Bio SeqIO
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SeqIO - Handler for SeqIO Formats
Package variables
Privates (from "my" definitions)
%valid_alphabet_cache;
$entry = 0
Included modules
Bio::Factory::FTLocationFactory
Bio::Factory::SequenceStreamI
Bio::Root::IO
Bio::Root::Root
Bio::Seq::SeqBuilder
Bio::Tools::GuessSeqFormat
Inherit
Bio::Factory::SequenceStreamI Bio::Root::IO Bio::Root::Root
Synopsis
    use Bio::SeqIO;

    $in  = Bio::SeqIO->new(-file => "inputfilename" , '-format' => 'Fasta');
    $out = Bio::SeqIO->new(-file => ">outputfilename" , '-format' => 'EMBL');
    # note: we quote -format to keep older Perls from complaining.

    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 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'); # read from standard input

    while ( $seq = <$stream> ) {
	# do something with $seq
    }
and
    print $stream $seq; # when stream is in output mode
This makes the simplest ever reformatter
    #!/usr/local/bin/perl

    $format1 = shift;
    $format2 = shift || die "Usage: reformat format1 format2 < input > output";

    use Bio::SeqIO;

    $in  = Bio::SeqIO->newFh(-format => $format1 );
    $out = Bio::SeqIO->newFh(-format => $format2 );
    #note: you might want to quote -format to keep older perl's from complaining.

    print $out $_ while <$in>;
Methods
BEGIN
No description
Code
newDescriptionCode
newFhDescriptionCode
fhDescriptionCode
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
alphabetDescriptionCode
_load_format_moduleDescriptionCode
_concatenate_linesDescriptionCode
_filehandleDescriptionCode
_guess_formatDescriptionCode
DESTROY
No description
Code
TIEHANDLEDescriptionCode
READLINE
No description
Code
PRINT
No description
Code
sequence_factoryDescriptionCode
object_factoryDescriptionCode
sequence_builderDescriptionCode
location_factoryDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : $stream = Bio::SeqIO->new(-file => $filename, -format => 'Format')
 Function: Returns a new seqstream
 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
newFhcodeprevnextTop
 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
fhcodeprevnextTop
 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_seqcodeprevnextTop
 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_seqcodeprevnextTop
 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
alphabetcodeprevnextTop
 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_modulecodeprevnextTop
 Title   : _load_format_module
 Usage   : *INTERNAL SeqIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :
_concatenate_linescodeprevnextTop
 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    :
_filehandlecodeprevnextTop
 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: This method is deprecated. Call _fh() instead.
 Example :
 Returns : value of _filehandle
 Args    : newvalue (optional)
_guess_formatcodeprevnextTop
 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
TIEHANDLE(), READLINE(), PRINT()codeprevnextTop
These provide the tie interface. See perltie for more details.
sequence_factorycodeprevnextTop
 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_factorycodeprevnextTop
 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_buildercodeprevnextTop
 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 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_factorycodeprevnextTop
 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.
Methods code
BEGINdescriptionprevnextTop
sub BEGIN {
    eval { require Bio::SeqIO::staden::read; };
}
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;

    # or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::SeqIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ); if( ! $format ) { if ($param{-file}) { $format = Bio::Tools::GuessSeqFormat->new(-file => $param{-file}||$ARGV[0] )->guess; } elsif ($param{-fh}) { $format = Bio::Tools::GuessSeqFormat->new(-fh => $param{-fh}||$ARGV[0] )->guess; } } $format = "\L$format"; # normalize capitalization to lower case
$class->throw("Unknown format given or could not determine it [$format]") unless $format; return undef unless( $class->_load_format_module($format) ); return "Bio::SeqIO::$format"->new(@args); }
}
newFhdescriptionprevnextTop
sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}
fhdescriptionprevnextTop
sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;

    # flush is initialized by the Root::IO init
my ($seqfact,$locfact,$objbuilder) = $self->_rearrange([qw(SEQFACTORY LOCFACTORY OBJBUILDER) ], @args); $locfact = Bio::Factory::FTLocationFactory->new(-verbose => $self->verbose) if ! $locfact; $objbuilder = Bio::Seq::SeqBuilder->new(-verbose => $self->verbose) unless $objbuilder; $self->sequence_builder($objbuilder); $self->location_factory($locfact); # note that this should come last because it propagates the sequence
# factory to the sequence builder
$seqfact && $self->sequence_factory($seqfact); # initialize the IO part
$self->_initialize_io(@args);
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self, $seq) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::SeqIO object.");
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic Bio::SeqIO object.");
}
alphabetdescriptionprevnextTop
sub alphabet {
   my ($self, $value) = @_;

   if ( defined $value) {
       $value = lc $value;
       unless ($valid_alphabet_cache{$value}) {
	   # instead of hard-coding the allowed values once more, we check by
# creating a dummy sequence object
eval { require Bio::PrimarySeq; my $seq = Bio::PrimarySeq->new('-verbose' => $self->verbose, '-alphabet' => $value); }; if ($@) { $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values."); } $valid_alphabet_cache{$value} = 1; } $self->{'alphabet'} = $value; } return $self->{'alphabet'};
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
    my ($self, $format) = @_;
    my $module = "Bio::SeqIO::" . $format;
    my $ok;

    eval {
	$ok = $self->_load_module($module);
    };
    if ( $@ ) {
    print STDERR <<END
$self: $format cannot be found
Exception $@
For more information about the SeqIO system please see the SeqIO docs.
This includes ways of checking for formats at compile time, not run time
END
; } return $ok;
}
_concatenate_linesdescriptionprevnextTop
sub _concatenate_lines {
    my ($self, $s1, $s2) = @_;

    $s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2);
    return ($s1 ? $s1 : "") . ($s2 ? $s2 : "");
}
_filehandledescriptionprevnextTop
sub _filehandle {
    my ($self,@args) = @_;
    return $self->_fh(@args);
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'fasta'   if /\.(fasta|fast|fas|seq|fa|fsa|nt|aa)$/i;
   return 'genbank' if /\.(gb|gbank|genbank|gbk|gbs)$/i;
   return 'scf'     if /\.scf$/i;
   return 'scf'     if /\.scf$/i;
   return 'abi'     if /\.ab[i1]$/i;
   return 'alf'     if /\.alf$/i;
   return 'ctf'     if /\.ctf$/i;
   return 'ztr'     if /\.ztr$/i;
   return 'pln'     if /\.pln$/i;
   return 'exp'     if /\.exp$/i;
   return 'pir'     if /\.pir$/i;
   return 'embl'    if /\.(embl|ebl|emb|dat)$/i;
   return 'raw'     if /\.(txt)$/i;
   return 'gcg'     if /\.gcg$/i;
   return 'ace'     if /\.ace$/i;
   return 'bsml'    if /\.(bsm|bsml)$/i;
   return 'swiss'   if /\.(swiss|sp)$/i;
   return 'phd'     if /\.(phd|phred)$/i;
   return 'fastq'   if /\.fastq$/i;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
    my ($class,$val) = @_;
    return bless {'seqio' => $val}, $class;
}
READLINEdescriptionprevnextTop
sub READLINE {
  my $self = shift;
  return $self->{'seqio'}->next_seq() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'seqio'}->next_seq();
  return @list;
}
PRINTdescriptionprevnextTop
sub PRINT {
  my $self = shift;
  $self->{'seqio'}->write_seq(@_);
}
sequence_factorydescriptionprevnextTop
sub sequence_factory {
   my ($self,$obj) = @_;   
   if( defined $obj ) {
       if( ! ref($obj) || ! $obj->isa('Bio::Factory::SequenceFactoryI') ) {
	   $self->throw("Must provide a valid Bio::Factory::SequenceFactoryI object to ".ref($self)."::sequence_factory()");
       }
       $self->{'_seqio_seqfactory'} = $obj;
       my $builder = $self->sequence_builder();
       if($builder && $builder->can('sequence_factory') &&
	  (! $builder->sequence_factory())) {
	   $builder->sequence_factory($obj);
       }
   }
   $self->{'_seqio_seqfactory'};
}
object_factorydescriptionprevnextTop
sub object_factory {
    return shift->sequence_factory(@_);
}
sequence_builderdescriptionprevnextTop
sub sequence_builder {
    my ($self,$obj) = @_;
    if( defined $obj ) {
	if( ! ref($obj) || ! $obj->isa('Bio::Factory::ObjectBuilderI') ) {
	    $self->throw("Must provide a valid Bio::Factory::ObjectBuilderI object to ".ref($self)."::sequence_builder()");
	}
	$self->{'_object_builder'} = $obj;
    }
    $self->{'_object_builder'};
}
location_factorydescriptionprevnextTop
sub location_factory {
    my ($self,$obj) = @_;   
    if( defined $obj ) {
	if( ! ref($obj) || ! $obj->isa('Bio::Factory::LocationFactoryI') ) {
	    $self->throw("Must provide a valid Bio::Factory::LocationFactoryI".
			 " object to ".ref($self)."->location_factory()");
	}
	$self->{'_seqio_locfactory'} = $obj;
    }
    $self->{'_seqio_locfactory'};
}
General documentation
CONSTRUCTORSTop
Bio::SeqIO->new()Top
   $seqIO = Bio::SeqIO->new(-file => 'filename',   -format=>$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
   '+
    -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$2|g;
      # print into STDOUT
      print $string;
  }
    -format
    Specify the format of the file. Supported formats include:
   AB1         ABI tracefile format
   ABI         ABI tracefile format
   ALF         ALF tracefile format
   CTF         CTF tracefile format
   EMBL        EMBL format
   EXP         Staden tagged experiment tracefile format
   Fasta       FASTA format
   Fastq       Fastq format
   GCG         GCG format
   GenBank     GenBank format
   PIR         Protein Information Resource format
   PLN         Staden plain tracefile format
   SCF         SCF tracefile format
   ZTR         ZTR tracefile format
   ace         ACeDB sequence format
   game        GAME XML format
   locuslink   LocusLink annotation (LL_tmpl format only)
   phd         phred output
   qual        Quality values (get a sequence of quality scores)
   raw         Raw format (one sequence per line, no ID)
   swiss       Swissprot format
    If no format is specified and a filename is given then the module
will attempt to deduce the format from the filename suffix. If this
is unsuccessful then Fasta format is assumed.
    The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are
all valid suffixes.
    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.
    -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 don't 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   => " "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()Top
   $fh = Bio::SeqIO->newFh(-fh   => \*FILEHANDLE, -format=>$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 METHODSTop
See below for more detailed summaries. The main methods are:
$sequence = $seqIO->next_seq()Top
Fetch the next sequence from the stream.
$seqIO->write_seq($sequence [,$another_sequence,...])Top
Write the specified sequence(s) to the stream.
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml      - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Ewan Birney, Lincoln SteinTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _