Bio::Structure::IO(3)                      User Contributed Perl Documentation




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-lATbioperl.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-lATbioperl.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 birneyATebi.uk, lsteinATcshl.org, kris.boulezATalgonomics.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    :



perl v5.12.2                                                 February 24, 2011