bp_seq_load.pl

gistfile1.pl

#!/usr/bin/perl -w

eval 'exec /usr/bin/perl  -S $0 ${1+"$@"}'
    if 0; # not running under some shell

use strict;

use Getopt::Long;

use Bio::DB::SeqFeature::Store;
use Bio::SeqIO;

my $DSN         = 'dbi:mysql:test';
my $SFCLASS     = 'Bio::DB::SeqFeature';
my $ADAPTOR     = 'DBI::mysql';
my $NAMESPACE;
my $VERBOSE  = 1;
my $FAST     = 0;
my $TMP      = File::Spec->tmpdir();
my $IGNORE_SEQREGION   = 0;
my $CREATE   = 0;
my $USER     = '';
my $PASS     = '';
my $COMPRESS = 0;
my $INDEX_SUB = 1;
my $NOALIAS_TARGET = 0;
my $SUMMARY_STATS  = 0;

GetOptions(
       'dsn=s'          => \$DSN,
       'seqfeature=s'   => \$SFCLASS,
       'namespace=s'    => \$NAMESPACE,
       'adaptor=s'      => \$ADAPTOR,
       'verbose!'       => \$VERBOSE,
       'create'         => \$CREATE,
       'user=s'         => \$USER,
       'password=s'     => \$PASS,
       'S|subfeatures!' => \$INDEX_SUB,
       'noalias-target' => \$NOALIAS_TARGET,
       ) || die <<END;
Usage: $0 [options] gff_file1 gff_file2...
  Options:
          -d --dsn        The database name ($DSN)
          -n --namespace  The table prefix, excluding ($NAMESPACE)
          -s --seqfeature The type of SeqFeature to create ($SFCLASS)
          -a --adaptor    The storage adaptor to use ($ADAPTOR)
          -v --verbose    Turn on verbose progress reporting
             --noverbose  Turn off verbose progress reporting
          -c --create     Create the database and reinitialize it (will erase contents)
          -u --user       User to connect to database as
          -p --password   Password to use to connect to database

END

my @options;
@options = ($USER,$PASS) if $USER || $PASS;

my $store = Bio::DB::SeqFeature::Store->new
(
    -dsn        => $DSN,
    -namespace  => $NAMESPACE,
    -adaptor    => $ADAPTOR,
    -user       => $USER,
    -pass       => $PASS,
    -write      => 1,
    -create     => $CREATE,
)
or die "Couldn't create connection to the database";

$store->init_database('erase') if $CREATE;
$SUMMARY_STATS++               if $CREATE; # this is a good thing



my $seq_io = Bio::SeqIO->
    new(-file => "<$ARGV[0]");

while (my $seq_obj = $seq_io->next_seq) {
  $store->
    insert_sequence( $seq_obj->accession_number,
		     $seq_obj->seq
		   );
}

exit 0;