Bio-DB-SeqFeature

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lib/Bio/DB/SeqFeature/Store.pm  view on Meta::CPAN

=head2 insert_sequence

 Title   : insert_sequence
 Usage   : $success = $db->insert_sequence($seqid,$sequence_string,$offset)
 Function: Inserts sequence data into the database at the indicated offset
 Returns : true if successful
 Args    : see below
 Status  : public

This method inserts the DNA or protein sequence fragment
$sequence_string, identified by the ID $seq_id, into the database at
the indicated offset $offset. It is used internally by the GFF3Loader
to load sequence data from the files.

=cut

###
# insert_sequence()
#
# insert a bit of primary sequence into the database

lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm  view on Meta::CPAN

     AND s.offset >= ?
     AND s.offset <= ?
   ORDER BY s.offset
END

  my $sth     = $self->_prepare($sql);
  my $seq = '';
  $self->_print_query($sql,$id,$offset1,$offset2) if DEBUG || $self->debug;
  $sth->execute($id,$offset1,$offset2) or $self->throw($sth->errstr);

  while (my($frag,$offset) = $sth->fetchrow_array) {
    substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset;
    $seq .= $frag;
  }  
  substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq);
  if ($reversed) {
    $seq = reverse $seq;
    $seq =~ tr/gatcGATC/ctagCTAG/;
  }
  $sth->finish;
  $seq;
}

lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm  view on Meta::CPAN

   WHERE s.id=ll.id
     AND ll.seqname= ?
     AND "offset" >= ?
     AND "offset" <= ?
   ORDER BY "offset"
END

  my $seq = '';
  $sth->execute($seqid,$offset1,$offset2) or $self->throw($sth->errstr);

  while (my($frag,$offset) = $sth->fetchrow_array) {
    substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset;
    $seq .= $frag;
  }
  substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq);
  if ($reversed) {
    $seq = reverse $seq;
    $seq =~ tr/gatcGATC/ctagCTAG/;
  }
  $sth->finish;
  $seq;
}

lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm  view on Meta::CPAN

   WHERE ll.id=s.id
     AND ll.seqname= ?
     AND offset >= ?
     AND offset <= ?
   ORDER BY offset
END

  my $seq = '';
  $sth->execute($seqid,$offset1,$offset2) or $self->throw($sth->errstr);

  while (my($frag,$offset) = $sth->fetchrow_array) {
    substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset;
    $seq .= $frag;
  }
  substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq);
  if ($reversed) {
    $seq = reverse $seq;
    $seq =~ tr/gatcGATC/ctagCTAG/;
  }
  $sth->finish;
  $seq;
}

lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm  view on Meta::CPAN

     AND s.offset >= ?
     AND s.offset <= ?
   ORDER BY s.offset
END

  my $sth     = $self->_prepare($sql);
  my $seq = '';
  $self->_print_query($sql,$id,$offset1,$offset2) if DEBUG || $self->debug;
  $sth->execute($id,$offset1,$offset2) or $self->throw($sth->errstr);

  while (my($frag,$offset) = $sth->fetchrow_array) {
    substr($frag,0,$start-$offset) = '' if defined $start && $start > $offset;
    $seq .= $frag;
  }  
  substr($seq,$end-$start+1) = '' if defined $end && $end-$start+1 < length($seq);
  if ($reversed) {
    $seq = reverse $seq;
    $seq =~ tr/gatcGATC/ctagCTAG/;
  }
  $sth->finish;
  $seq;
}

lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm  view on Meta::CPAN

 	yk53c10.3	15000-15500,15700-15800
 	yk53c10.5	18892-19154

This example is declaring that the ESTs named yk53c10.3 and yk53c10.5
belong to the same group named yk53c10.

=head2 Comments and the #include Directive

Lines that begin with the # sign are treated as comments and
ignored. When a # sign appears within a line, everything to the right
of the symbol is also ignored, unless it looks like an HTML fragment or
an HTML color, e.g.:

 # this is ignored
 [Example]
 glyph   = generic   # this comment is ignored
 bgcolor = #FF0000
 link    = http://www.google.com/search?q=$name#results

Be careful, because the processing of # signs uses a regexp heuristic. To be safe, 
always put a space after the # sign to make sure it is treated as a comment.