Mercurial > repos > fgiacomoni > hmdb_ms_search

comparison t/hmdb_managerTest.pl @ 23:2d8a310e86ce draft

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Prod branch Updating with v.:CI_COMMIT_TAG- - Fxx
author fgiacomoni
date Thu, 19 May 2022 13:43:09 +0000
parents 4eb2de7c24d1
children
comparison
equal deleted inserted replaced
22:453fbe98925a 23:2d8a310e86ce
41 print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++; 41 print "\n** Test $current_test prepare_multi_masses_query with a list of mzs **\n" ; $current_test++;
42 is_deeply( prepare_multi_masses_queryTest( 42 is_deeply( prepare_multi_masses_queryTest(
43 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ), 43 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ),
44 '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 44 '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A',
45 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying'); 45 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying');
46 46
47 print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++; 47 print "\n** Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs **\n" ; $current_test++;
48 is_deeply( get_matches_from_hmdb_uaTest( 48 is_deeply( getMatchesFromHmdb5WithUATest(
49 '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'), 49 '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'),
50 [ 50 [
51 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', 51 'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',
52 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', 52 '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,',
53 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', 53 '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,',
54 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', 54 '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
55 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', 55 '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
56 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', 56 '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
57 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', 57 '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,',
58 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' 58 '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,',
59 ## Update format - 2018-01-19... HMDB V04 59 '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
60 # '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', 60 '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,',
61 # '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', 61 '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,',
62 # '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', 62 '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,',
63 # '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', 63 '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
64 # '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', 64 '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
65 # '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', 65 '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,',
66 # '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', 66 '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,',
67 ## Update results - 2018-09-20... HMDBv4 67 '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,',
68 #'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', 68 '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,',
69 '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', 69 '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,',
70 '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', 70 '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,'
71 '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',
72 '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',
73 '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',
74 '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',
75 '175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
76 '175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
77 '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',
78 '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',
79 '175.01,HMDB0135622,{4-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
80 '175.01,HMDB0135448,{3-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
81 '175.01,HMDB0240280,Methanesulfonic acid,C11145,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4',
82 '175.01,HMDB0003745,Coenzyme m,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
83 '175.01,HMDB0142159,[2-hydroxy-2-(2-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
84 '175.01,HMDB0142160,[2-hydroxy-1-(2-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
85 '175.01,HMDB0142162,"[3-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
86 '175.01,HMDB0142166,"[4-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
87 '175.01,HMDB0142164,[2-hydroxy-1-(3-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
88 '175.01,HMDB0142163,[2-hydroxy-2-(3-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
89 '175.01,HMDB0142167,[2-hydroxy-2-(4-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
90 '175.01,HMDB0142168,[2-hydroxy-1-(4-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
91 '175.01,HMDB0129951,"{3-[2-(3,5-dihydroxyphenyl)ethyl]phenyl}oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
92 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
93 '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',
94 '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',
95 '175.01,HMDB0155176,5-Hydroxy-6-hydrouracil,n/a,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6',
96 '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
97 '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
98 '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',
99 '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',
100 '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',
101 '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',
102 '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'
103 ], 71 ],
104 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb'); 72 'Method \'getMatchesFromHmdb5WithUA\' works again (API v5.0 compatible) with a well-formated string of mzs and return a complete csv from hmdb');
105 73
106 print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++; 74 print "\n** Test $current_test test_matches_from_hmdb_ua to get hmdb status **\n" ; $current_test++;
107 is_deeply (test_matches_from_hmdb_uaTest (), 75 is_deeply (testMatchesFromHmdb5WithUATest (),
108 \'200', 76 \'200',
109 'The HMDB server is available: returns successful HTTP requests' ) ; 77 'The HMDB server is available: returns successful HTTP requests' ) ;
110 78
111 print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++; 79 print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++;
112 is_deeply (check_state_from_hmdb_uaTest (\'200'), 80 is_deeply (check_state_from_hmdb_uaTest (\'200'),
113 1, 81 1,
114 'The status 200 returns no error/warn' ) ; 82 'The status 200 returns no error/warn' ) ;
115 83
116 print "\n** Test $current_test prepare_multi_masses_query with an empty list of mzs **\n" ; $current_test++; 84 print "\n** Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status **\n" ; $current_test++;
117 throws_ok{ check_state_from_hmdb_uaTest(\'504')} 85 throws_ok{ check_state_from_hmdb_uaTest(\'504')}
118 '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/', 86 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\./,
119 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ; 87 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ;
120 88
121 print "\n** Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++; 89
122 is_deeply ( parse_hmdb_csv_resultsTest ( 90 print "\n** Test $current_test parseHmdb5CSVResults (version 5.0) with the correct inputs for hmdb outputs parsing (csv format) **\n" ; $current_test++;
91 is_deeply ( parseHmdb5CSVResultsTest (
123 [ 92 [
124 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', 93 'query_mass,compound_id,compound_name,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,"delta(ppm),",ccs_value',
125 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125', 94 '175.01,HMDB0259477,"S-(N,N-Diethyldithiocarbamoyl)-N-acetyl-L-cysteine",C10H18N2O3S3,310.04795597,M+H+K,+,175.009195,5,',
126 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676', 95 '175.01,HMDB0258038,9-(Formyloxymethyl)-9H-fluorene-2-sulfonic acid,C15H12O5S,304.04054466,M+2Na,+,175.00949,3,',
127 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895', 96 '175.01,HMDB0257737,"4,5-Dihydroxy-3-methyl-1H-imidazol-2-one",C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
128 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', 97 '175.01,HMDB0240502,Dihydroresveratrol 4\'-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
129 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914', 98 '175.01,HMDB0240500,Dihydroresveratrol 3-sulfate,C14H14O6S,310.051109345,M+H+K,+,175.010772,4,',
130 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683', 99 '175.01,HMDB0246744,"5-Amino-1,3,4-thiadiazole-2-thiol",C2H3N3S2,132.976839457,M+ACN+H,+,175.010662,4,',
131 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683' 100 '175.01,HMDB0252977,Phosphoaminophosphonic acid-guanylate ester,C10H17N6O13P3,522.006645625,M+3H,+,175.009491,3,',
132 ## Update format - 2018-01-19... HMDB V04 101 '175.01,HMDB0246800,5-Hydroxy-1-methylhydantoin,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6,',
133 '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1', 102 '175.01,HMDB0258677,Tafamidis,C14H7Cl2NO3,306.980298509,M+ACN+2H,+,175.010699,4,',
134 '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4', 103 '175.01,HMDB0240280,Mesylate,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4,',
135 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5', 104 '175.01,HMDB0000257,Thiosulfate,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1,',
136 '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5', 105 '175.01,HMDB0035230,Aurantricholide B,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
137 '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', 106 '175.01,HMDB0033657,De-O-methylsterigmatocystin,C17H10O6,310.047738052,M+H+K,+,175.009086,5,',
138 '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', 107 '175.01,HMDB0003745,Mesna,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4,',
139 '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2', 108 '420.16,HMDB0250452,Core oligosaccharide,C27H48O24,756.253552426,M+2ACN+2H,+,420.160599,1,',
109 '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,',
110 '420.16,HMDB0256144,Pazopanib,C21H23N7O2S,437.163393705,M+H-H2O,+,420.160694,2,',
111 '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,',
112 '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2,'
140 ], 113 ],
141 ['175.01', '238.19', '420.16'], 114 ['175.01', '238.19', '420.16'],
142 10 115 10
143 ), 116 ),
144 [ 117 [
145 [ 118 [
146 { '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' }, 119 { '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' },
147 {'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'}, 120 { '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' },
148 {'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'}, 121 { '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' },
149 {'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'}, 122 { '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' },
150 {'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'} 123 { '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' },
124 { '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' },
125 { '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' },
126 { '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' },
127 { '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' },
128 { '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' }
151 ], 129 ],
152 [], 130 [],
153 [ 131 [
154 {'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'}, 132 { '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' },
155 {'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'} 133 { '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' },
134 { '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' },
135 { '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' }
156 ] 136 ]
157 ], 137 ],
158 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; 138 'Method \'parseHmdb5CSVResults\' works with a well-formated csv output and returns a a well formated array' ) ;
159 139
160 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++; 140
161 is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ), 141 # print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs **\n" ; $current_test++;
162 [ [], [], [] ], 142 # is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
163 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ; 143 # [ [], [], [] ],
164 144 # 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
165 print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++; 145 #
166 is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ), 146 # print "\n** Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list **\n" ; $current_test++;
167 [], 147 # is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
168 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ; 148 # [],
169 149 # 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
170 ## Other example... from mz 265.0567515 150 #
171 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++; 151 # ## Other example... from mz 265.0567515
172 is_deeply ( parse_hmdb_csv_resultsTest ( 152 # 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++;
173 [ 153 # is_deeply ( parse_hmdb_csv_resultsTest (
174 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)', 154 # [
175 '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2', 155 # 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
176 '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', 156 # '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2',
177 '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', 157 # '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
178 '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', 158 # '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
179 '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2', 159 # '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
180 '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3', 160 # '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
181 '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', 161 # '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3',
182 '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', 162 # '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
183 '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3', 163 # '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
184 '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4', 164 # '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
185 ], 165 # '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4',
186 ['265.0567515'], 166 # ],
187 5 167 # ['265.0567515'],
188 ), 168 # 5
189 [ 169 # ),
190 [ 170 # [
191 { 171 # [
192 'ENTRY_DELTA' => '2', 172 # {
193 'ENTRY_FORMULA' => 'C5H8O2S', 173 # 'ENTRY_DELTA' => '2',
194 'ENTRY_ENTRY_ID' => 'HMDB0059667', 174 # 'ENTRY_FORMULA' => 'C5H8O2S',
195 'ENTRY_ADDUCT_MZ' => '265.056276', 175 # 'ENTRY_ENTRY_ID' => 'HMDB0059667',
196 'ENTRY_ADDUCT_TYPE' => '+', 176 # 'ENTRY_ADDUCT_MZ' => '265.056276',
197 'ENTRY_CPD_MZ' => '132.02450019', 177 # 'ENTRY_ADDUCT_TYPE' => '+',
198 'ENTRY_ADDUCT' => '2M+H' 178 # 'ENTRY_CPD_MZ' => '132.02450019',
199 }, 179 # 'ENTRY_ADDUCT' => '2M+H'
200 { 180 # },
201 'ENTRY_ADDUCT_MZ' => '265.056128', 181 # {
202 'ENTRY_ENTRY_ID' => 'HMDB0038767', 182 # 'ENTRY_ADDUCT_MZ' => '265.056128',
203 'ENTRY_ADDUCT_TYPE' => '+', 183 # 'ENTRY_ENTRY_ID' => 'HMDB0038767',
204 'ENTRY_CPD_MZ' => '726.200729034', 184 # 'ENTRY_ADDUCT_TYPE' => '+',
205 'ENTRY_ADDUCT' => 'M+3Na', 185 # 'ENTRY_CPD_MZ' => '726.200729034',
206 'ENTRY_DELTA' => '2', 186 # 'ENTRY_ADDUCT' => 'M+3Na',
207 'ENTRY_FORMULA' => 'C32H38O19' 187 # 'ENTRY_DELTA' => '2',
208 }, 188 # 'ENTRY_FORMULA' => 'C32H38O19'
209 { 189 # },
210 'ENTRY_DELTA' => '2', 190 # {
211 'ENTRY_FORMULA' => 'C32H38O19', 191 # 'ENTRY_DELTA' => '2',
212 'ENTRY_ENTRY_ID' => 'HMDB0039759', 192 # 'ENTRY_FORMULA' => 'C32H38O19',
213 'ENTRY_ADDUCT_MZ' => '265.056128', 193 # 'ENTRY_ENTRY_ID' => 'HMDB0039759',
214 'ENTRY_ADDUCT_TYPE' => '+', 194 # 'ENTRY_ADDUCT_MZ' => '265.056128',
215 'ENTRY_CPD_MZ' => '726.200729034', 195 # 'ENTRY_ADDUCT_TYPE' => '+',
216 'ENTRY_ADDUCT' => 'M+3Na' 196 # 'ENTRY_CPD_MZ' => '726.200729034',
217 }, 197 # 'ENTRY_ADDUCT' => 'M+3Na'
218 { 198 # },
219 'ENTRY_FORMULA' => 'C32H38O19', 199 # {
220 'ENTRY_DELTA' => '2', 200 # 'ENTRY_FORMULA' => 'C32H38O19',
221 'ENTRY_ADDUCT_TYPE' => '+', 201 # 'ENTRY_DELTA' => '2',
222 'ENTRY_ADDUCT_MZ' => '265.056128', 202 # 'ENTRY_ADDUCT_TYPE' => '+',
223 'ENTRY_ENTRY_ID' => 'HMDB0040875', 203 # 'ENTRY_ADDUCT_MZ' => '265.056128',
224 'ENTRY_CPD_MZ' => '726.200729034', 204 # 'ENTRY_ENTRY_ID' => 'HMDB0040875',
225 'ENTRY_ADDUCT' => 'M+3Na' 205 # 'ENTRY_CPD_MZ' => '726.200729034',
226 }, 206 # 'ENTRY_ADDUCT' => 'M+3Na'
227 { 207 # },
228 'ENTRY_ADDUCT_TYPE' => '+', 208 # {
229 'ENTRY_ENTRY_ID' => 'HMDB0040878', 209 # 'ENTRY_ADDUCT_TYPE' => '+',
230 'ENTRY_ADDUCT_MZ' => '265.056128', 210 # 'ENTRY_ENTRY_ID' => 'HMDB0040878',
231 'ENTRY_ADDUCT' => 'M+3Na', 211 # 'ENTRY_ADDUCT_MZ' => '265.056128',
232 'ENTRY_CPD_MZ' => '726.200729034', 212 # 'ENTRY_ADDUCT' => 'M+3Na',
233 'ENTRY_FORMULA' => 'C32H38O19', 213 # 'ENTRY_CPD_MZ' => '726.200729034',
234 'ENTRY_DELTA' => '2' 214 # 'ENTRY_FORMULA' => 'C32H38O19',
235 } 215 # 'ENTRY_DELTA' => '2'
236 ] 216 # }
237 ], 217 # ]
238 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ; 218 # ],
239 219 # 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
240 220 #
221 #
222
241 } 223 }
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259 ## END of the script 224 ## END of the script