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
'command |' # open a pipe from the command
'| command' # open a pipe to the command
- -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;
}
- -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.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.
- -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
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
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'
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)
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.