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

	   use Bio::SeqIO;

	   my $in  = Bio::SeqIO->newFh(-format => $format1, -fh	=> \*ARGV );
	   my $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   => 'seqs.fasta', -format => $format);
	  $seqIO = Bio::SeqIO->new(-fh	   => \*FILEHANDLE, -format => $format);
	  $seqIO = Bio::SeqIO->new(-string => $string	  , -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

	    To read from or write to a piped command, open a filehandle	and
	    use	the -fh	option.

       -fh  You	may use	new() with a opened filehandle,	provided as a glob
	    reference. For example, to read from STDIN:

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

	    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;
	      }

	    Filehandles	can also be used to read from or write to a piped
	    command:

	      use Bio::SeqIO;
	      #convert .fastq.gz to .fasta
	      open my $zcat, 'zcat seq.fastq.gz	|' or die $!;
	      my $in=Bio::SeqIO->new(-fh=>$zcat,
				     -format=>'fastq');
	      my $out=Bio::SeqIO->new(-file=>'>seq.fasta',
				      -format=>'fasta');
	      while (my	$seq=$in->next_seq) {
		  $out->write_seq($seq)
	      }

       -string
	    A string to	read the sequences from. For example:

	       my $string = ">seq1\nACGCTAGCTAGC\n";
	       my $seqIO = Bio::SeqIO->new(-string => $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.org/howtos/SeqIO_HOWTO.html>).

	    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.

       -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) }

       -seqfactory
	    Provide a Bio::Factory::SequenceFactoryI object. See the
	    sequence_factory() method.

       -locfactory
	    Provide a Bio::Factory::LocationFactoryI object. See the
	    location_factory() method.

       -objbuilder
	    Provide a Bio::Factory::ObjectBuilderI object. See the
	    object_builder() method.

   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:

	 https://github.com/bioperl/bioperl-live/issues

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 => 'sequences.fasta',
					    -format => 'fasta');
	Function: Returns a new	sequence stream
	Returns	: A Bio::SeqIO stream initialised with the appropriate format
	Args	: Named	parameters indicating where to read the	sequences from or to
		  write	them to:
		    -file   => filename, OR
		    -fh	    => filehandle to attach to,	OR
		    -string => string

		  Additional arguments,	all with reasonable defaults:
		    -format	=> format of the sequences, usually auto-detected
		    -alphabet	=> 'dna', 'rna', or 'protein'
		    -flush	=> 0 or	1 (default: flush filehandles after each write)
		    -seqfactory	=> sequence factory
		    -locfactory	=> location factory
		    -objbuilder	=> object builder

       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: Get or set the IO filehandle
	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

   format
	Title	: format
	Usage	: $format = $stream->format()
	Function: Get the sequence format
	Returns	: sequence format, e.g.	fasta, fastq
	Args	: none

   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. This	applies	to rich	sequence formats only, e.g. genbank
		  but not fasta.

		  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 v5.32.0			  2019-12-07			 Bio::SeqIO(3)

NAME | SYNOPSIS | DESCRIPTION | CONSTRUCTORS | OBJECT METHODS | FEEDBACK | AUTHOR - Ewan Birney, Lincoln Stein | APPENDIX

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