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