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

NAME
       Bio::AlignIO - Handler for AlignIO Formats

SYNOPSIS
	   use Bio::AlignIO;

	   $inputfilename = "testaln.fasta";
	   $in	= Bio::AlignIO->new(-file   => $inputfilename ,
				    -format => 'fasta');
	   $out	= Bio::AlignIO->new(-file   => ">out.aln.pfam" ,
				    -format => 'pfam');

	   while ( my $aln = $in->next_aln() ) {
	       $out->write_aln($aln);
	   }

	   # OR

	   use Bio::AlignIO;

	   open	MYIN, '<', 'testaln.fasta' or die "Could not read file 'testaln.fasta':	$!\n";
	   $in	= Bio::AlignIO->newFh(-fh     => \*MYIN,
				      -format => 'fasta');
	   open	my $MYOUT, '>',	'testaln.pfam' or die "Could not write file 'testaln.pfam': $!\n";
	   $out	= Bio::AlignIO->newFh(-fh     =>  $MYOUT,
				      -format => 'pfam');

	   # World's smallest Fasta<->pfam format converter:
	   print $out $_ while <$in>;

DESCRIPTION
       Bio::AlignIO is a handler module	for the	formats	in the AlignIO set,
       for example, Bio::AlignIO::fasta. It is the officially sanctioned way
       of getting at the alignment objects. The	resulting alignment is a
       Bio::Align::AlignI-compliant object.

       The idea	is that	you request an object for a particular format.	All
       the objects have	a notion of an internal	file that is read from or
       written to. A particular	AlignIO	object instance	is configured for
       either input or output, you can think of	it as a	stream object.

       Each object has functions:

	  $stream->next_aln();

       And:

	  $stream->write_aln($aln);

       Also:

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

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

	   use Bio::AlignIO;

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

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

       And:

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

       Bio::AlignIO is patterned on the	Bio::SeqIO module and shares most of
       its features.  One significant difference is that Bio::AlignIO usually
       handles IO for only a single alignment at a time, whereas Bio::SeqIO
       handles IO for multiple sequences in a single stream.  The principal
       reason for this is that whereas simultaneously handling multiple
       sequences is a common requirement, simultaneous handling	of multiple
       alignments is not. The only current exception is	format "bl2seq"	which
       parses results of the BLAST "bl2seq" program and	which may produce
       several alignment pairs.	 This set of alignment pairs can be read using
       multiple	calls to next_aln.

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

       The new class method constructs a new Bio::AlignIO object.  The
       returned	object can be used to retrieve or print	alignment 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::AlignIO->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.

       -format
	   Specify the format of the file.  Supported formats include:

	      bl2seq	  Bl2seq Blast output
	      clustalw	  clustalw (.aln) format
	      emboss	  EMBOSS water and needle format
	      fasta	  FASTA	format
	      maf	  Multiple Alignment Format
	      mase	  mase (seaview) format
	      mega	  MEGA format
	      meme	  MEME format
	      msf	  msf (GCG) format
	      nexus	  Swofford et al NEXUS format
	      pfam	  Pfam sequence	alignment format
	      phylip	  Felsenstein PHYLIP format
	      prodom	  prodom (protein domain) format
	      psi	  PSI-BLAST format
	      selex	  selex	(hmmer)	format
	      stockholm	  stockholm format

	   Currently only those	formats	which were implemented in
	   Bio::SimpleAlign have been incorporated into	Bio::AlignIO.
	   Specifically, "mase", "stockholm" and "prodom" have only been
	   implemented for input. See the specific module (e.g.
	   Bio::AlignIO::prodom) for notes on supported	versions.

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

	   The format name is case insensitive;	"FASTA", "Fasta" and "fasta"
	   are all treated equivalently.

   Bio::AlignIO->newFh()
	  $fh =	Bio::AlignIO->newFh(-fh	  => \*FILEHANDLE, -format=>$format);
	  # read from STDIN or use @ARGV:
	  $fh =	Bio::AlignIO->newFh(-format => $format);

       This constructor	behaves	like new, but returns a	tied filehandle	rather
       than a Bio::AlignIO 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.

       -flush
	By default, all	files (or filehandles) opened for writing alignments
	will be	flushed	after each write_aln() 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 $clustal =	Bio::AlignIO->new( -file   => "<prot.aln",
					   -format => "clustalw" );
	  my $msf = Bio::AlignIO->new(-file   => ">prot.msf",
				      -format => "msf",
				      -flush  => 0 ); #	go as fast as we can!
	  while($seq = $clustal->next_aln) { $msf->write_aln($seq) }

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

   $alignment =	$AlignIO->next_aln()
       Fetch an	alignment from a formatted file.

   $AlignIO->write_aln($aln)
       Write the specified alignment to	a file..

   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
       reponsive 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 - Peter Schattner
       Email: schattner@alum.mit.edu

CONTRIBUTORS
       Jason Stajich, jason@bioperl.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::AlignIO->new(-file => $filename,
					      -format => 'Format')
	Function: Returns a new	seqstream
	Returns	: A Bio::AlignIO::Handler initialised with
		  the appropriate format
	Args	: -file	=> $filename
		  -format => format
		  -fh => filehandle to attach to
		  -displayname_flat => 1 [optional]
				       to force	the displayname	to not show start/end
				       information

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

   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 the Bio::AlignIO::Fh class
	Args	:

   format
	Title	: format
	Usage	: $format = $stream->format()
	Function: Get the alignment format
	Returns	: alignment format
	Args	: none

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

   next_aln
	Title	: next_aln
	Usage	: $aln = stream->next_aln
	Function: reads	the next $aln object from the stream
	Returns	: a Bio::Align::AlignI compliant object
	Args	:

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln($aln)
	Function: writes the $aln object into the stream
	Returns	: 1 for	success	and 0 for error
	Args	: Bio::Seq object

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

   force_displayname_flat
	Title	: force_displayname_flat
	Usage	: $obj->force_displayname_flat($newval)
	Function:
	Example	:
	Returns	: value	of force_displayname_flat (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   alphabet
	Title	: alphabet
	Usage	: $obj->alphabet($newval)
	Function: Get/Set alphabet for purpose of passing to Bio::LocatableSeq creation
	Example	: $obj->alphabet('dna');
	Returns	: value	of alphabet (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

perl v5.24.1			  2017-07-08		       Bio::AlignIO(3)

NAME | SYNOPSIS | DESCRIPTION | CONSTRUCTORS | OBJECT METHODS | FEEDBACK | AUTHOR - Peter Schattner | CONTRIBUTORS | APPENDIX

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