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)