Summary

Bio::SeqIO::MultiFile - Treating a set of files as a single input stream

Package variables

Inherit

Bio::SeqIO

Synopsis

   $seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta',
                                   '-files'  => ['file1','file2'] );
   while((my $seq = $seqin->next_seq)) {
       # do something with $seq
   }

Description

Bio::SeqIO::MultiFile provides a simple way of bundling a whole
set of identically formatted sequence input files as a single stream.

Methods

Methods description

 Title   : next_seq
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

 Title   : next_primary_seq
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

 Title   : _load_file
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

 Title   : _set_file
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

 Title   : _current_seqio
 Usage   : $obj->_current_seqio($newval)
 Function:
 Example :
 Returns : value of _current_seqio
 Args    : newvalue (optional)

 Title   : _format
 Usage   : $obj->_format($newval)
 Function:
 Example :
 Returns : value of _format
 Args    : newvalue (optional)

Methods code

sub _initialize {

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

  $self->SUPER::_initialize(@args);

  my ($file_array,$format) = $self->_rearrange([qw(
					 FILES
					 FORMAT
					)],
				     @args,
				     );
  if( !defined $file_array || ! ref $file_array ) {
      $self->throw("Must have an array files for MultiFile");
  }

  if( !defined $format ) {
      $self->throw("Must have a format for MultiFile");
  }

  $self->{'_file_array'} = [];

  $self->_set_file(@$file_array);
  $self->_format($format);
  if( $self->_load_file() == 0 ) {
     $self->throw("Unable even to initialise the first file");
  }

}

sub next_seq {

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

   my $seq = $self->_current_seqio->next_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return;
       } else {
	   return $self->next_seq();
       }
   } else {
       return $seq;
   }

}

sub next_primary_seq {

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

   my $seq = $self->_current_seqio->next_primary_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return;
       } else {
	   return $self->next_primary_seq();
       }
   } else {
       return $seq;
   }

}

sub _load_file {

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

   my $file = shift(@{$self->{'_file_array'}});
   if( !defined $file ) {
       return 0;
   }
   my $seqio = Bio::SeqIO->new( '-format' => $self->_format(), -file => $file);
   # should throw an exception - but if not...
   if( !defined $seqio) {
       $self->throw("no seqio built for $file!");
   }

   $self->_current_seqio($seqio);
   return 1;

}

sub _set_file {

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

   push(@{$self->{'_file_array'}},@files);

}

sub _current_seqio {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_current_seqio'} = $value;
    }
    return $obj->{'_current_seqio'};

}

sub _format {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_format'} = $value;
    }
    return $obj->{'_format'};

}

General documentation

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

Email birney@ebi.ac.uk

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