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

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";
	   $in	= Bio::AlignIO->newFh(-fh     => *MYIN,
				      -format => 'fasta');
	   open my $MYOUT, '>', 'testaln.pfam';
	   $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://redmine.open-bio.org/projects/bioperl/

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	:

   _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 v5.14.2							    2012-03-02							 Bio::AlignIO(3pm)