Modware

Bioseq

   Modware::Bioseq - Bio::SeqI implementing Object that queries a sequence in Chado instead of in memory.

     # USE CASE: PRINT THE FIRST 1000 BASES OF FEATURE_ID 1000
      
       my $chr = Modware::Bioseq->new( -feature_id => 1000 );

       print $chr->subseq (1, 1000);

     # USE CASE: ADD A Bio::SeqFeatureI COMPLIANT FEATURE TO CHROMOSOME 1, THEN PRINT THE SEQUENCE
      
         my $chr = Modware::Bioseq->new( -feature_id  => 1000 );

         my $generic_feature = new Bio::SeqFeature::Generic( 
                                  -start  => 10,
                                  -end    => 100,
                                  -strand => -1
         );

         print $generic_feature->seq->seq();

     # USE CASE: CHANGE THE SEQUENCE OF FEATURE_ID 1000
      
         my $chr = Modware::Bioseq->new( -feature_id  => 1000 );

         my $seq = 'ATCGATAGGCATAGA';#...# # this would be much longer in reality!!

         $chr->seq( $seq );

         # the new sequence is now in the database

   This class is mainly used for chromosomes and contigs on which Bio::SeqFeature annotations will be placed,
   it is mainly used internally and should not generally be used as a part of the API.

   This class behaves as a Bio::PrimarySeq object.  The sequence remains in the database while calls
   to subseq and trunc are translated into sql statements to fetch only portions of that sequence from 
   the database.

   Beware of calling the 'seq' method on one of these objects, it will pull the whole sequence into 
   memory.  If it is a chromosome, this can be very large!

Methods description

 Title   : length
 Usage   : $len = $seq->length()
 Function:
 Returns : integer representing the length of the sequence.
 Args    :

 Title    : seq
 Note     : get/set chromsoome sequence in database
 Function : returns entire seq 
 Returns  : feature_id string
 Args     : none (for now)

 Title   : subseq
 Usage   : $substring = $obj->subseq(10,40);
 Function: returns the subseq from start to end, where the first base
           is 1 and the number is inclusive, ie 1-2 are the first two
           bases of the sequence
 Returns : a string
 Args    : integer for start position
           integer for end position

 Title   : trunc
 Usage   : $subseq = $myseq->trunc(10,100);
 Function: Provides a truncation of a sequence,

 Example :
 Returns : a fresh Bio::PrimarySeqI implementing object
 Args    : Two integers denoting first and last base of the sub-sequence.

Methods code

   my ( $self, $start, $end ) = @_;

   my $dbh = new Modware::DBH;

   my $sth = $dbh->prepare("
      SELECT SEQLEN
        FROM FEATURE
       WHERE FEATURE_ID = ?
   ");

   $sth->execute( $self->primary_id() );

   return $sth->fetchrow();

   my ($self, $seq) = @_;

   if($seq) {
      my $dbh = new Modware::DBH;

      my $sth = $dbh->prepare("
            UPDATE FEATURE
               SET RESIDUES        = ?,
                   SEQLEN          = ?
             WHERE FEATURE_ID      = ?
      ");

      $sth->execute( $seq, length( $seq ), $self->primary_id() );
      return $seq;

   }
   else {

      my $dbh = new Modware::DBH;

      my $sth = $dbh->prepare("
         SELECT RESIDUES
           FROM FEATURE
          WHERE FEATURE_ID = ?
      ");

      $sth->execute( $self->primary_id() );

      return $sth->fetchrow();

   }

   my ( $self, $start, $end ) = @_;
   
   if(  defined  $start && defined $end ) {
      if( $start > $end ){
         $self->throw("Bad start,end parameters. Start [$start] has to be ".
         "less than end [$end]");
      }
      if( $start <= 0 ) {
          $self->throw("Bad start parameter ($start). Start must be positive.");
      }
      if( $end > $self->length ) {
         $self->throw("Bad end parameter ($end). End must be less than the total length of sequence (total=".$self->length.")");
      }

      my $dbh = new Modware::DBH;
      my $sth = $dbh->prepare("
         SELECT SUBSTR( RESIDUES, ?, ? )
           FROM FEATURE
          WHERE FEATURE_ID = ?
      ");

      my $subseq_length = $end - $start + 1;
      $sth->execute( $start, $subseq_length, $self->primary_id() );

      return $sth->fetchrow();

   }
   else {
      $self->warn("Incorrect parameters to subseq - must be two integers ".
      "or a Bio::LocationI object not ($start,$end)");
   }

   my ($self,$start,$end) = @_;

   my $str;
   if( defined $start && ref($start) &&
       $start->isa('Bio::LocationI') ) {
       $str = $self->subseq($start); # start is a location actually
   } elsif( !$end ) {
       $self->throw("trunc start,end -- there was no end for $start");
   } elsif( $end < $start ) {
       my $msg = "start [$start] is greater than end [$end].\n ".
       "If you want to truncated and reverse complement,\n ".
       "you must call trunc followed by revcom. Sorry.";
       $self->throw($msg);
   } else {
       $str = $self->subseq($start,$end);
   }

   my $out = Bio::PrimarySeq->new( 
        '-seq'              => $str,
        '-display_id'       => $self->display_id,
        '-accession_number' => $self->accession_number,
        '-alphabet'         => $self->alphabet,
        '-desc'             => $self->desc(),
        '-verbose'          => $self->verbose
     );
   return $out;

General documentation

   Eric Just e-just@northwestern.edu

   The rest of the documentation details each of the object
   methods. Internal methods are usually preceded with a _

Copyright © 2006, Northwestern University All rights reserved.