Bio::SeqIO MultiFile
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Summary
Bio::SeqIO::MultiFile - Treating a set of files as a single input stream
Package variables
No package variables defined.
Included modules
Bio::SeqIO
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
_current_seqioDescriptionCode
_formatDescriptionCode
_initialize
No description
Code
_load_fileDescriptionCode
_set_fileDescriptionCode
next_primary_seqDescriptionCode
next_seqDescriptionCode
Methods description
_current_seqiocode    nextTop
 Title   : _current_seqio
Usage : $obj->_current_seqio($newval)
Function:
Example :
Returns : value of _current_seqio
Args : newvalue (optional)
_formatcodeprevnextTop
 Title   : _format
Usage : $obj->_format($newval)
Function:
Example :
Returns : value of _format
Args : newvalue (optional)
_load_filecodeprevnextTop
 Title   : _load_file
Usage :
Function:
Example :
Returns :
Args :
_set_filecodeprevnextTop
 Title   : _set_file
Usage :
Function:
Example :
Returns :
Args :
next_primary_seqcodeprevnextTop
 Title   : next_primary_seq
Usage :
Function:
Example :
Returns :
Args :
next_seqcodeprevnextTop
 Title   : next_seq
Usage :
Function:
Example :
Returns :
Args :
Methods code
_current_seqiodescriptionprevnextTop
sub _current_seqio {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_current_seqio'} = $value;
    }
    return $obj->{'_current_seqio'};
}
_formatdescriptionprevnextTop
sub _format {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_format'} = $value;
    }
    return $obj->{'_format'};

}

1;
}
_initializedescriptionprevnextTop
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 ) {
     $self->throw("Unable even to initialise the first file");
  }
}
_load_filedescriptionprevnextTop
sub _load_file {
   my ($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;
}
_set_filedescriptionprevnextTop
sub _set_file {
   my ($self,@files) = @_;

   push(@{$self->{'_file_array'}},@files);
}
next_primary_seqdescriptionprevnextTop
sub next_primary_seq {
   my ($self,@args) = @_;

   my $seq = $self->_current_seqio->next_primary_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return undef;
       } else {
	   return $self->next_primary_seq();
       }
   } else {
       return $seq;
   }
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self,@args) = @_;

   my $seq = $self->_current_seqio->next_seq();
   if( !defined $seq ) {
       if( $self->_load_file() == 0) {
	   return undef;
       } else {
	   return $self->next_seq();
       }
   } else {
       return $seq;
   }
}
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/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _