Bio::EnsEMBL::DBSQL CompressedSequenceAdaptor
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Summary
Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor - Facilitates DB storage and retrieval of compressed sequence
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::SequenceAdaptor
Inherit
Bio::EnsEMBL::DBSQL::SequenceAdaptor
Synopsis
  $seq_adptr = $database_adaptor->get_SequenceAdaptor();
$dna = ${ $seq_adptr->fetch_by_Slice_start_end_strand( $slice, 1, 1000, -1 ) };
Description
An adaptor for the retrieval of compressed DNA sequence from the EnsEMBL
database
Methods
_fetch_seq
No description
Code
storeDescriptionCode
Methods description
storecode    nextTop
  Arg [1]    : string $seq_region_id the id of the sequence region this dna
will be associated with.
Arg [2] : string reference $sequence the dna sequence to be stored in
the database
Example : $dbID = $seq_adaptor->store(12,\'ACTGGGTACCAAACAAACACAACA');
Description: stores a dna sequence in the databases dna table and returns the
database identifier for the new record.
Returntype : int
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::RawContigAdaptor::store
Status : Stable
Methods code
_fetch_seqdescriptionprevnextTop
sub _fetch_seq {
  my $self          = shift;
  my $seq_region_id = shift;
  my $start         = shift;
  my $len           = shift;

  #calculate the offset and start in the compressed sequence 
my $comp_start = ($start-1 >> 2) + 1; my $comp_len = ($len >> 2) + 2; my ($bvector, $nline); my $sth = $self->prepare( "SELECT SUBSTRING( d.sequence, ?, ?), n_line FROM dnac d WHERE d.seq_region_id = ?"); $sth->bind_param(1,$comp_start,SQL_INTEGER); $sth->bind_param(2,$comp_len ,SQL_INTEGER); $sth->bind_param(3,$seq_region_id,SQL_INTEGER); $sth->execute(); $sth->bind_columns(\$bvector,\$ nline); $sth->fetch(); $sth->finish(); #convert sequence from binary string to 0123 string
my $bitlen = length($bvector) << 2;
my $str = '';
for(my $i=0; $i < $bitlen; $i++) {
$str .= vec($bvector, $i, 2);
}

#convert from 0123 to ACTG
$str =~ tr/0123/ACTG/;

$str = substr($str, ($start-1)%4, $len);

#expand the nlines and place them back in the sequence
my @nlines = split(/:/, $nline);
foreach my $nl (@nlines) {
my ($offset,$char,$nlen) = $nl =~ /(\d+)(\D)(\d+)/;

#skip nlines entirely out of range
next if(($offset+$nlen-1) < $start || $offset > ($start+$len-1));

#obtain relative offset into requested region
$offset = $offset - $start + 1;

#nlines that partially overlap requested region have to be shrunk
if($offset < 1) {
$nlen = $nlen - (1-$offset);
$offset = 1;
}
if($offset + $nlen > $start+$len) {
$nlen = $len - $offset + 1;
}

substr($str,$offset-1,$nlen) = $char x $nlen;
}

return \$str;
}
storedescriptionprevnextTop
sub store {
  my ($self, $seq_region_id, $sequence) = @_;

  if(!$seq_region_id) {
    throw('seq_region_id is required');
  }

  $sequence = uc($sequence);

  my $bvector = '';

  #convert sequence to 0s,1s,2s and 3s
$sequence =~ tr/ACTG/0123/; #nlines cover sequence which is not ACTG such as N
#nline format is a set of colon delimited int, char, int triplets:
#<offset><code><length>
my($nline_char,$nline_len,$nline_off); my @nlines; my $len = length($sequence); for(my $i=0; $i < $len; $i++) { my $char = substr($sequence,$i,1); #quickly check if this character was an A,C,T or G (and was converted to
# a 0,1,2,3)
if($char =~ /[0-3]/) { vec($bvector, $i,2) = $char; if($nline_char) { #end of an nline
push @nlines, "$nline_off$nline_char$nline_len"; $nline_char = undef; $nline_len = 0; $nline_off = 0; } } else { #this was not an ACTG
if($nline_char) { if($nline_char eq $char) { #continuation of an nline
$nline_len++; } else { #end of a previous nline and start of a new one
push @nlines, "$nline_off$nline_char$nline_len"; $nline_char = $char; $nline_len = 1; $nline_off = $i+1; } } else { #start of a new nline
$nline_char = $char; $nline_len = 1; $nline_off = $i+1; } $char = 0; #need to put numeric val into bitvector despite nline
} vec($bvector, $i,2) = $char; } my $nline = join(':', @nlines); my $statement = $self->prepare( "INSERT INTO dnac(seq_region_id, sequence, n_line) VALUES(?,?,?)"); $statement->bind_param(1,$seq_region_id,SQL_INTEGER); $statement->bind_param(2,$bvector,SQL_BLOB); $statement->bind_param(3,$nline,SQL_LONGVARCHAR); $statement->execute(); $statement->finish(); return; } 1;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html
CONTACTTop
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developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.