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Bio::SeqIO(3)	      User Contributed Perl Documentation	 Bio::SeqIO(3)

NAME
       Bio::SeqIO - Handler for SeqIO Formats

SYNOPSIS
	   use Bio::SeqIO;

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

	   while ( my $seq = $in->next_seq() ) {
		   $out->write_seq($seq);
	   }

	 # Now, to actually get at the sequence object, use the standard Bio::Seq
	 # methods (look at Bio::Seq if you don't know what they are)

	   use Bio::SeqIO;

	   $in	= Bio::SeqIO->new(-file => "inputfilename" ,
				  -format => 'genbank');

	   while ( my $seq = $in->next_seq() ) {
	      print "Sequence ",$seq->id, " first 10 bases ",
		    $seq->subseq(1,10), "\n";
	   }

	 # The SeqIO system does have a filehandle binding. Most people find this
	 # a little confusing, but it does mean you can write the world's
	 # smallest reformatter

	   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 $out $_ while <$in>;

DESCRIPTION
       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 Bio::SeqIO system can be thought of like biological file handles.
       They are attached to filehandles with smart formatting rules (eg,
       genbank format, or EMBL format, or binary trace file format) and can
       either read or write sequence objects (Bio::Seq objects, or more
       correctly, Bio::SeqI implementing objects, of which Bio::Seq is one
       such object). If you want to know what to do with a Bio::Seq object,
       read Bio::Seq.

       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->next_seq();

       and

	  $stream->write_seq($seq);

       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',
				       -fh     => \*ARGV);
	   # read from standard input or the input filenames

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

       and

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

       This makes the simplest ever reformatter

	   #!/usr/bin/perl

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

	   use Bio::SeqIO;

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

	   print $out $_ while <$in>;

CONSTRUCTORS
   Bio::SeqIO->new()
	  $seqIO = Bio::SeqIO->new(-file => 'filename',	  -format=>$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 Seq objects. new()
       accepts the following parameters:

       -file
	    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

       -fh  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.

	    A string filehandle is handy if you want to modify the output in
	    the memory, before printing it out. The following program reads in
	    EMBL formatted entries from a file and prints them out in fasta
	    format with some HTML tags:

	      use Bio::SeqIO;
	      use IO::String;
	      my $in  = Bio::SeqIO->new(-file => "emblfile",
					-format => 'EMBL');
	      while ( my $seq = $in->next_seq() ) {
		  # the output handle is reset for every file
		  my $stringio = IO::String->new($string);
		  my $out = Bio::SeqIO->new(-fh => $stringio,
					    -format => 'fasta');
		  # output goes into $string
		  $out->write_seq($seq);
		  # modify $string
		  $string =~ s|(>)(\w+)|$1<font color="Red">$2</font>|g;
		  # print into STDOUT
		  print $string;
	      }

       -format
	    Specify the format of the file.  Supported formats include fasta,
	    genbank, embl, swiss (SwissProt), Entrez Gene and tracefile
	    formats such as abi (ABI) and scf. There are many more, for a
	    complete listing see the SeqIO HOWTO
	    (http://bioperl.open-bio.org/wiki/HOWTO:SeqIO
	    <http://bioperl.open-bio.org/wiki/HOWTO:SeqIO>).

	    If no format is specified and a filename is given then the module
	    will attempt to deduce the format from the filename suffix. If
	    there is no suffix that Bioperl understands then it will attempt
	    to guess the format based on file content. If this is unsuccessful
	    then SeqIO will throw a fatal error.

	    The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta'
	    are all valid.

	    Currently, the tracefile formats (except for SCF) require
	    installation of the external Staden "io_lib" package, as well as
	    the Bio::SeqIO::staden::read package available from the bioperl-
	    ext repository.

       -alphabet
	    Sets the alphabet ('dna', 'rna', or 'protein'). When the alphabet
	    is set then Bioperl will not attempt to guess what the alphabet
	    is. This may be important because Bioperl does not always guess
	    correctly.

       -flush
	    By default, all files (or filehandles) opened for writing
	    sequences will be flushed after each write_seq() (making the file
	    immediately usable).  If you do not need this facility and would
	    like to marginally improve the efficiency of writing multiple
	    sequences to the same file (or filehandle), pass the -flush option
	    '0' or any other value that evaluates as defined but false:

	      my $gb = Bio::SeqIO->new(-file   => "<gball.gbk",
				       -format => "gb");
	      my $fa = Bio::SeqIO->new(-file   => ">gball.fa",
				       -format => "fasta",
				       -flush  => 0); # go as fast as we can!
	      while($seq = $gb->next_seq) { $fa->write_seq($seq) }

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

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

   $sequence = $seqIO->next_seq()
       Fetch the next sequence from the stream, or nothing if no more.

   $seqIO->write_seq($sequence [,$another_sequence,...])
       Write the specified sequence(s) to the stream.

   TIEHANDLE(), READLINE(), PRINT()
       These provide the tie interface.	 See perltie for more details.

FEEDBACK
   Mailing Lists
       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

   Support
       Please direct usage questions or support issues to the mailing list:

	bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and
       responsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   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 the
       web:

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

AUTHOR - Ewan Birney, Lincoln Stein
       Email birney@ebi.ac.uk
	     lstein@cshl.org

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

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

		  Additional arguments may be used to set factories and
		  builders involved in the sequence object creation. None of
		  these must be provided, they all have reasonable defaults.
		    -seqfactory	  the Bio::Factory::SequenceFactoryI object
		    -locfactory	  the Bio::Factory::LocationFactoryI object
		    -objbuilder	  the Bio::Factory::ObjectBuilderI object

       See Bio::SeqIO::Handler

   newFh
	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	:

       See Bio::SeqIO::Fh

   fh
	Title	: fh
	Usage	: $obj->fh
	Function:
	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 Bio::SeqIO class
	Args	: none

   next_seq
	Title	: next_seq
	Usage	: $seq = stream->next_seq
	Function: Reads the next sequence object from the stream and returns it.

		  Certain driver modules may encounter entries in the stream
		  that are either misformatted or that use syntax not yet
		  understood by the driver. If such an incident is
		  recoverable, e.g., by dismissing a feature of a feature
		  table or some other non-mandatory part of an entry, the
		  driver will issue a warning. In the case of a
		  non-recoverable situation an exception will be thrown.  Do
		  not assume that you can resume parsing the same stream
		  after catching the exception. Note that you can always turn
		  recoverable errors into exceptions by calling
		  $stream->verbose(2).

	Returns : a Bio::Seq sequence object, or nothing if no more sequences
		  are available

	Args	: none

       See Bio::Root::RootI, Bio::Factory::SeqStreamI, Bio::Seq

   write_seq
	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

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

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

   _concatenate_lines
	Title	: _concatenate_lines
	Usage	: $s = _concatenate_lines($line, $continuation_line)
	Function: Private. Concatenates two strings assuming that the second stems
		  from a continuation line of the first. Adds a space between both
		  unless the first ends with a dash.

		  Takes care of either arg being empty.
	Example :
	Returns : A string.
	Args	:

   _filehandle
	Title	: _filehandle
	Usage	: $obj->_filehandle($newval)
	Function: This method is deprecated. Call _fh() instead.
	Example :
	Returns : value of _filehandle
	Args	: newvalue (optional)

   _guess_format
	Title	: _guess_format
	Usage	: $obj->_guess_format($filename)
	Function: guess format based on file suffix
	Example :
	Returns : guessed format of filename (lower case)
	Args	:
	Notes	: formats that _filehandle() will guess include fasta,
		  genbank, scf, pir, embl, raw, gcg, ace, bsml, swissprot,
		  fastq and phd/phred

   sequence_factory
	Title	: sequence_factory
	Usage	: $seqio->sequence_factory($seqfactory)
	Function: Get/Set the Bio::Factory::SequenceFactoryI
	Returns : Bio::Factory::SequenceFactoryI
	Args	: [optional] Bio::Factory::SequenceFactoryI

   object_factory
	Title	: object_factory
	Usage	: $obj->object_factory($newval)
	Function: This is an alias to sequence_factory with a more generic name.
	Example :
	Returns : value of object_factory (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   sequence_builder
	Title	: sequence_builder
	Usage	: $seqio->sequence_builder($seqfactory)
	Function: Get/Set the Bio::Factory::ObjectBuilderI used to build sequence
		  objects.

		  If you do not set the sequence object builder yourself, it
		  will in fact be an instance of L<Bio::Seq::SeqBuilder>, and
		  you may use all methods documented there to configure it.

	Returns : a Bio::Factory::ObjectBuilderI compliant object
	Args	: [optional] a Bio::Factory::ObjectBuilderI compliant object

   location_factory
	Title	: location_factory
	Usage	: $seqio->location_factory($locfactory)
	Function: Get/Set the Bio::Factory::LocationFactoryI object to be used for
		  location string parsing
	Returns : a Bio::Factory::LocationFactoryI implementing object
	Args	: [optional] on set, a Bio::Factory::LocationFactoryI implementing
		  object.

perl v5.14.1			  2011-07-22			 Bio::SeqIO(3)
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