hmdb_ms_search: t/hmdb_managerTest.pl annotate

annotate t/hmdb_managerTest.pl @ 16:8b2fbd449ffd draft

Master branch Updating - - Fxx

author	fgiacomoni
date	Wed, 16 Jan 2019 10:56:59 -0500
parents	4eb2de7c24d1
children	2d8a310e86ce

rev	line source
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	1 #! perl
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	2 use diagnostics;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	3 use warnings;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	4 no warnings qw/void/;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	5 use strict;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	6 no strict "refs" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	7 use Test::More qw( no_plan );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	8 use Test::Exception;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	9 use FindBin ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	10 use Carp ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	11
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	12 ## Specific Modules
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	13 use lib $FindBin::Bin ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	14 my $binPath = $FindBin::Bin ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	15 use lib::hmdbTest qw( :ALL ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	16
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	17
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	18 ## To launch the right sequence : API, MAPPER, THREADER, ...
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	19 #my $sequence = 'MAPPER' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	20 my $sequence = 'MAIN' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	21 my $current_test = 1 ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	22
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	23 if ($sequence eq "MAIN") {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	24 print "\n\t\t\t\t * * * * * * \n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	25 print "\t * * * - - - Test HMDB Main script - - - * * * \n\n" ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	26
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	27
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	28 print "\n Test $current_test extract_sub_mz_lists with an empty list of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	29
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	30 throws_ok{ extract_sub_mz_listsTest([], 3)} '/The provided mzs list is empty/', 'Method \'extract_sub_mz_lists\' detects empty argument and died correctly' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	31
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	32 print "\n Test $current_test extract_sub_mz_lists with a list of mzs and a limit of 3 \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	33 is_deeply( extract_sub_mz_listsTest(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	34 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ], 3),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	35 [ [ '175.01', '238.19', '420.16' ], [ '780.32', '956.25', '1100.45' ] ],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	36 'Method \'extract_sub_mz_lists\' works with a list and return a well formated list of sublist of mzs');
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	37
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	38 print "\n Test $current_test prepare_multi_masses_query with an empty list of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	39 throws_ok{ prepare_multi_masses_queryTest([])} '/The input method parameter mass list is empty/', 'Method \'prepare_multi_masses_query\' detects empty argument and died correctly' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	40
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	41 print "\n Test $current_test prepare_multi_masses_query with a list of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	42 is_deeply( prepare_multi_masses_queryTest(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	43 ['175.01', '238.19', '420.16', '780.32', '956.25', '1100.45' ] ),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	44 '175.01%0D%0A238.19%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	45 'Method \'prepare_multi_masses_query\' works with a list of and return a well formated string for hmdb querying');
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	46
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	47 print "\n Test $current_test get_matches_from_hmdb_ua with a well-formated string of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	48 is_deeply( get_matches_from_hmdb_uaTest(
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	49 '175.01%0D%0A420.16%0D%0A780.32%0D%0A956.25%0D%0A1100.45%0D%0A', 0.001, 'positive'),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	50 [
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	51 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	52 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	53 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	54 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	55 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	56 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	57 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	58 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	59 ## Update format - 2018-01-19... HMDB V04
10 4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	60 # '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	61 # '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	62 # '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	63 # '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	66 # '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	67 ## Update results - 2018-09-20... HMDBv4
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	68 #'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	75 '175.01,HMDB0000257,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	76 '175.01,HMDB0060293,Thiosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	79 '175.01,HMDB0135622,{4-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	80 '175.01,HMDB0135448,{3-[(2E)-3-phenylprop-2-enoyl]phenyl}oxidanesulfonic acid,n/a,C15H12O5S,304.04054466,M+2Na,+,175.00949,3',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	81 '175.01,HMDB0240280,Methanesulfonic acid,C11145,CH4O3S,95.988114684,M+DMSO+H,+,175.009335,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	82 '175.01,HMDB0003745,Coenzyme m,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	83 '175.01,HMDB0142159,[2-hydroxy-2-(2-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	84 '175.01,HMDB0142160,[2-hydroxy-1-(2-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	85 '175.01,HMDB0142162,"[3-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	86 '175.01,HMDB0142166,"[4-(1,2-dihydroxy-2-phenylethyl)phenyl]oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	87 '175.01,HMDB0142164,[2-hydroxy-1-(3-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	88 '175.01,HMDB0142163,[2-hydroxy-2-(3-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	89 '175.01,HMDB0142167,[2-hydroxy-2-(4-hydroxyphenyl)-1-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	90 '175.01,HMDB0142168,[2-hydroxy-1-(4-hydroxyphenyl)-2-phenylethoxy]sulfonic acid,n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	91 '175.01,HMDB0129951,"{3-[2-(3,5-dihydroxyphenyl)ethyl]phenyl}oxidanesulfonic acid",n/a,C14H14O6S,310.051109345,M+H+K,+,175.010772,4',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	92 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	95 '175.01,HMDB0155176,5-Hydroxy-6-hydrouracil,n/a,C4H6N2O3,130.037842061,M+2Na-H,+,175.009002,6',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	96 '420.16,HMDB0060838,N-Desmethyl-p-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	97 '420.16,HMDB0060836,N-Desmethyl-O-hydroxy rosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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',
4eb2de7c24d1 Master branch Updating - - Fxx fgiacomoni parents: 9 diff changeset	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'
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	103 ],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	104 'Method \'get_matches_from_hmdb_ua\' works with a well-formated string of mzs and return a complete csv from hmdb');
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	105
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	106 print "\n Test $current_test test_matches_from_hmdb_ua to get hmdb status \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	107 is_deeply (test_matches_from_hmdb_uaTest (),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	108 \'200',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	109 'The HMDB server is available: returns successful HTTP requests' ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	110
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	111 print "\n Test $current_test check_state_from_hmdb_ua to manage script execution with the hmdb server status \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	112 is_deeply (check_state_from_hmdb_uaTest (\'200'),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	113 1,
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	114 'The status 200 returns no error/warn' ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	115
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	116 print "\n Test $current_test prepare_multi_masses_query with an empty list of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	117 throws_ok{ check_state_from_hmdb_uaTest(\'504')}
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	118 '/Gateway Timeout: The HMDB server was acting as a gateway or proxy and did not receive a timely response from the upstream server/',
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	119 'Method \'check_state_from_hmdb_ua\' detects HTTP error code returned by HMDB and died correctly' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	120
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	121 print "\n Test $current_test parse_hmdb_csv_results with the correct inputs for hmdb outputs parsing (csv format) \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	122 is_deeply ( parse_hmdb_csv_resultsTest (
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	123 [
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	124 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	125 # '175.01,HMDB60293,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,0.000125',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	126 # '175.01,HMDB03745,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,0.000676',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	127 # '175.01,HMDB31436,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,0.000895',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	128 # '175.01,HMDB33657,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	129 # '175.01,HMDB35230,C17H10O6,310.047738052,M+H+K,+,175.009086,0.000914',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	130 # '420.16,HMDB60838,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	131 # '420.16,HMDB60836,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,0.000683'
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	132 ## Update format - 2018-01-19... HMDB V04
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	133 '175.01,HMDB0060293,Hydroxidodioxidosulfidosulfate,C05529,H2O3S2,113.94453531,M+IsoProp+H,+,175.009875,1',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	134 '175.01,HMDB0003745,Mesna,C03576,C2H6O3S2,141.975835438,M+CH3OH+H,+,175.009324,4',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	135 '175.01,HMDB0031436,Silicic acid,n/a,H4O4Si,95.987885149,M+DMSO+H,+,175.009105,5',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	136 '175.01,HMDB0033657,De-o-methylsterigmatocystin,C03683,C17H10O6,310.047738052,M+H+K,+,175.009086,5',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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',
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	139 '420.16,HMDB0060836,N-Desmethyl O-hydroxyrosiglitazone,n/a,C17H17N3O4S,359.093976737,M+IsoProp+H,+,420.159317,2',
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	140 ],
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	141 ['175.01', '238.19', '420.16'],
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	142 10
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	143 ),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	144 [
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	145 [
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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' },
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'},
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'},
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'},
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	151 ],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	152 [],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	153 [
4 6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'},
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98 fgiacomoni parents: 1 diff changeset	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'}
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	156 ]
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	157 ],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	158 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	159
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	160 print "\n Test $current_test parse_hmdb_csv_results with a void hmdb output and a list of mzs \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	161 is_deeply ( parse_hmdb_csv_resultsTest ( [], ['175.01', '238.19', '420.16'] ),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	162 [ [], [], [] ],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	163 'Method \'parse_hmdb_csv_results\' works with a empty csv output and returns an empty but well formatted array' ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	164
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	165 print "\n Test $current_test parse_hmdb_csv_results with a void hmdb output and a void mz list \n" ; $current_test++;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	166 is_deeply ( parse_hmdb_csv_resultsTest ( [], [] ),
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	167 [],
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	168 'Method \'parse_hmdb_csv_results\' works with a empty csv output/mz list and returns an empty but well formatted array' ) ;
9 c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	169
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	170 ## Other example... from mz 265.0567515
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	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++;
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	172 is_deeply ( parse_hmdb_csv_resultsTest (
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	173 [
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	174 'query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m/z,delta(ppm)',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	175 '265.0567515,HMDB0059667,3-Methylsulfolene,n/a,C5H8O2S,132.02450019,2M+H,+,265.056276,2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	176 '265.0567515,HMDB0038767,Camelliaside b,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	177 '265.0567515,HMDB0039759,Kaempferol 3-(2g-apiosylrobinobioside),n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	178 '265.0567515,HMDB0040875,Isoschaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	179 '265.0567515,HMDB0040878,Schaftoside 4\'-glucoside,n/a,C32H38O19,726.200729034,M+3Na,+,265.056128,2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	180 '265.0567515,HMDB0059600,erythro-5-Phosphonooxy-L-lysine,C03366,C6H15N2O6P,242.066772734,M+Na,+,265.055991,3',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	181 '265.0567515,HMDB0061174,"2,4-Imidazolidinedione, 3-ethyl-5-(4-hydroxyphenyl)-",n/a,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	182 '265.0567515,HMDB0015571,Oxitriptan,C00643,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	183 '265.0567515,HMDB0000472,5-hydroxy-l-tryptophan,C01017,C11H12N2O3,220.08479226,M+2Na-H,+,265.055952,3',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	184 '265.0567515,HMDB0030584,Silidianin,n/a,C25H24O10,484.136946988,M+2Na,+,265.057691,4',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	185 ],
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	186 ['265.0567515'],
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	187 5
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	188 ),
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	189 [
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	190 [
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	191 {
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	192 'ENTRY_DELTA' => '2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	193 'ENTRY_FORMULA' => 'C5H8O2S',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	194 'ENTRY_ENTRY_ID' => 'HMDB0059667',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	195 'ENTRY_ADDUCT_MZ' => '265.056276',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	196 'ENTRY_ADDUCT_TYPE' => '+',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	197 'ENTRY_CPD_MZ' => '132.02450019',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	198 'ENTRY_ADDUCT' => '2M+H'
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	199 },
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	200 {
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	201 'ENTRY_ADDUCT_MZ' => '265.056128',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	202 'ENTRY_ENTRY_ID' => 'HMDB0038767',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	203 'ENTRY_ADDUCT_TYPE' => '+',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	204 'ENTRY_CPD_MZ' => '726.200729034',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	205 'ENTRY_ADDUCT' => 'M+3Na',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	206 'ENTRY_DELTA' => '2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	207 'ENTRY_FORMULA' => 'C32H38O19'
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	208 },
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	209 {
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	210 'ENTRY_DELTA' => '2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	211 'ENTRY_FORMULA' => 'C32H38O19',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	212 'ENTRY_ENTRY_ID' => 'HMDB0039759',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	213 'ENTRY_ADDUCT_MZ' => '265.056128',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	214 'ENTRY_ADDUCT_TYPE' => '+',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	215 'ENTRY_CPD_MZ' => '726.200729034',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	216 'ENTRY_ADDUCT' => 'M+3Na'
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	217 },
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	218 {
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	219 'ENTRY_FORMULA' => 'C32H38O19',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	220 'ENTRY_DELTA' => '2',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	221 'ENTRY_ADDUCT_TYPE' => '+',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	222 'ENTRY_ADDUCT_MZ' => '265.056128',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	223 'ENTRY_ENTRY_ID' => 'HMDB0040875',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	224 'ENTRY_CPD_MZ' => '726.200729034',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	225 'ENTRY_ADDUCT' => 'M+3Na'
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	226 },
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	227 {
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	228 'ENTRY_ADDUCT_TYPE' => '+',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	229 'ENTRY_ENTRY_ID' => 'HMDB0040878',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	230 'ENTRY_ADDUCT_MZ' => '265.056128',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	231 'ENTRY_ADDUCT' => 'M+3Na',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	232 'ENTRY_CPD_MZ' => '726.200729034',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	233 'ENTRY_FORMULA' => 'C32H38O19',
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	234 'ENTRY_DELTA' => '2'
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	235 }
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	236 ]
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	237 ],
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	238 'Method \'parse_hmdb_csv_results\' works with a well-formated csv output and returns a a well formated array' ) ;
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	239
c32280662103 Master branch Updating - - Fxx fgiacomoni parents: 4 diff changeset	240
1 6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	241 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	242
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	243
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	244
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	245
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	246
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	247
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	248
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	249
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	250
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	251
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	252
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	253
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	254
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	255
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	256
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	257
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	258
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471 fgiacomoni parents: diff changeset	259 ## END of the script

Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate t/hmdb_managerTest.pl @ 16:8b2fbd449ffd draft