Mercurial > repos > fgiacomoni > hmdb_ms_search

annotate t/lib/hmdbTest.pm @ 16:8b2fbd449ffd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Master branch Updating - - Fxx
author fgiacomoni
date Wed, 16 Jan 2019 10:56:59 -0500
parents 4eb2de7c24d1
children 2d8a310e86ce
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
1 package lib::hmdbTest ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
2
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
3 use diagnostics; # this gives you more debugging information
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
4 use warnings; # this warns you of bad practices
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
5 use strict; # this prevents silly errors
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
6 use Exporter ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
7 use Carp ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
8
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
9 our $VERSION = "1.0";
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
10 our @ISA = qw(Exporter);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
11 our @EXPORT = qw( 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);
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
12 our %EXPORT_TAGS = ( ALL => [qw( 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)] );
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
13
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
14 use lib '/Users/fgiacomoni/Inra/labs/perl/galaxy_tools/hmdb' ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
15 use lib::hmdb qw( :ALL ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
16
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
17 use Data::Dumper ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
18
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
19 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
20 sub extract_sub_mz_listsTest {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
21
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
22 my ($masses, $hmdb_limits, ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
23
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
24 my $oHmdb = lib::hmdb->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
25 my $submasses = $oHmdb->extract_sub_mz_lists($masses, $hmdb_limits ) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
26
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
27 return ($submasses) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
28 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
29
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
30 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
31 sub prepare_multi_masses_queryTest {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
32
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
33 my ($mzs ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
34
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
35 my $oHmdb = lib::hmdb->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
36 my ( $hmdb_masses, $nb_masses_to_submit ) = $oHmdb->prepare_multi_masses_query($mzs) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
37
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
38 return ($hmdb_masses) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
39 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
40
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
41 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
42 sub get_matches_from_hmdb_uaTest {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
43
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
44 my ( $hmdb_masses, $delta, $molecular_species ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
45
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
46 my $oHmdb = lib::hmdb->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
47 my $hmdb_pages = $oHmdb->get_matches_from_hmdb_ua($hmdb_masses, $delta, $molecular_species) ;
10
4eb2de7c24d1 Master branch Updating - - Fxx
fgiacomoni
parents: 9
diff changeset
48 print Dumper $hmdb_pages ;
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
49 return ($hmdb_pages) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
50 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
51
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
52
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
53 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
54 sub test_matches_from_hmdb_uaTest {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
55
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
56 my $oHmdb = lib::hmdb->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
57 my $status = $oHmdb->test_matches_from_hmdb_ua() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
58 return ($status) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
59 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
60
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
61
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
62 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
63 sub check_state_from_hmdb_uaTest {
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
64 my ($status ) = @_ ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
65
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
66 my $oHmdb = lib::hmdb->new() ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
67 my $res = $oHmdb->check_state_from_hmdb_ua($status) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
68 return($res) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
69 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
70
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
71
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
72
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
73 ## sub
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
74 sub parse_hmdb_csv_resultsTest {
4
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98
fgiacomoni
parents: 1
diff changeset
75 my ($hmdb_pages, $mzs, $max ) = @_ ;
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
76
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
77 my $oHmdb = lib::hmdb->new() ;
4
6091a80df951 planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98
fgiacomoni
parents: 1
diff changeset
78 my $result = $oHmdb->parse_hmdb_csv_results($hmdb_pages, $mzs, $max) ; ## hash format result
9
c32280662103 Master branch Updating - - Fxx
fgiacomoni
parents: 4
diff changeset
79 print Dumper $result ;
1
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
80 return($result) ;
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
81 }
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
82
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
83
6d0a0f8f672a planemo upload commit f67323ae4fa7fdbd9f4518ede105a7d7cd44b471
fgiacomoni
parents:
diff changeset
84 1 ;