Bio::SeqIO - Handler for SeqIO Formats


    use Bio::SeqIO;

    $in  = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta');
    $out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL');
    # note: we quote -format to keep older perl's from complaining.

    while ( my $seq = $in->next_seq() ) {


    use Bio::SeqIO;

    $in  = Bio::SeqIO->newFh(-file => "inputfilename" , '-format' => 'Fasta');
    $out = Bio::SeqIO->newFh('-format' => 'EMBL');

    # World's shortest Fasta<->EMBL format converter:
    print $output $_ while <$in>;


Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use.

The SeqIO system replaces the old parse_XXX functions in the Seq object.

The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular SeqIO object instance is configured for either input or output. A specific example of a stream object is the Bio::SeqIO::fasta object.

Each stream object has functions





   $stream->type() # returns 'INPUT' or 'OUTPUT'

As an added bonus, you can recover a filehandle that is tied to the SeqIO object, allowing you to use the standard <> and print operations to read and write sequence objects:

    use Bio::SeqIO;

    $stream = Bio::SeqIO->newFh(-format => 'Fasta'); # read from standard input

    while ( $seq = <$stream> ) {
        # do something with $seq


    print $stream $seq; # when stream is in output mode

This makes the simplest ever reformatter


    $format1 = shift;
    $format2 = shift || die "Usage: reformat format1 format2 < input > output";

    use Bio::SeqIO;

    $in  = Bio::SeqIO->newFh(-format => $format1 );
    $out = Bio::SeqIO->newFh(-format => $format2 );
    #note: you might want to quote -format to keep older perl's from complaining.

    print $out $_ while <$in>;



   $seqIO = Bio::SeqIO->new(-file => 'filename',   -format=>$format);
   $seqIO = Bio::SeqIO->new(-fh   => \*FILEHANDLE, -format=>$format);
   $seqIO = Bio::SeqIO->new(-format => $format);

The new() class method constructs a new Bio::SeqIO object. The returned object can be used to retrieve or print BioSeq objects. new() accepts the following parameters:


A file path to be opened for reading or writing. The usual Perl conventions apply:

   'file'       # open file for reading
   '>file'      # open file for writing
   '>>file'     # open file for appending
   '+<file'     # open file read/write
   'command |'  # open a pipe from the command
   '| command'  # open a pipe to the command

You may provide new() with a previously-opened filehandle. For example, to read from STDIN:

   $seqIO = Bio::SeqIO->new(-fh => \*STDIN);

Note that you must pass filehandles as references to globs.

If neither a filehandle nor a filename is specified, then the module will read from the @ARGV array or STDIN, using the familiar <> semantics.


Specify the format of the file. Supported formats include:

   Fasta       FASTA format
   EMBL        EMBL format
   GenBank     GenBank format
   swiss       Swissprot format
   SCF         SCF tracefile format
   PIR         Protein Information Resource format
   GCG         GCG format
   raw         Raw format (one sequence per line, no ID)

If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, Fasta format is assumed.

The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are all supported.


   $fh = Bio::SeqIO->newFh(-fh   => \*FILEHANDLE, -format=>$format);
   $fh = Bio::SeqIO->newFh(-format => $format);
   # etc.

This constructor behaves like new(), but returns a tied filehandle rather than a Bio::SeqIO object. You can read sequences from this object using the familiar <> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this:

  @sequences = <$fh>;

Other operations, such as read(), sysread(), write(), close(), and printf() are not supported.


See below for more detailed summaries. The main methods are:

$sequence = $seqIO->next_seq()

Fetch the next sequence from the stream.

$seqIO->write_seq($sequence [,$another_sequence,...])

Write the specified sequence(s) to the stream.


These provide the tie interface. See perltie for more details.


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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.          - General discussion     - Technically-oriented discussion             - About the mailing lists

Reporting Bugs

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:

AUTHOR - Ewan Birney, Lincoln Stein


Describe contact details here


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


 Title   : new
 Usage   : $stream = Bio::SeqIO->new(-file => $filename, -format => 'Format')
 Function: Returns a new seqstream
 Returns : A Bio::SeqIO::Handler initialised with the appropriate format
 Args    : -file => $filename 
           -format => format
           -fh => filehandle to attach to


 Title   : newFh
 Usage   : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
 Function: does a new() followed by an fh()
 Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
           $sequence = <$fh>;   # read a sequence object
           print $fh $sequence; # write a sequence object
 Returns : filehandle tied to the Bio::SeqIO::Fh class
 Args    : 


 Title   : fh
 Usage   : $obj->fh
 Example : $fh = $obj->fh;      # make a tied filehandle
           $sequence = <$fh>;   # read a sequence object
           print $fh $sequence; # write a sequence object
 Returns : filehandle tied to the Bio::SeqIO::Fh class
 Args    : 


 Title   : _load_format_module
 Usage   : *INTERNAL SeqIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns : 
 Args    :


 Title   : next_seq
 Usage   : $seq = stream->next_seq
 Function: reads the next $seq object from the stream
 Returns : a Bio::Seq sequence object
 Args    : 


 Title   : next_primary_seq
 Usage   : $seq = $stream->next_primary_seq
 Function: Provides a primaryseq type of sequence object
 Returns : A Bio::PrimarySeqI object
 Args    : none


 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    : Bio::Seq object


 Title   : moltype
 Usage   : $self->moltype($newval)
 Function: Set/get the molecule type for the Seq objects to be created.
 Example : $seqio->moltype('protein')
 Returns : value of moltype: 'dna', 'rna', or 'protein'
 Args    : newvalue (optional) 
 Throws  : Exception if the argument is not one of 'dna', 'rna', or 'protein' 


 Title   : close
 Usage   : $seqio->close()
 Function: Closes the file handle associated with this seqio system
 Example :
 Returns : 
 Args    :


 Title   : _print
 Usage   : $obj->_print(@lines)
 Example : 
 Returns : writes output


 Title   : _readline
 Usage   : $obj->_readline($newval)
 Example : 
 Returns : reads a line of input


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


 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Example : 
 Returns : guessed format of filename (lower case)
 Args    :