Bio::Variation IO
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Summary
Bio::Variation::IO - Handler for sequence variation IO Formats
Package variables
No package variables defined.
Inherit
Bio::Root::IO Bio::SeqIO
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>;
Methods
newDescriptionCode
_load_format_module
No description
Code
nextDescriptionCode
next_seq
No description
Code
writeDescriptionCode
write_seq
No description
Code
_guess_formatDescriptionCode
Methods description
newcode    nextTop
 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
nextcodeprevnextTop
 Title   : next
Usage : $seqDiff = $stream->next
Function: reads the next $seqDiff object from the stream
Returns : a Bio::Variation::SeqDiff object
Args :
writecodeprevnextTop
 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_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
Methods code
newdescriptionprevnextTop
sub new {
   my ($class, %param) = @_;
   my ($format);

   @param{ map { lc $_ } keys %param } = values %param;  # lowercase keys
$format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ) || 'flat'; $format = "\L$format"; # normalize capitalization to lower case
return unless $class->_load_format_module($format); return "Bio::Variation::IO::$format"->new(%param);
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($class, $format) = @_;
  my $module = "Bio::Variation::IO::" . $format;
  my $ok;  
  eval {
      $ok = $class->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$class: $format cannot be found
Exception $@
For more information about the IO system please see the IO docs.
This includes ways of checking for formats at compile time, not run time
END
; } return $ok;
}
nextdescriptionprevnextTop
sub next {
   my ($self, $seq) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Variation::IO object.");
}
next_seqdescriptionprevnextTop
sub next_seq {
   my ($self, $seq) = @_;
   $self->throw("These are not sequence objects. Use method 'next' instead of 'next_seq'.");
   $self->next($seq);
}
writedescriptionprevnextTop
sub write {
    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic Bio::Variation::IO object.");
}
write_seqdescriptionprevnextTop
sub write_seq {
   my ($self, $seq) = @_;
   $self->warn("These are not sequence objects. Use method 'write' instead of 'write_seq'.");
   $self->write($seq);
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'flat'     if /\.dat$/i;
   return 'xml'     if /\.xml$/i;
}


1;
}
General documentation
CONSTRUCTORSTop
Bio::Variation::IO->new()Top
   $seqIO = Bio::Variation::IO->new(-file => 'filename',   -format=>$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()Top
   $fh = Bio::Variation::IO->newFh(-fh   => \*FILEHANDLE, -format=>$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 METHODSTop
See below for more detailed summaries. The main methods are:
$sequence = $seqIO->next()Top
Fetch the next sequence from the stream.
$seqIO->write($sequence [,$another_sequence,...])Top
Write the specified sequence(s) to the stream.
TIEHANDLE(), READLINE(), PRINT()Top
These provide the tie interface. See perltie for more details.
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $stream->format()
Function: Get the variation format
Returns : variation format
Args : none