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Bio::Structure::IO.3pm

NAME

Bio::Structure::IO - Handler for Structure Formats

SYNOPSIS

     use Bio::Structure::IO;
 
     $in  = Bio::Structure::IO->new(-file => "inputfilename",
                                    -format => 'pdb');
 
     while ( my $struc = $in->next_structure() ) {
        print "Structure ", $struc->id, " number of models: ",
              scalar $struc->model,"\n";
     }
 
 

DESCRIPTION

Bio::Structure::IO is a handler module for the formats in the Structure::IO set (e.g. Bio::Structure::IO::pdb). It is the officially sanctioned way of getting at the format objects, which most people should use.

The Bio::Structure::IO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (e.g. PDB format) and can either read or write structure objects (Bio::Structure objects, or more correctly, Bio::Structure::StructureI implementing objects, of which Bio::Structure is one such object). If you want to know what to do with a Bio::Structure object, read Bio::Structure.

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 Structure::IO object instance is configured for either input or output. A specific example of a stream object is the Bio::Structure::IO::pdb object.

Each stream object has functions

    $stream->next_structure();
 
 

and

    $stream->write_structure($struc);
 
 

also

    $stream->type() # returns 'INPUT' or 'OUTPUT'
 
 

As an added bonus, you can recover a filehandle that is tied to the Structure::IOIO object, allowing you to use the standard <> and print operations to read and write structure::IOuence objects:

     use Bio::Structure::IO;
 
     $stream = Bio::Structure::IO->newFh(-format => 'pdb'); # read from standard input
 
     while ( $structure = <$stream> ) {
         # do something with $structure
     }
 
 

and

     print $stream $structure; # when stream is in output mode
 
 

CONSTRUCTORS

Bio::Structure::IO->new()

    $stream = Bio::Structure::IO->new(-file => 'filename',   -format=>$format);
    $stream = Bio::Structure::IO->new(-fh   => \*FILEHANDLE, -format=>$format);
    $stream = Bio::Structure::IO->new(-format => $format);
 
 

The new() class method constructs a new Bio::Structure::IO object. The returned object can be used to retrieve or print Bio::Structure 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:

    $strucIO = Bio::Structure::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:

    pdb         Protein Data Bank 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, PDB format is assumed.

The format name is case insensitive. 'PDB', 'Pdb' and 'pdb' are all supported.

Bio::Structure::IO->newFh()

    $fh = Bio::Structure::IO->newFh(-fh   => \*FILEHANDLE, -format=>$format);
    $fh = Bio::Structure::IO->newFh(-format => $format);
    # etc.
 
 

This constructor behaves like new(), but returns a tied filehandle rather than a Bio::Structure::IO object. You can read structures 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 structure objects into an array like this:

   @structures = <$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:

$structure = $structIO->next_structure()

Fetch the next structure from the stream.

$structIO->write_structure($struc [,$another_struc,...])

Write the specified structure(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 one of 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:

   http://bugzilla.open-bio.org/
 
 

AUTHORS - Ewan Birney, Lincoln Stein, Kris Boulez

Email birney@ebi.ac.uk, lstein@cshl.org, kris.boulez@algonomics.com

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::Structure::IO->new(-file => $filename, -format => 'Format')
  Function: Returns a new structIOstream
  Returns : A Bio::Structure::IO handler initialised with the appropriate format
  Args    : -file => $filename
            -format => format
            -fh => filehandle to attach to
 
 

newFh

  Title   : newFh
  Usage   : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
  Function: does a new() followed by an fh()
  Example : $fh = Bio::Structure::IO->newFh(-file=>$filename,-format=>'Format')
            $structure = <$fh>;   # read a structure object
            print $fh $structure; # write a structure object
  Returns : filehandle tied to the Bio::Structure::IO::Fh class
  Args    :
 
 

fh

  Title   : fh
  Usage   : $obj->fh
  Function:
  Example : $fh = $obj->fh;      # make a tied filehandle
            $structure = <$fh>;   # read a structure object
            print $fh $structure; # write a structure object
  Returns : filehandle tied to the Bio::Structure::IO::Fh class
  Args    :
 
 

next_structure

  Title   : next_structure
  Usage   : $structure = stream->next_structure
  Function: Reads the next structure object from the stream and returns a
            Bio::Structure::Entry object.
 
            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::Structure::Entry object
  Args    : none
 
 

write_structure

  Title   : write_structure
  Usage   : $stream->write_structure($structure)
  Function: writes the $structure object into the stream
  Returns : 1 for success and 0 for error
  Args    : Bio::Structure object
 
 

_load_format_module

  Title   : _load_format_module
  Usage   : *INTERNAL Structure::IO stuff*
  Function: Loads up (like use) a module at run time on demand
  Example :
  Returns :
  Args    :
 
 

_concatenate_lines

  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    :
 
 

_filehandle

  Title   : _filehandle
  Usage   : $obj->_filehandle($newval)
  Function: This method is deprecated. Call _fh() instead.
  Example :
  Returns : value of _filehandle
  Args    : newvalue (optional)
 
 

_guess_format

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