# BioPerl module for Bio::SeqIO
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
#
# _history
# October 18, 1999 Largely rewritten by Lincoln Stein
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO - Handler for SeqIO Formats
=head1 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>;
=head1 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 L<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 E<lt>E<gt> 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
use strict;
my $format1 = shift;
my $format2 = shift || die
"Usage: reformat format1 format2 < input > output";
use Bio::SeqIO;
my $in = Bio::SeqIO->newFh(-format => $format1, -fh => \*ARGV );
my $out = Bio::SeqIO->newFh(-format => $format2 );
# Note: you might want to quote -format to keep older
# perl's from complaining.
print $out $_ while <$in>;
=head1 CONSTRUCTORS
=head2 Bio::SeqIO-E<gt>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:
=over 5
=item -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
=item -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 E<lt>E<gt>
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;
}
=item -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 (L<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 SeqIO will
throw a fatal error.
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.
=item -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.
=item -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 = Bio::SeqIO->new(-file => "<gball.gbk",
-format => "gb");
my $fa = Bio::SeqIO->new(-file => ">gball.fa",
-format => "fasta",
-flush => 0); # go as fast as we can!
while($seq = $gb->next_seq) { $fa->write_seq($seq) }
=back
=head2 Bio::SeqIO-E<gt>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 E<lt>E<gt> 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.
=head1 OBJECT METHODS
See below for more detailed summaries. The main methods are:
=head2 $sequence = $seqIO-E<gt>next_seq()
Fetch the next sequence from the stream, or nothing if no more.
=head2 $seqIO-E<gt>write_seq($sequence [,$another_sequence,...])
Write the specified sequence(s) to the stream.
=head2 TIEHANDLE(), READLINE(), PRINT()
These provide the tie interface. See L<perltie> for more details.
=head1 FEEDBACK
=head2 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
=head2 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
responsive 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.
=head2 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/
=head1 AUTHOR - Ewan Birney, Lincoln Stein
Email birney@ebi.ac.uk
lstein@cshl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#' Let the code begin...
package Bio::SeqIO;
use strict;
use Bio::Factory::FTLocationFactory;
use Bio::Seq::SeqBuilder;
use Bio::Tools::GuessSeqFormat;
use Symbol;
use base qw(Bio::Root::Root Bio::Root::IO Bio::Factory::SequenceStreamI);
my %valid_alphabet_cache;
=head2 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 L<Bio::SeqIO::Handler>
=cut
my $entry = 0;
sub new {
my ($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
unless( defined $param{-file} ||
defined $param{-fh} ||
defined $param{-string} ) {
$class->throw("file argument provided, but with an undefined value")
if exists $param{'-file'};
$class->throw("fh argument provided, but with an undefined value")
if exists $param{'-fh'};
$class->throw("string argument provided, but with an undefined value")
if exists($param{'-string'});
# $class->throw("No file, fh, or string argument provided"); # neither defined
}
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;
}
}
# changed 1-3-11; no need to print out an empty string (only way this
# exception is triggered) - cjfields
$class->throw("Could not guess format from file/fh") unless $format;
$format = "\L$format"; # normalize capitalization to lower case
if ($format =~ /-/) {
($format, my $variant) = split('-', $format, 2);
push @args, (-variant => $variant);
}
return unless( $class->_load_format_module($format) );
return "Bio::SeqIO::$format"->new(@args);
}
}
=head2 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 L<Bio::SeqIO::Fh>
=cut
sub newFh {
my $class = shift;
return unless my $self = $class->new(@_);
return $self->fh;
}
=head2 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
=cut
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
# _initialize is chained for all SeqIO classes
sub _initialize {
my($self, @args) = @_;
# flush is initialized by the Root::IO init
my ($seqfact,$locfact,$objbuilder, $alphabet) =
$self->_rearrange([qw(SEQFACTORY
LOCFACTORY
OBJBUILDER
ALPHABET)
], @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);
#bug 2160
$alphabet && $self->alphabet($alphabet);
# initialize the IO part
$self->_initialize_io(@args);
}
=head2 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
$stream->verbose(2).
Returns : a Bio::Seq sequence object, or nothing if no more sequences
are available
Args : none
See L<Bio::Root::RootI>, L<Bio::Factory::SeqStreamI>, L<Bio::Seq>
=cut
sub next_seq {
my ($self, $seq) = @_;
$self->throw("Sorry, you cannot read from a generic Bio::SeqIO object.");
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object
=cut
sub write_seq {
my ($self, $seq) = @_;
$self->throw("Sorry, you cannot write to a generic Bio::SeqIO object.");
}
=head2 alphabet
Title : alphabet
Usage : $self->alphabet($newval)
Function: Set/get the molecule type for the Seq objects to be created.
Example : $seqio->alphabet('protein')
Returns : value of alphabet: 'dna', 'rna', or 'protein'
Args : newvalue (optional)
Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein'
=cut
sub alphabet {
my ($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 $self->{'alphabet'};
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL SeqIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($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;
}
=head2 _concatenate_lines
Title : _concatenate_lines
Usage : $s = _concatenate_lines($line, $continuation_line)
Function: Private. Concatenates two strings assuming that the second stems
from a continuation line of the first. Adds a space between both
unless the first ends with a dash.
Takes care of either arg being empty.
Example :
Returns : A string.
Args :
=cut
sub _concatenate_lines {
my ($self, $s1, $s2) = @_;
$s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2);
return ($s1 ? $s1 : "") . ($s2 ? $s2 : "");
}
=head2 _filehandle
Title : _filehandle
Usage : $obj->_filehandle($newval)
Function: This method is deprecated. Call _fh() instead.
Example :
Returns : value of _filehandle
Args : newvalue (optional)
=cut
sub _filehandle {
my ($self,@args) = @_;
return $self->_fh(@args);
}
=head2 _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
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'abi' if /\.ab[i1]$/i;
return 'ace' if /\.ace$/i;
return 'alf' if /\.alf$/i;
return 'bsml' if /\.(bsm|bsml)$/i;
return 'ctf' if /\.ctf$/i;
return 'embl' if /\.(embl|ebl|emb|dat)$/i;
return 'entrezgene' if /\.asn$/i;
return 'exp' if /\.exp$/i;
return 'fasta' if /\.(fasta|fast|fas|seq|fa|fsa|nt|aa|fna|faa)$/i;
return 'fastq' if /\.fastq$/i;
return 'gcg' if /\.gcg$/i;
return 'genbank' if /\.(gb|gbank|genbank|gbk|gbs)$/i;
return 'phd' if /\.(phd|phred)$/i;
return 'pir' if /\.pir$/i;
return 'pln' if /\.pln$/i;
return 'qual' if /\.qual$/i;
return 'raw' if /\.txt$/i;
return 'scf' if /\.scf$/i;
return 'swiss' if /\.(swiss|sp)$/i;
# from Strider 1.4 Release Notes: The file name extensions used by
# Strider 1.4 are ".xdna", ".xdgn", ".xrna" and ".xprt" for DNA,
# DNA Degenerate, RNA and Protein Sequence Files, respectively
return 'strider' if /\.(xdna|xdgn|xrna|xprt)$/i;
return 'ztr' if /\.ztr$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my ($class,$val) = @_;
return bless {'seqio' => $val}, $class;
}
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;
}
sub PRINT {
my $self = shift;
$self->{'seqio'}->write_seq(@_);
}
=head2 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
=cut
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'};
}
=head2 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)
=cut
sub object_factory{
return shift->sequence_factory(@_);
}
=head2 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
=cut
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'};
}
=head2 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.
=cut
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'};
}
1;