[Bio] / Sprout / BBHCheck.pl Repository:
ViewVC logotype

Diff of /Sprout/BBHCheck.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.1, Mon Aug 14 04:58:30 2006 UTC revision 1.2, Mon Aug 14 05:25:50 2006 UTC
# Line 20  Line 20 
20  as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory,  as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory,
21  where I<User> is the value of the B<user> option above.  where I<User> is the value of the B<user> option above.
22    
23    =item fig
24    
25    Check the SEED for genomes that have no BBHs in Sprout.
26    
27  =item sql  =item sql
28    
29  If specified, turns on tracing of SQL activity.  If specified, turns on tracing of SQL activity.
# Line 57  Line 61 
61  # Get the command-line options and parameters.  # Get the command-line options and parameters.
62  my ($options, @parameters) = StandardSetup([qw(Sprout) ],  my ($options, @parameters) = StandardSetup([qw(Sprout) ],
63                                             {                                             {
64                                                  fig => [0, "check the SEED database as well as the Sprout"],
65                                                phone => ["", "phone number (international format) to call when load finishes"],                                                phone => ["", "phone number (international format) to call when load finishes"],
66                                             },                                             },
67                                             "",                                             "",
# Line 67  Line 72 
72  eval {  eval {
73      # Get a sprout object.      # Get a sprout object.
74      my $sprout = SFXlate->new_sprout_only();      my $sprout = SFXlate->new_sprout_only();
75        # Get the FIG object's DB handle.
76        my $fig = FIG->new();
77        my $fDBH = $fig->db_handle();
78      # Get the list of genomes.      # Get the list of genomes.
79      my @genomes = $sprout->Genomes();      my @genomes = $sprout->Genomes();
80      # Get the genome names.      # Get the genome names.
# Line 89  Line 97 
97          if ($count) {          if ($count) {
98              Trace("$name BBH count is $count.") if T(3);              Trace("$name BBH count is $count.") if T(3);
99          } else {          } else {
100                if ($options->{fig}) {
101                    # Check to see if the SEED is bad, too.
102                    my $response = $fDBH->SQL("SELECT * FROM bbh WHERE peg1 LIKE ? LIMIT 10", "", ["fig|$genome.peg%"]);
103                    if (@$response == 0) {
104                        # Here there are no BBHs anywhere.
105                        Trace("$name has no BBHs in SEED or Sprout. ***") if T(1);
106                    } else {
107                        # Here we can fix the problem by reloading the Sprout.
108                        Trace("$name has no BBHs in Sprout but is okay in SEED.") if T(1);
109                    }
110                } else {
111                        # Here we don't care about the SEED.
112              Trace("$name has no BBHs. ***") if T(1);              Trace("$name has no BBHs. ***") if T(1);
113                }
114              $badGenomes++;              $badGenomes++;
115          }          }
116      }      }
Legend:
Removed from v.1.1  
changed lines
  Added in v.1.2
MCS Webmaster
 ViewVC Help
Powered by ViewVC 1.0.3