Provided by: libbio-perl-perl_1.7.2-2_all 
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
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>;
CONSTRUCTORS
Bio::SeqIO->new()
$seqIO = Bio::SeqIO->new(-file => 'seqs.fasta', -format => $format);
$seqIO = Bio::SeqIO->new(-fh => \*FILEHANDLE, -format => $format);
$seqIO = Bio::SeqIO->new(-string => $string , -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
To read from or write to a piped command, open a filehandle and use the -fh option.
-fh You may use new() with a opened filehandle, provided as a glob reference. For
example, to read from STDIN:
my $seqIO = Bio::SeqIO->new(-fh => \*STDIN);
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;
}
Filehandles can also be used to read from or write to a piped command:
use Bio::SeqIO;
#convert .fastq.gz to .fasta
open my $zcat, 'zcat seq.fastq.gz |' or die $!;
my $in=Bio::SeqIO->new(-fh=>$zcat,
-format=>'fastq');
my $out=Bio::SeqIO->new(-file=>'>seq.fasta',
-format=>'fasta');
while (my $seq=$in->next_seq) {
$out->write_seq($seq)
}
-string
A string to read the sequences from. For example:
my $string = ">seq1\nACGCTAGCTAGC\n";
my $seqIO = Bio::SeqIO->new(-string => $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.org/howtos/SeqIO_HOWTO.html>).
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.
-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 = 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) }
-seqfactory
Provide a Bio::Factory::SequenceFactoryI object. See the sequence_factory() method.
-locfactory
Provide a Bio::Factory::LocationFactoryI object. See the location_factory() method.
-objbuilder
Provide a Bio::Factory::ObjectBuilderI object. See the object_builder() method.
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, or nothing if no more.
$seqIO->write_seq($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
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.
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 - 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 => 'sequences.fasta',
-format => 'fasta');
Function: Returns a new sequence stream
Returns : A Bio::SeqIO stream initialised with the appropriate format
Args : Named parameters indicating where to read the sequences from or to
write them to:
-file => filename, OR
-fh => filehandle to attach to, OR
-string => string
Additional arguments, all with reasonable defaults:
-format => format of the sequences, usually auto-detected
-alphabet => 'dna', 'rna', or 'protein'
-flush => 0 or 1 (default: flush filehandles after each write)
-seqfactory => sequence factory
-locfactory => location factory
-objbuilder => object builder
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: Get or set the IO filehandle
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, or nothing if no more sequences
are available
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
format
Title : format
Usage : $format = $stream->format()
Function: Get the sequence format
Returns : sequence format, e.g. fasta, fastq
Args : none
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. This applies to rich sequence formats only, e.g. genbank
but not fasta.
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.