Bio::AlignIO - Handler for AlignIO Formats
use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , '-format' => 'fasta'); $out = Bio::AlignIO->new(-file => ">outputfilename" , '-format' => 'pfam'); # note: we quote -format to keep older perl's from complaining. while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); }
or
use Bio::AlignIO; $in = Bio::AlignIO->newFh(-file => "inputfilename" , '-format' => 'fasta'); $out = Bio::AlignIO->newFh('-format' => 'pfam'); # World's shortest Fasta<->pfam format converter: print $out $_ while <$in>;
Bio::AlignIO is a handler module for the formats in the AlignIO set (eg, Bio::AlignIO::fasta). It is the officially sanctioned way of getting at the alignment objects, which most people should use.
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 AlignIO object instance is configured for either input or output. A specific example of a stream object is the Bio::AlignIO::fasta object.
Each stream object has functions
$stream->next_aln();
and
$stream->write_aln($aln);
also
$stream->type() # returns 'INPUT' or 'OUTPUT'
As an added bonus, you can recover a filehandle that is tied to the AlignIO object, allowing you to use the standard <> and print operations to read and write sequence objects:
use Bio::AlignIO; $stream = Bio::AlignIO->newFh(-format => 'Fasta'); # read from standard input while ( $aln = <$stream> ) { # do something with $aln }
print $stream $aln; # 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::AlignIO; $in = Bio::AlignIO->newFh(-format => $format1 ); $out = Bio::AlignIO->newFh(-format => $format2 ); #note: you might want to quote -format to keep older perl's from complaining. print $out $_ while <$in>;
AlignIO.pm is patterned on the module SeqIO.pm and shares most the SeqIO.pm features. One significant difference currently is that AlignIO.pm only handles IO for a single alignment at a time (SeqIO.pm handles IO for multiple sequences in a single stream.) The principal reason for this is that whereas simultaneously handling multiple sequences is a common requirement, simultaneous handling of multiple alignments is not. Capability for IO for more than one multiple alignment (which may be of use for certain applications such as IO for Pfam libraries) may be included in the future. For this reason we keep the name "next_aln()" for the alignment input routine, even though currently only one alignment is read (or written) at a time and the name "read_aln()" might be more appropriate.
$seqIO = Bio::AlignIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::AlignIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::AlignIO->new(-format => $format);
The new() class method constructs a new Bio::AlignIO object. The returned object can be used to retrieve or print BioAlign 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::AlignIO->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.
Specify the format of the file. Supported formats include:
fasta FASTA format pfam pfam format selex selex (hmmer) format stockholm stockholm format prodom prodom (protein domain) format clustalw clustalw (.aln) format msf msf (GCG) format mase mase (seaview) format
Currently only those formats which were implemented in SimpleAlign.pm have been incorporated in AlignIO.pm. Specifically, mase, stockholm and prodom have only been implemented for input. Clustalw format has only been implemented for output.
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.
$fh = Bio::AlignIO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::AlignIO->newFh(-format => $format); # etc.
This constructor behaves like new(), but returns a tied filehandle rather than a Bio::AlignIO 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 an alignment from a formatted file.
Write the specified alignment to a file..
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.
bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists
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/
Email: schattner@alum.mit.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $stream = Bio::AlignIO->new(-file => $filename, -format => 'Format') Function: Returns a new seqstream Returns : A Bio::AlignIO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to
Title : newFh Usage : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::AlignIO::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::AlignIO::Fh class Args :
Title : _load_format_module Usage : *INTERNAL AlignIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : next_aln Usage : $aln = stream->next_aln Function: reads the next $aln object from the stream Returns : a Bio::Seq sequence object Args :
Title : write_aln Usage : $stream->write_aln($aln) Function: writes the $aln object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object
Title : close Usage : $seqio->close() Function: Closes the file handle associated with this seqio system Example : Returns : Args :
Title : _print Usage : $obj->_print(@lines) Function: Example : Returns : writes output
Title : _readline Usage : $obj->_readline($newval) Function: Example : Returns : reads a line of input
Title : _filehandle Usage : $obj->_filehandle($newval) Function: 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.