Provided by: libbio-perl-perl_1.6.923-1_all bug


       Bio::AlignIO - Handler for AlignIO Formats


           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() ) {

           # 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>;


       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->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

           use Bio::AlignIO;

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

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


           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.


          $seqIO = Bio::AlignIO->new(-file => 'filename',   -format=>$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:

           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

              $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.

           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

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

          $fh = Bio::AlignIO->newFh(-fh   => \*FILEHANDLE, -format=>$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

        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) }


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

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

       Write the specified alignment to a file..

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


   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.
                  - General discussion  - About the mailing lists

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

       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:

AUTHOR - Peter Schattner



       Jason Stajich,


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

        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

        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    :

        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::AlignIO::Fh class
        Args    :

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

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

        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    :

        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

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

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

        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)