conversion script for vega 19 -> 20

misc-scripts/surgery/vega_convert_seqstore.pl

+use strict;
+use warnings;
+
+use Getopt::Long;
+use Cwd;
+
+use vars qw(@INC);
+
+#effectively add this directory to the PERL5LIB automatically
+my $dir = cwd() . '/' . __FILE__;
+my @d = split(/\//, $dir);
+pop(@d);
+$dir = join('/', @d);
+unshift @INC, $dir;
+
+
+my ($file, $user, $password, $verbose, $force, $help, $schema, $limit);
+
+GetOptions ('file=s'      => \$file,
+            'schema=s'    => \$schema,
+            'user=s'      => \$user,
+            'password=s'  => \$password,
+            'verbose'     => \$verbose,
+            'force'       => \$force,
+            'limit=s'     => \$limit,
+            'help'        => sub { &show_help(); exit 1;} );
+
+usage("-file option is required")   if(!$file);
+usage("-schema option is required") if(!$schema);
+usage() if($help);
+
+open(FILE, $file) or die("Could not open input file '$file'");
+
+
+my @all_species_converters;
+
+while( my $line = <FILE> ) {
+  chomp($line);
+  next if $line =~ /^#/;
+  next if !$line;
+
+  my ( $species, $host, $source_db_name, $target_db_name ) = 
+    split( "\t", $line );
+
+  my $converter;
+
+  eval "require SeqStoreConverter::$species";
+
+  if($@) {
+    warn("Could not require conversion module SeqStoreConverter::$species\n" .
+         "Using SeqStoreConverter::VegaBasicConverter instead:\n$@");
+
+    require SeqStoreConverter::VegaBasicConverter;
+    $species = "VegaBasicConverter";
+  }
+
+  {
+    no strict 'refs';
+
+    $converter = "SeqStoreConverter::$species"->new
+      ( $user, $password, $host, $source_db_name, $target_db_name, 
+        $schema, $force, $verbose, $limit );
+  }
+
+  push @all_species_converters, $converter;
+}
+
+for my $converter ( @all_species_converters ) {
+  $converter->debug( "\n\n*** converting " . $converter->source . " to " . 
+                     $converter->target() . " ***");
+  $converter->transfer_meta();
+  $converter->create_coord_systems();
+  $converter->create_seq_regions();
+  $converter->create_assembly();
+  $converter->create_attribs();
+  $converter->set_top_level();
+
+  $converter->transfer_dna();
+  $converter->transfer_genes();
+  $converter->transfer_prediction_transcripts();
+  $converter->transfer_features();
+  $converter->transfer_stable_ids();
+  $converter->copy_other_tables();
+  $converter->copy_repeat_consensus();
+}
+
+
+print STDERR "*** All finished ***\n";
+
+sub usage {
+  my $msg = shift;
+
+  print STDERR "$msg\n\n" if($msg);
+
+  print STDERR <<EOF;
+usage:   perl convert_seqstore <options>
+
+options: -file <input_file>     input file with tab delimited 'species',
+                                'host', 'source_db', 'target_db' values
+                                on each line
+
+         -schema <table_file>   file containing SQL schema definition
+
+         -user <user>           a mysql db user with read/write priveleges
+
+         -password <password>   the mysql user's password
+
+         -verbose               print out debug statements
+
+         -force                 replace any target dbs that already exists
+
+         -limit <num_rows>      limit the number of features transfered to
+                                speed up testing
+
+         -help                  display this message
+
+example: perl convert_seqstore.pl -file converter.input \\
+              -schema ../../sql/table.sql -user ensadmin -password secret \\
+              -force -verbose
+
+EOF
+#'
+
+  exit;
+}