Bio::SeqIO - Handler for SeqIO Formats 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 L<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>; 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>;

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 Seq objects. new() accepts the following parameters: 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 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<font color="Red">$2</font>|g; # print into STDOUT print $string; } 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. 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 => "<gball.gbk", -format => "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()
$fh = Bio::SeqIO->newFh(-fh => \*FILEHANDLE, -format=>$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. 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.

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/MailList.shtml - 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@bioperl.org http://bugzilla.bioperl.org/ Email birney@ebi.ac.uk 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 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 L<Bio::Factory::SequenceFactoryI> object -locfactory the L<Bio::Factory::LocationFactoryI> object -objbuilder the L<Bio::Factory::ObjectBuilderI> object 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: 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 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

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 L<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 L<Bio::Factory::ObjectBuilderI> compliant object Args : [optional] a L<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 L<Bio::Factory::LocationFactoryI> implementing object Args : [optional] on set, a L<Bio::Factory::LocationFactoryI> implementing object.