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');
    # note: we quote -format to keep older perl's from complaining.

    while ( my $seq = $in->next_seq() ) {
	$out->write_seq($seq);
    }

or

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 $output $_ while <$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 SeqIO system replaces the old parse_XXX functions in the Seq object.

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);

also

$stream->type() # returns 'INPUT' or 'OUTPUT'

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>;

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 BioSeq 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.

-format

Specify the format of the file. Supported formats include:

Fasta       FASTA format
EMBL        EMBL format
GenBank     GenBank format
swiss       Swissprot format
SCF         SCF tracefile format
PIR         Protein Information Resource format
GCG         GCG format
raw         Raw format (one sequence per line, no ID)

If no format is specified and a filename is given, then the module will attempt to deduce it from the filename. If this is unsuccessful, Fasta format is assumed.

The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are all supported.

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.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - 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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney, Lincoln Stein

Email birney@sanger.ac.uk

Describe contact details here

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 seqstream
Returns : A Bio::SeqIO::Handler initialised with the appropriate format
Args    : -file => $filename 
          -format => format
          -fh => filehandle to attach to

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    : 

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 the Bio::SeqIO::Fh class
Args    : 

_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    :

next_seq

Title   : next_seq
Usage   : $seq = stream->next_seq
Function: reads the next $seq object from the stream
Returns : a Bio::Seq sequence object
Args    : 

next_primary_seq

Title   : next_primary_seq
Usage   : $seq = $stream->next_primary_seq
Function: Provides a primaryseq type of sequence object
Returns : A Bio::PrimarySeqI object
Args    : none

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

moltype

Title   : moltype
Usage   : $self->moltype($newval)
Function: Set/get the molecule type for the Seq objects to be created.
Example : $seqio->moltype('protein')
Returns : value of moltype: 'dna', 'rna', or 'protein'
Args    : newvalue (optional) 
Throws  : Exception if the argument is not one of 'dna', 'rna', or 'protein' 

close

Title   : close
Usage   : $seqio->close()
Function: Closes the file handle associated with this seqio system
Example :
Returns : 
Args    :

_print

Title   : _print
Usage   : $obj->_print(@lines)
Function: 
Example : 
Returns : writes output

_readline

Title   : _readline
Usage   : $obj->_readline($newval)
Function: 
Example : 
Returns : reads a line of input

_filehandle

Title   : _filehandle
Usage   : $obj->_filehandle($newval)
Function: 
Example : 
Returns : value of _filehandle
Args    : newvalue (optional)

_guess_format

Title   : _guess_format
Usage   : $obj->_guess_format($filename)
Function: 
Example : 
Returns : guessed format of filename (lower case)
Args    : 

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq