Public Member Functions
public	create_coord_systems ()

public	create_seq_regions ()

public	chromosome_to_seq_region ()

public	create_assembly ()

public	assembly_contig_clone ()

public	clone_to_seq_region ()

Detailed Description

Definition at line 3 of file CaenorhabditisBriggsae.pm.

Member Function Documentation

◆ assembly_contig_clone()

public SeqStoreConverter::CaenorhabditisBriggsae::assembly_contig_clone ( )

Undocumented method

Code:

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◆ chromosome_to_seq_region()

public SeqStoreConverter::CaenorhabditisBriggsae::chromosome_to_seq_region ( )

Undocumented method

Code:

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◆ clone_to_seq_region()

public SeqStoreConverter::CaenorhabditisBriggsae::clone_to_seq_region ( )

Undocumented method

Code:

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sub clone_to_seq_region {
  my $self = shift;
  my $target_cs_name = shift;
 
  my $target = $self->target();
  my $source = $self->source();
  my $dbh    = $self->dbh();
 
  # target coord_system will have a different ID
  $target_cs_name ||= "clone";
  my $cs_id = $self->get_coord_system_id($target_cs_name);
 
  $self->debug("CaenorhabditisBriggsae Specific:Transforming clones " .
               "into $target_cs_name seq_regions");
 
  #
  # We don't want to make clones out of the WGS contigs, only out of
  # the clones with proper embl accessions.  Also for some reason the embl_offset
  # is not set in the briggsae 17/18/19 databases, which means we have to deduce the
  # length from the name of the contigs!
  #
  my $select_sth = $dbh->prepare
    ("SELECT cl.clone_id,
             CONCAT(cl.embl_acc, '.', cl.embl_version),
             ctg.name
     FROM   $source.clone cl, $source.contig ctg
         WHERE  cl.clone_id = ctg.clone_id
     AND    cl.embl_acc not like 'c%'
     ORDER BY cl.clone_id");
 
  $select_sth->execute();
 
  my ($clone_id, $embl_acc, $ctg_name);
  $select_sth->bind_columns(\$clone_id, \$embl_acc, \$ctg_name);
 
  my $highest_end = undef;
  my $current_clone = undef;
  my $current_clone_id = undef;
  my $length;
 
  my $insert_sth = $dbh->prepare
    ("INSERT INTO $target.seq_region (name, coord_system_id, length) " .
     "VALUES(?,?,?)");
 
  my $tmp_insert_sth = $dbh->prepare
    ("INSERT INTO $target.tmp_cln_map (old_id, new_id) VALUES (?, ?)");
 
  while ($select_sth->fetch()) {
    #extract the end position of the contig
    my $ctg_end;
    (undef,undef,$ctg_end) = split(/\./, $ctg_name);
 
    if(!defined($current_clone)) {
      $current_clone = $embl_acc;
      $current_clone_id = $clone_id;
      $highest_end   = $ctg_end;
    }
 
    if($current_clone ne $embl_acc) {
      #started new clone, store last one
 
      $insert_sth->execute($current_clone, $cs_id, $highest_end);
      #store mapping of old -> new ids in temp table
      $tmp_insert_sth->execute($current_clone_id, $insert_sth->{'mysql_insertid'});
 
      $current_clone = $embl_acc;
      $current_clone_id = $clone_id;
      $highest_end = $ctg_end;
    } elsif($ctg_end > $highest_end) {
      #same clone, adjust end if end of contig is highest yet seen
      $highest_end = $ctg_end;
    }
  }
 
  #insert the last clone
  $insert_sth->execute($current_clone, $cs_id, $highest_end);
  $tmp_insert_sth->execute($current_clone_id, $insert_sth->{'mysql_insertid'});
 
 
  $select_sth->finish();
  $insert_sth->finish();
  $tmp_insert_sth->finish();
 
  return;
}

◆ create_assembly()

public SeqStoreConverter::CaenorhabditisBriggsae::create_assembly ( )

Undocumented method

Code:

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◆ create_coord_systems()

public SeqStoreConverter::CaenorhabditisBriggsae::create_coord_systems ( )

Undocumented method

Code:

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◆ create_seq_regions()

public SeqStoreConverter::CaenorhabditisBriggsae::create_seq_regions ( )

Undocumented method

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/misc-scripts/surgery/SeqStoreConverter/CaenorhabditisBriggsae.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ assembly_contig_clone()

◆ chromosome_to_seq_region()

◆ clone_to_seq_region()

◆ create_assembly()

◆ create_coord_systems()

◆ create_seq_regions()