY_ENTRY_ID' => 'HMDB0038767', - 'ENTRY_ADDUCT_TYPE' => '+', - 'ENTRY_CPD_MZ' => '726.200729034', - 'ENTRY_ADDUCT' => 'M+3Na', - 'ENTRY_DELTA' => '2', - 'ENTRY_FORMULA' => 'C32H38O19' - }, - { - 'ENTRY_DELTA' => '2', - 'ENTRY_FORMULA' => 'C32H38O19', - 'ENTRY_ENTRY_ID' => 'HMDB0039759', - 'ENTRY_ADDUCT_MZ' => '265.056128', - 'ENTRY_ADDUCT_TYPE' => '+', - 'ENTRY_CPD_MZ' => '726.200729034', - 'ENTRY_ADDUCT' => 'M+3Na' - }, - { - 'ENTRY_FORMULA' => 'C32H38O19', - 'ENTRY_DELTA' => '2', - 'ENTRY_ADDUCT_TYPE' => '+', - 'ENTRY_ADDUCT_MZ' => '265.056128', - 'ENTRY_ENTRY_ID' => 'HMDB0040875', - 'ENTRY_CPD_MZ' => '726.200729034', - 'ENTRY_ADDUCT' => 'M+3Na' - }, - { - 'ENTRY_ADDUCT_TYPE' => '+', - 'ENTRY_ENTRY_ID' => 'HMDB0040878', - 'ENTRY_ADDUCT_MZ' => '265.056128', - 'ENTRY_ADDUCT' => 'M+3Na', - 'ENTRY_CPD_MZ' => '726.200729034', - 'ENTRY_FORMULA' => 'C32H38O19', - 'ENTRY_DELTA' => '2' - } - ] - ], - 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; - - -} + 'Method \'parseHmdb5CSVResults\' works with a well-formated csv output and returns a a well formated array' ) ; - - - - - - - +# print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++; +# is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ), +# [ [], [], [] ], +# 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ; +# +# print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++; +# is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), +# [], +# 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; +# +# ## Other example... from mz 265.0567515 +# print "\n** Test $current_test parse_hmdb_csv_results with mz 265.0567515 and the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; +# is_deeply ( parse_hmdb_csv_resultsTest ( +# [ +# 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', +# '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2', +# '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', +# '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', +# '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', +# '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', +# '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3', +# '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', +# '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', +# '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', +# '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4', +# ], +# ['265.0567515'], +# 5 +# ), +# [ +# [ +# { +# 'ENTRY_DELTA' => '2', +# 'ENTRY_FORMULA' => 'C5H8O2S', +# 'ENTRY_ENTRY_ID' => 'HMDB0059667', +# 'ENTRY_ADDUCT_MZ' => '265.056276', +# 'ENTRY_ADDUCT_TYPE' => '+', +# 'ENTRY_CPD_MZ' => '132.02450019', +# 'ENTRY_ADDUCT' => '2M+H' +# }, +# { +# 'ENTRY_ADDUCT_MZ' => '265.056128', +# 'ENTRY_ENTRY_ID' => 'HMDB0038767', +# 'ENTRY_ADDUCT_TYPE' => '+', +# 'ENTRY_CPD_MZ' => '726.200729034', +# 'ENTRY_ADDUCT' => 'M+3Na', +# 'ENTRY_DELTA' => '2', +# 'ENTRY_FORMULA' => 'C32H38O19' +# }, +# { +# 'ENTRY_DELTA' => '2', +# 'ENTRY_FORMULA' => 'C32H38O19', +# 'ENTRY_ENTRY_ID' => 'HMDB0039759', +# 'ENTRY_ADDUCT_MZ' => '265.056128', +# 'ENTRY_ADDUCT_TYPE' => '+', +# 'ENTRY_CPD_MZ' => '726.200729034', +# 'ENTRY_ADDUCT' => 'M+3Na' +# }, +# { +# 'ENTRY_FORMULA' => 'C32H38O19', +# 'ENTRY_DELTA' => '2', +# 'ENTRY_ADDUCT_TYPE' => '+', +# 'ENTRY_ADDUCT_MZ' => '265.056128', +# 'ENTRY_ENTRY_ID' => 'HMDB0040875', +# 'ENTRY_CPD_MZ' => '726.200729034', +# 'ENTRY_ADDUCT' => 'M+3Na' +# }, +# { +# 'ENTRY_ADDUCT_TYPE' => '+', +# 'ENTRY_ENTRY_ID' => 'HMDB0040878', +# 'ENTRY_ADDUCT_MZ' => '265.056128', +# 'ENTRY_ADDUCT' => 'M+3Na', +# 'ENTRY_CPD_MZ' => '726.200729034', +# 'ENTRY_FORMULA' => 'C32H38O19', +# 'ENTRY_DELTA' => '2' +# } +# ] +# ], +# 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; +# +# - - - - - - - +} ## END of the script \ No newline at end of file