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 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>;
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 }
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>;
$seqIO = Bio::SeqIO->new(-file => 'filename', -format=>$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:
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:
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) ace ACeDB sequence format
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.
$fh = Bio::SeqIO->newFh(-fh => \*FILEHANDLE, -format=>$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:
Fetch the next sequence from the stream.
Write the specified sequence(s) to the stream.
These provide the tie interface. See perltie for more details.
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.
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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:
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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 :
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 :
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) (see Bio::RootI POD page). Returns : a Bio::Seq sequence object Args :
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
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 : 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'
Title : _load_format_module Usage : *INTERNAL SeqIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
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 :
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: Example : Returns : guessed format of filename (lower case) Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.