plucky (3) Bio::Variation::IO.3pm.gz
NAME
Bio::Variation::IO - Handler for sequence variation IO Formats
SYNOPSIS
use Bio::Variation::IO;
$in = Bio::Variation::IO->new(-file => "inputfilename" ,
-format => 'flat');
$out = Bio::Variation::IO->new(-file => ">outputfilename" ,
-format => 'xml');
while ( my $seq = $in->next() ) {
$out->write($seq);
}
# or
use Bio::Variation::IO;
#input file format can be read from the file extension (dat|xml)
$in = Bio::Variation::IO->newFh(-file => "inputfilename");
$out = Bio::Variation::IO->newFh(-format => 'xml');
# World's shortest flat<->xml format converter:
print $out $_ while <$in>;
DESCRIPTION
Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg,
Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which
most people should use.
The structure, conventions and most of the code is inherited from Bio::SeqIO module. The main difference
is that instead of using methods next_seq and write_seq, you drop '_seq' from the method names.
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::Variation::IO::flat object.
Each stream object has functions
$stream->next();
and
$stream->write($seqDiff);
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::Variation::IO;
$stream = Bio::Variation::IO->newFh(-format => 'flat');
# 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;
use Bio::Variation::IO;
$in = Bio::Variation::IO->newFh(-format => $format1 );
$out = Bio::Variation::IO->newFh(-format => $format2 );
print $out $_ while <$in>;
CONSTRUCTORS
Bio::Variation::IO->new()
$seqIO = Bio::Variation::IO->new(-file => 'filename', -format=>$format);
$seqIO = Bio::Variation::IO->new(-fh => \*FILEHANDLE, -format=>$format);
$seqIO = Bio::Variation::IO->new(-format => $format);
The new() class method constructs a new Bio::Variation::IO 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::Variation::IO->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:
flat pseudo EMBL format
xml seqvar xml 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. 'FLAT', 'Flat' and 'flat' are all supported.
Bio::Variation::IO->newFh()
$fh = Bio::Variation::IO->newFh(-fh => \*FILEHANDLE, -format=>$format);
$fh = Bio::Variation::IO->newFh(-format => $format);
# etc.
#e.g.
$out = Bio::Variation::IO->newFh( '-FORMAT' => 'flat');
print $out $seqDiff;
This constructor behaves like new(), but returns a tied filehandle rather than a Bio::Variation::IO
object. You can read sequences from this object using the familiar <> operator, and write to it using
print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an
array like this:
@mutations = <$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()
Fetch the next sequence from the stream.
$seqIO->write($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 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 reponsive 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 - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-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::Variation::IO->new(-file => $filename, -format => 'Format')
Function: Returns a new seqstream
Returns : A Bio::Variation::IO::Handler initialised with the appropriate format
Args : -file => $filename
-format => format
-fh => filehandle to attach to
format
Title : format
Usage : $format = $stream->format()
Function: Get the variation format
Returns : variation format
Args : none
next
Title : next
Usage : $seqDiff = $stream->next
Function: reads the next $seqDiff object from the stream
Returns : a Bio::Variation::SeqDiff object
Args :
write
Title : write
Usage : $stream->write($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Variation::SeqDiff object
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :