t/CXGN/Genomic/clone.t

   1 #!/usr/bin/env perl
   2 use strict;
   3 use warnings;
   4
   5 use UNIVERSAL qw/isa/;
   6
   7 use Bio::SeqUtils;
   8
   9 use List::MoreUtils;
  10
  11 use CXGN::DB::Connection;
  12 use CXGN::DB::DBICFactory;
  13
  14 use CXGN::Tools::Text qw/commify_number/;
  15 use CXGN::CDBI::Class::DBI::TestSampler;
  16 use CXGN::Genomic::CloneIdentifiers qw/parse_clone_ident/;
  17
  18 my %config;
  19 BEGIN {
  20     %config = ( packagename => 'CXGN::Genomic::Clone',
  21                 test_repeats => 4,
  22                 numtests     => 28,
  23                );
  24
  25 }
  26 ;
  27 use Test::More;
  28 use_ok('CXGN::Genomic::Clone');
  29
  30 my $chado = CXGN::DB::DBICFactory->open_schema('Bio::Chado::Schema');
  31 my $dbh = CXGN::Genomic::Clone->db_Main;
  32 foreach my $cid ( 2, 55724,119416 ) {
  33     test_random_clone( $dbh, $cid );
  34 }
  35
  36 done_testing;
  37
  38 ############# SUBROUTINES #########
  39
  40 sub test_random_clone {
  41   my $dbh = shift;
  42   my $id = shift;
  43
  44   #test that we can retrieve it
  45   my $clone = CXGN::Genomic::Clone->retrieve($id);
  46   isa_ok $clone, 'CXGN::Genomic::Clone';
  47
  48   #diag 'testing with clone id '.$clone->clone_id;
  49
  50   #check estimated length
  51   my ($estlen) = $dbh->selectrow_array('select estimated_length from genomic.clone where clone_id=?',undef,$id);
  52   ok(!defined($estlen) && !defined($clone->estimated_length)
  53      || $clone->estimated_length == $estlen
  54     );
  55
  56   ok($clone->clone_name_with_chromosome || 'does not die','clone_name_with_chromosome method does not die');
  57
  58   #check has_a relations
  59   ok( isa($clone->library_id,'CXGN::Genomic::Library') );
  60   ok( isa($clone->clone_type_id,'CXGN::Genomic::CloneType') );
  61   #check has_many relations
  62   my $bad_chromats = grep {! isa($_,'CXGN::Genomic::Chromat')} $clone->chromat_objects;
  63   ok($bad_chromats == 0);
  64
  65   #cursory checks of sql
  66   my @sql_args = ( $clone->library_object->shortname,
  67                    $clone->platenum,
  68                    $clone->wellrow,
  69                    $clone->wellcol,
  70                  );
  71   ok($clone->clone_name_mysql(@sql_args) =~ /concat/i);
  72   ok($clone->clone_name_postgresql(@sql_args) =~ /\|\|/i);
  73   ok($clone->cornell_clone_name_mysql(@sql_args) =~ /concat/i);
  74   ok($clone->cornell_clone_name_postgresql(@sql_args) =~ /\|\|/i);
  75
  76   #clone name and cornell clone name
  77   my $valid_name_pattern = qr/^[A-Z]{2}_\w+\d{4}[A-Z]\d{2}$/;
  78   ok($clone->clone_name =~ $valid_name_pattern);
  79   ok($clone->clone_name eq $clone->arizona_clone_name);
  80   my $valid_cornell_name_pattern =
  81     $clone->library_id->shortname eq 'LE_HBa' ? qr/^P\d{3}[A-Z]\d{2}$/ :
  82       $valid_name_pattern;
  83   ok($clone->cornell_clone_name =~ $valid_cornell_name_pattern);
  84   #  warn "clone name was ".$clone->cornell_clone_name;
  85
  86   #check that we can retrieve from clone name
  87   is(CXGN::Genomic::Clone->retrieve_from_clone_name($clone->clone_name),
  88      $clone,
  89      'can retrieve self by clone name'
  90     );
  91
  92   ok($clone->library_id->library_id == $clone->library_object->library_id);
  93
  94   #test the chado_feature method
  95   my $features = $clone->chado_feature_rs( $chado );
  96   can_ok( $features, 'next', 'first', 'all' );
  97   my $feature = $features->single; #< actually execute the query also
  98
  99   #check that clone_type_object returns the right stuff
 100   ok(ref($clone->clone_type_object) eq ref($clone->clone_type_id));
 101   ok($clone->clone_type_object->clone_type_id == $clone->clone_type_id->clone_type_id);
 102
 103   #check that the sequencing status is a valid value
 104   my $seqstatus = $clone->sequencing_status;
 105   ok(grep {$seqstatus eq $_} qw/in_progress none complete/);
 106
 107   #check that the clone's sequence is valid
 108   unlike( $clone->seq || '', qr/[^ACTGXN]/i, 'clone has valid sequence or no sequence');
 109
 110   #check that the latest sequence name is kosher
 111   my $chado_name = $clone->latest_sequence_name;
 112   my $chado_name_parsable = parse_clone_ident($chado_name,'versioned_bac_seq');
 113   ok( !defined($chado_name) || $chado_name_parsable, 'latest_sequence_name returns a valid value');
 114
 115   #check restriction fragment functions
 116
 117   #check that intl_clone_name returns something that looks right
 118   is( $clone->intl_clone_name, $clone->library_object->shortname.'-'.$clone->platenum.$clone->wellrow.$clone->wellcol,
 119       'intl_clone_name looks OK');
 120
 121   my $acc = $clone->genbank_accession( $chado );
 122   my @acc = $clone->genbank_accession( $chado );
 123   if($acc) {
 124     ok(@acc == 1,'genbank_accession returns 1-element list if has genbank accession');
 125     like($acc,qr/^[A-Z]{2}\d+\.\d+$/,'genbank accession looks correctly formed');
 126   } else {
 127     ok(! defined $acc, 'genbank_accession returns undef in scalar context if no accession');
 128     ok(@acc == 0,'genbank_accession returns empty list in list context if no accession');
 129   }
 130
 131
 132   #check clone restriction fragments methods
 133   my @seqs = $clone->seq;
 134   if( @seqs == 1 ) {
 135     my $f = $clone->in_silico_restriction_fragment_sizes('HindIII');
 136     is ref($f), 'ARRAY', 'in-silico restriction func returns arrayref';
 137     ok !grep ref,@$f, 'and the arrayref is flat';
 138
 139     if( my @iv = $clone->in_vitro_restriction_fragment_sizes('HindIII') ) {
 140       my $iv = shift @iv;
 141       is ref($iv), 'ARRAY', 'in-vitro restriction func returns arrayref';
 142       ok !(grep {ref} @$iv), 'invitro arrayref is flat';
 143     } else {
 144       ok @iv == 0, 'in_vitro properly returned empty list';
 145       SKIP: { skip 'no in-vitro restriction record',1 };
 146     }
 147
 148   } else {
 149     ok !defined $clone->in_silico_restriction_fragment_sizes('HindIII'), 'no sequence, so no in silico restriction fragments';
 150     SKIP: {skip 'no finished sequence', 3}
 151   }
 152
 153 ##############################################################################
 154 }
 155