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annotate t/lib/hmdbTest.pm @ 23:2d8a310e86ce draft

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author fgiacomoni
date Thu, 19 May 2022 13:43:09 +0000
parents 4eb2de7c24d1
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1 package lib::hmdbTest ;
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3 use diagnostics; # this gives you more debugging information
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4 use warnings; # this warns you of bad practices
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5 use strict; # this prevents silly errors
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6 use Exporter ;
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7 use Carp ;
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8
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9 our $VERSION = "1.0";
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10 our @ISA = qw(Exporter);
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11 our @EXPORT = qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest);
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12 our %EXPORT_TAGS = ( ALL => [qw( testMatchesFromHmdb5WithUATest parseHmdb5CSVResultsTest getMatchesFromHmdb5WithUATest parse_hmdb_csv_resultsTest check_state_from_hmdb_uaTest test_matches_from_hmdb_uaTest extract_sub_mz_listsTest prepare_multi_masses_queryTest get_matches_from_hmdb_uaTest)] );
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14 use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ;
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15 use lib::hmdb qw( :ALL ) ;
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17 use Data::Dumper ;
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19 ## sub
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20 sub extract_sub_mz_listsTest {
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22 my ($masses, $hmdb_limits, ) = @_ ;
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24 my $oHmdb = lib::hmdb->new() ;
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25 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $hmdb_limits ) ;
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27 return ($submasses) ;
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28 }
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30 ## sub
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31 sub prepare_multi_masses_queryTest {
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33 my ($mzs ) = @_ ;
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35 my $oHmdb = lib::hmdb->new() ;
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36 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
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37
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38 return ($hmdb_masses) ;
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39 }
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41 ## sub
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42 sub get_matches_from_hmdb_uaTest {
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43
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44 my ( $hmdb_masses, $delta, $molecular_species ) = @_ ;
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45
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46 my $oHmdb = lib::hmdb->new() ;
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47 my $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
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48 print Dumper $hmdb_pages ;
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49 return ($hmdb_pages) ;
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50 }
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51
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52 ## sub
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53 sub getMatchesFromHmdb5WithUATest {
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54
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55 my ( $hmdb_masses, $delta, $molecular_species ) = @_ ;
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56
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57 my $oHmdb = lib::hmdb->new() ;
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58 my ($hmdb_pages, $status) = $oHmdb->getMatchesFromHmdb5WithUA($hmdb_masses, $delta, $molecular_species) ;
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59 print Dumper $hmdb_pages ;
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60 return ($hmdb_pages) ;
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61 }
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62
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64 ## sub
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65 sub test_matches_from_hmdb_uaTest {
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66
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67 my $oHmdb = lib::hmdb->new() ;
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68 my $status = $oHmdb->test_matches_from_hmdb_ua() ;
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69 return ($status) ;
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70 }
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71
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72 ## sub
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73 sub testMatchesFromHmdb5WithUATest {
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74
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75 my $oHmdb = lib::hmdb->new() ;
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76 my $status = $oHmdb->testMatchesFromHmdb5WithUA() ;
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77 return ($status) ;
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78 }
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80 ## sub
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81 sub check_state_from_hmdb_uaTest {
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82 my ($status ) = @_ ;
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83
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84 my $oHmdb = lib::hmdb->new() ;
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85 my $res = $oHmdb->check_state_from_hmdb_ua($status) ;
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86 return($res) ;
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87 }
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89
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90 ## sub
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91 sub parseHmdb5CSVResultsTest {
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92 my ($hmdb_pages, $mzs, $max ) = @_ ;
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93
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94 my $oHmdb = lib::hmdb->new() ;
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95 my $result = $oHmdb->parseHmdb5CSVResults($hmdb_pages, $mzs, $max) ; ## hash format result
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96 #print Dumper $result ;
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97 return($result) ;
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98 }
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100 ## sub
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101 sub parse_hmdb_csv_resultsTest {
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102 my ($hmdb_pages, $mzs, $max ) = @_ ;
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103
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104 my $oHmdb = lib::hmdb->new() ;
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105 my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max) ; ## hash format result
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106 print Dumper $result ;
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107 return($result) ;
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108 }
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111 1 ;