Bio::SeqIO raw
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Summary
Bio::SeqIO::raw - raw sequence file input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::SeqFactory
Bio::SeqIO
Inherit
Bio::SeqIO
Synopsis
Do not use this module directly. Use it via the Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from raw flat
file databases.
Methods
_initialize
No description
Code
next_seqDescriptionCode
write_qualDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
write_qualcodeprevnextTop
 Title   : write_qual
Usage : $stream->write_qual($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);    
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq'));      
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self,@args) = @_;
   ## When its 1 sequence per line with no formatting at all,
## grabbing it should be easy :)
my $nextline = $self->_readline(); if( !defined $nextline ){ return undef; } my $sequence = uc($nextline); $sequence =~ s/\W//g; return $self->sequence_factory->create(-seq => $sequence);
}
write_qualdescriptionprevnextTop
sub write_qual {
   my ($self,@seq) = @_;
   my @qual = ();
   foreach (@seq) {
     unless ($_->isa("Bio::Seq::SeqWithQuality")){
        warn("You cannot write raw qualities without supplying a Bio::Seq::SeqWithQuality object! You passed a ", ref($_), "\n");
        next;
     } 
     @qual = @{$_->qual};
     if(scalar(@qual) == 0) {
	    $qual[0] = "\n";
     }
     
     $self->_print (join " ", @qual,"\n") or return;

   }
   return 1;
}
1;
}
write_seqdescriptionprevnextTop
sub write_seq {
   my ($self,@seq) = @_;
   foreach my $seq (@seq) {
       $self->throw("Must provide a valid Bio::PrimarySeqI object") 
	   unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
     $self->_print($seq->seq, "\n") or return;
   }
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bioperl.org                 - General discussion
http://www.bioperl.org/MailList.shtml - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
AUTHORSTop
  Ewan Birney   <birney@ebi.ac.uk>
Lincoln Stein <lstein@cshl.org>
CONTRIBUTORSTop
  Jason Stajich <jason@bioperl.org<gt>
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _