Bio::Structure IO
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Summary
Bio::Structure::IO - Handler for Structure Formats
Package variables
Privates (from "my" definitions)
$entry = 0
Included modules
Bio::PrimarySeq
Symbol
Inherit
Bio::Root::IO Bio::Root::Root
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
Methods
newDescriptionCode
newFhDescriptionCode
fhDescriptionCode
_initialize
No description
Code
next_structureDescriptionCode
write_seq
No description
Code
_load_format_moduleDescriptionCode
_concatenate_linesDescriptionCode
_filehandleDescriptionCode
_guess_formatDescriptionCode
DESTROY
No description
Code
TIEHANDLEDescriptionCode
READLINE
No description
Code
PRINT
No description
Code
Methods description
newcode    nextTop
 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
newFhcodeprevnextTop
 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 :
fhcodeprevnextTop
 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_structurecodeprevnextTop
 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
_load_format_modulecodeprevnextTop
 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_linescodeprevnextTop
 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 :
_filehandlecodeprevnextTop
 Title   : _filehandle
Usage : $obj->_filehandle($newval)
Function: This method is deprecated. Call _fh() instead.
Example :
Returns : value of _filehandle
Args : newvalue (optional)
_guess_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
TIEHANDLE(), READLINE(), PRINT()codeprevnextTop
These provide the tie interface. See perltie for more details.
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller,@args) = @_;
    my $class = ref($caller) || $caller;

    # or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::Structure::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} || $class->_guess_format( $param{-file} || $ARGV[0] ) || 'pdb'; $format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return unless( &_load_format_module($format) ); return "Bio::Structure::IO::$format"->new(@args); }
}
newFhdescriptionprevnextTop
sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}
fhdescriptionprevnextTop
sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;

    # not really necessary unless we put more in RootI
$self->SUPER::_initialize(@args); # initialize the IO part
$self->_initialize_io(@args);
}
next_structuredescriptionprevnextTop
sub next_structure {
   my ($self, $struc) = @_;
   $self->throw("Sorry, you cannot read from a generic Bio::Structure::IO object.");
}

# Do we want people to read out the sequence directly from a $structIO stream
#
##=head2 next_primary_seq
##
## Title : next_primary_seq
## Usage : $seq = $stream->next_primary_seq
## Function: Provides a primaryseq type of sequence object
## Returns : A Bio::PrimarySeqI object
## Args : none
##
##
##=cut
##
##sub next_primary_seq {
## my ($self) = @_;
##
## # in this case, we default to next_seq. This is because
## # Bio::Seq's are Bio::PrimarySeqI objects. However we
## # expect certain sub classes to override this method to provide
## # less parsing heavy methods to retrieving the objects
##
## return $self->next_seq();
##
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self, $struc) = @_;
    $self->throw("Sorry, you cannot write to a generic Bio::Structure::IO object.");
}


# De we need this here
#
##=head2 alphabet
##
## Title : alphabet
## Usage : $self->alphabet($newval)
## Function: Set/get the molecule type for the Seq objects to be created.
## Example : $seqio->alphabet('protein')
## Returns : value of alphabet: 'dna', 'rna', or 'protein'
## Args : newvalue (optional)
## Throws : Exception if the argument is not one of 'dna', 'rna', or 'protein'
##
##=cut
##
##sub alphabet {
## my ($self, $value) = @_;
##
## if ( defined $value) {
## # instead of hard-coding the allowed values once more, we check by
## # creating a dummy sequence object
## eval {
## my $seq = Bio::PrimarySeq->new('-alphabet' => $value);
## };
## if($@) {
## $self->throw("Invalid alphabet: $value\n. See Bio::PrimarySeq for allowed values.");
## }
## $self->{'alphabet'} = "\L$value";
## }
## return $self->{'alphabet'};
##
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($format) = @_;
  my ($module, $load, $m);

  $module = "_<Bio/Structure/IO/$format.pm";
  $load = "Bio/Structure/IO/$format.pm";

  return 1 if $main::{$module};
  eval {
    require $load;
  };
  if ( $@ ) {
    print STDERR <<END;
$load: $format cannot be found
Exception $@
For more information about the Structure::IO system please see the
Bio::Structure::IO docs. This includes ways of checking for formats at
compile time, not run time
END
; return; } return 1;
}
_concatenate_linesdescriptionprevnextTop
sub _concatenate_lines {
    my ($self, $s1, $s2) = @_;
    $s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2);
    return ($s1 ? $s1 : "") . ($s2 ? $s2 : "");
}
_filehandledescriptionprevnextTop
sub _filehandle {
    my ($self,@args) = @_;
    return $self->_fh(@args);
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'fasta'   if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i;
   return 'genbank' if /\.(gb|gbank|genbank)$/i;
   return 'scf'     if /\.scf$/i;
   return 'pir'     if /\.pir$/i;
   return 'embl'    if /\.(embl|ebl|emb|dat)$/i;
   return 'raw'     if /\.(txt)$/i;
   return 'gcg'     if /\.gcg$/i;
   return 'ace'     if /\.ace$/i;
   return 'bsml'    if /\.(bsm|bsml)$/i;
   return 'pdb'     if /\.(ent|pdb)$/i;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
    my ($class,$val) = @_;
    return bless {'structio' => $val}, $class;
}
READLINEdescriptionprevnextTop
sub READLINE {
  my $self = shift;
  return $self->{'structio'}->next_seq() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'structio'}->next_seq();
  return @list;
}
PRINTdescriptionprevnextTop
sub PRINT {
  my $self = shift;
  $self->{'structio'}->write_seq(@_);
}

1;
}
General documentation
CONSTRUCTORSTop
Bio::Structure::IO->new()Top
   $stream = Bio::Structure::IO->new(-file => 'filename',   -format=>$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()Top
   $fh = Bio::Structure::IO->newFh(-fh   => \*FILEHANDLE, -format=>$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 METHODSTop
See below for more detailed summaries. The main methods are:
$structure = $structIO->next_structure()Top
Fetch the next structure from the stream.
$structIO->write_structure($struc [,$another_struc,...])Top
Write the specified structure(s) to the stream.
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 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 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/
AUTHORS - Ewan Birney, Lincoln Stein, Kris BoulezTop
Email birney@ebi.ac.uk, lstein@cshl.org, kris.boulez@algonomics.com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $obj->format()
Function: Get the structure format
Returns : structure format
Args : none
write_structureTop
 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