convert_seqstore.pl

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#!/usr/bin/env perl
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
 
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, $vega_schema, $limit);
 
GetOptions ('file=s'      => \$file,
            'schema=s'    => \$schema,
            'vega_schema=s' => \$vega_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 $converter;
  if ($vega_schema) {
      $species = "vega::".$species;
      eval "require SeqStoreConverter::$species";
      if($@) {
      warn("Could not require conversion module SeqStoreConverter::$species\n" .
           "Using SeqStoreConverter::BasicConverter instead:\n$@");
      require SeqStoreConverter::BasicConverter;
      $species = "BasicConverter";
      }
      else {
      warn "Using conversion module SeqStoreConverter::$species\n";
      }
  }
  
  else {
    eval "require SeqStoreConverter::$species";
    if($@) {
      warn("Could not require conversion module SeqStoreConverter::$species\n" .
           "Using SeqStoreConverter::BasicConverter instead:\n$@");
      require SeqStoreConverter::BasicConverter;
      $species = "BasicConverter";
    }
  }
 
  {
      no strict 'refs';
      $converter = "SeqStoreConverter::$species"->new
          ( $user, $password, $host, $source_db_name, $target_db_name, 
            $schema, $vega_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();
  $converter->transfer_features();
  if ($vega_schema) {
      $converter->transfer_vega_stable_ids();
  } else {
      $converter->transfer_stable_ids();
  }
  $converter->copy_other_tables();
  $converter->copy_repeat_consensus();
  $converter->create_meta_coord();
  if ($vega_schema) {
      $converter->update_clone_info();
      $converter->remove_supercontigs();
      $converter->copy_internal_clone_names();
  }
}
 
 
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
 
         -vega_schema <table_file> file containing SQL for additional Vega tables
 
         -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;
}