BasicMapper.pm

package XrefMapper::BasicMapper;

use strict;
use DBI;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Translation;
use  XrefMapper::db;

use vars '@ISA';

@ISA = qw{ XrefMapper::db };


=head1 NAME

XrefMapper::BasicMapper

=head1 DESCIPTION

This is the basic mapper routine. It will create the necessary fasta files for
both the xref and ensembl sequences. These will then be matched using exonerate
and the results written to another file. By creating a <species>.pm file and 
inheriting from this base class different matching routines, parameters, data 
sets etc can be set.

=head1 CONTACT

Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk


=cut


sub dump_seqs{
  my ($self, $xref) = @_;
  $self->dump_ensembl();
  $self->dump_xref($xref);
}

sub run_matching{
  print "NOT done yet:-)\n";
}

sub store{
  print "NOT done yet Either :-)\n";
}

sub dump_xref{
  my ($self,$xref) = @_;

  if(!defined($xref->species())){
    $xref->species($self->species);
  }
  if(!defined($xref->dir())){
    if(defined($self->species)){
      $xref->species($self->species)
    }
    else{
      $xref->species(".");
    }
  }
  #
  # the species specified must be in the database and hence have a species_id
  #
  my $sql = "select species_id from species where name = '".$xref->species."'";
  my $dbi = $xref->dbi();
  my $sth = $dbi->prepare($sql);
  $sth->execute();
  my @row = $sth->fetchrow_array();
  my $species_id;
  if (defined @row) {
    $species_id = $row[0];
  } else {
    print STDERR "Couldn't get ID for species ".$xref->species."\n";
    print STDERR "It must be one of :-\n";
    $sql = "select name from species";
    $sth = dbi()->prepare($sql);
    $sth->execute();
    while(my @row = $sth->fetchrow_array()){
      print STDERR $row[0]."\n";
    }
    die("Please try again\n");
  }

  #
  # Dump out the sequences where the species has an id of species_id
  # and the sequence type is 'dna'
  #
  $self->xref_dna_file($xref->dir."/".$xref->species."_xref_dna.fasta");
  open(XDNA,">".$xref->dir."/".$xref->species."_xref_dna.fasta") || die "Could not open xref_dna.fasta";
  my $sql = "select p.xref_id, p.sequence from primary_xref p, xref x ";
  $sql   .= "where p.xref_id = x.xref_id and ";
  $sql   .= "      p.sequence_type ='dna' and ";
  $sql   .= "      x.species_id = ".$species_id." ";
  $sth = $xref->dbi()->prepare($sql);
  $sth->execute();
  my $i = 0;
  while(my @row = $sth->fetchrow_array()){
    $i++;
    $row[1] =~ s/(.{60})/$1\n/g;
    print XDNA ">".$row[0]."\n".$row[1]."\n";
    if($i > 10){
      goto ENDDNA;
    }
  }
ENDDNA:
  close XDNA;

  #
  # Dump out the sequences where the species has an id of species_id
  # and the sequence type is 'peptide'
  #
  $self->xref_protein_file($xref->dir."/".$self->species."_xref_prot.fasta");
  open(XPEP,">".$xref->dir."/".$self->species."_xref_prot.fasta") || die "Could not open xref_prot.fasta";
  $sql    = "select p.xref_id, p.sequence from primary_xref p, xref x ";
  $sql   .= "where p.xref_id = x.xref_id and ";
  $sql   .= "      p.sequence_type ='peptide' and ";
  $sql   .= "      x.species_id = ".$species_id." ";
  $sth = $xref->dbi()->prepare($sql);
  $sth->execute();
  $i = 0;
  while(my @row = $sth->fetchrow_array()){
    $i++;
    $row[1] =~ s/(.{60})/$1\n/g;
    print XPEP ">".$row[0]."\n".$row[1]."\n";
    if($i > 10){
      goto ENDXPEP;
    }
  }
ENDXPEP:
  close XPEP;

}


sub dump_ensembl{
  my ($self) = @_;

  $self->fetch_and_dump_seq();

}


sub fetch_and_dump_seq{
  my ($self) = @_;

  my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
                           -dbname  => $self->dbname(),
                           -host    => $self->host(),
                           -port    => $self->port(),
                           -password => $self->password(),
                           -user     => $self->user(),
                           -group    => 'core');

  #
  # store ensembl dna file name and open it
  #
  
  # if no directory set then dump in the current directory.
  if(!defined($self->dir())){
    $self->dir(".");
  }
  $self->ensembl_dna_file($self->dir."/".$self->species."_dna.fasta");
  open(DNA,">".$self->ensembl_dna_file()) 
    || die("Could not open dna file for writing: ".$self->ensembl_dna_file."\n");

  #
  # store ensembl protein file name and open it
  #
  $self->ensembl_protein_file($self->dir."/".$self->species."_protein.fasta");
  open(PEP,">".$self->ensembl_protein_file()) 
    || die("Could not open dna file for writing: ".$self->ensembl_protein_file."\n");

  my $gene_adap = $db->get_GeneAdaptor();
  my @gene_ids = @{$gene_adap->list_dbIDs()};
  my $i =0;
  foreach my $gene_id (@gene_ids){
    $i++;
    my $gene = $gene_adap->fetch_by_dbID($gene_id);
    print "gene ".$gene."\n";
    foreach my $transcript (@{$gene->get_all_Transcripts()}) {
      my $seq = $transcript->spliced_seq(); 
      $seq =~ s/(.{60})/$1\n/g;
      print DNA ">" . $transcript->dbID() . "\n" .$seq."\n";
      my $trans = $transcript->translation();
      my $translation = $transcript->translate();
      print "tranlation ".$translation."\n";
      my $pep_seq = $translation->seq();
      $pep_seq =~ s/(.{60})/$1\n/g;
      print PEP ">".$trans->dbID()."\n".$pep_seq."\n";
    }
    if($i > 10){
      goto FIN;
    }
  }
FIN:
  close DNA;
  close PEP;
}



###
# Getter/Setter methods
###

sub xref_protein_file{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_xref_prot_file} = $arg );
  return $self->{_xref_prot_file};
}

sub xref_dna_file{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_xref_dna_file} = $arg );
  return $self->{_xref_dna_file};
}

sub ensembl_protein_file{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_ens_prot_file} = $arg );
  return $self->{_ens_prot_file};
}

sub ensembl_dna_file{
  my ($self, $arg) = @_;

  (defined $arg) &&
    ($self->{_ens_dna_file} = $arg );
  return $self->{_ens_dna_file};
}


#sub get_ensembl_type{
#  my %type;
#
#  $type{'Translation'} = "peptide";
#  $type{'Transcript'} = "dna";
#
#  return \%type;
#}

1;