BioSeqIO_____perldoc

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
 
        $format1 = shift;
        $format2 = shift || die
           "Usage: reformat format1 format2 < input > output";
 
        use Bio::SeqIO;
 
        $in  = Bio::SeqIO->newFh(-format => $format1, -fh => /*ARGV );
        $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()
       $seqIO = Bio::SeqIO->new(-file => 'filename',   -format=>$format);
       $seqIO = Bio::SeqIO->new(-fh   => /*FILEHANDLE, -format=>$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
            '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::SeqIO->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.
 
         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;
           }
 
    -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.open-bio.org/wiki/HOWTO:SeqIO>).
 
         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 Fasta format is assumed.
 
         The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta'
         are all valid.
 
         Currently, the tracefile formats (except for SCF) require
         installation of the external Staden "io_lib" package, as well as
         the Bio::SeqIO::staden::read package available from the bioperl-ext
         repository.
 
    -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 = new Bio::SeqIO -file   => "<gball.gbk",
                                   -format => "gb";
           my $fa = new Bio::SeqIO -file   => ">gball.fa",
                                   -format => "fasta",
                                   -flush  => 0; # go as fast as we can!
           while($seq = $gb->next_seq) { $fa->write_seq($seq) }
 
  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.
 
  $seqIO->write_seq($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
 
  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:
 
      http://bugzilla.open-bio.org/
 
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 => $filename,
                                         -format => 'Format')
     Function: Returns a new sequence stream
     Returns : A Bio::SeqIO stream initialised with the appropriate format
     Args    : Named parameters:
                 -file => $filename
                 -fh => filehandle to attach to
                 -format => format
 
               Additional arguments may be used to set factories and
               builders involved in the sequence object creation. None of
               these must be provided, they all have reasonable defaults.
                 -seqfactory   the Bio::Factory::SequenceFactoryI object
                 -locfactory   the Bio::Factory::LocationFactoryI object
                 -objbuilder   the Bio::Factory::ObjectBuilderI object
 
    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:
     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
     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
 
  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.
 
               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.