Raw content of Bio::Structure::IO # $Id: IO.pm,v 1.3 2002/10/22 07:45:21 lapp Exp $ # # BioPerl module for Bio::Structure::IO # # Cared for by Ewan Birney <birney@sanger.ac.uk> # and Lincoln Stein <lstein@cshl.org> # and Kris Boulez <kris.boulez@algonomics.com> # # Copyright 2001, 2002 Kris Boulez # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 Largely rewritten by Lincoln Stein # November 16, 2001 Copied Bio::SeqIO to Bio::Structure::IO and modified # where needed. Factoring out common methods # (to Bio::Root::IO) might be a good idea. # POD documentation - main docs before the code =head1 NAME Bio::Structure::IO - Handler for Structure Formats =head1 SYNOPSIS use Bio::Structure::IO; $in = Bio::Structure::IO->new(-file => "inputfilename" , '-format' => 'pdb'); $out = Bio::Structure::IO->new(-file => ">outputfilename" , '-format' => 'pdb'); # note: we quote -format to keep older perl's from complaining. while ( my $struc = $in->next_structure() ) { $out->write_structure($struc); } now, to actually get at the structure object, use the standard Bio::Structure methods (look at L<Bio::Structure> if you don't know what they are) 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"; } =head1 DESCRIPTION [ The following description is a copy-paste from the Bio::SeqIO description. This is not surprising as the code is also mostly a copy. ] Bio::Structure::IO is a handler module for the formats in the Structure::IO set (eg, 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 (eg, 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 L<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 E<lt>E<gt> 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 =head1 CONSTRUCTORS =head2 Bio::Structure::IO-E<gt>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: =over 4 =item -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 =item -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 E<lt>E<gt> semantics. A string filehandle is handy if you want to modify the output in the memory, before printing it out. The following program reads in EMBL formatted entries from a file and prints them out in fasta format with some HTML tags: [ not relevant for Bio::Structure::IO as only one format is supported at the moment ] use Bio::SeqIO; use IO::String; my $in = Bio::SeqIO->new('-file' => "emblfile" , '-format' => 'EMBL'); while ( my $seq = $in->next_seq() ) { # the output handle is reset for every file my $stringio = IO::String->new($string); my $out = Bio::SeqIO->new('-fh' => $stringio, '-format' => 'fasta'); # output goes into $string $out->write_seq($seq); # modify $string $string =~ s|(>)(\w+)|$1<font color="Red">$2</font>|g; # print into STDOUT print $string; } =item -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. =back =head2 Bio::Structure::IO-E<gt>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 E<lt>E<gt> 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. =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $structure = $structIO-E<gt>next_structure() Fetch the next structure from the stream. =head2 $structIO-E<gt>write_structure($struc [,$another_struc,...]) Write the specified structure(s) to the stream. =head2 TIEHANDLE(), READLINE(), PRINT() These provide the tie interface. See L<perltie> for more details. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Ewan Birney, Lincoln Stein, Kris Boulez Email birney@ebi.ac.uk, kris.boulez@algonomics Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Structure::IO; use strict; use vars qw(@ISA); use Bio::Root::Root; use Bio::Root::IO; use Bio::PrimarySeq; use Symbol(); @ISA = qw(Bio::Root::Root Bio::Root::IO); =head2 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 =cut my $entry = 0; sub new { my ($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 undef unless( &_load_format_module($format) ); return "Bio::Structure::IO::$format"->new(@args); } } =head2 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 : =cut sub newFh { my $class = shift; return unless my $self = $class->new(@_); return $self->fh; } =head2 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 : =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } # _initialize is chained for all SeqIO classes sub _initialize { my($self, @args) = @_; # not really necessary unless we put more in RootI $self->SUPER::_initialize(@args); # initialize the IO part $self->_initialize_io(@args); } =head2 next_structure Title : next_structure Usage : $structure = stream->next_structure Function: Reads the next structure object from the stream and returns it. 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 $stream->verbose(2) (see Bio::RootI POD page). Returns : a Bio::Structure structure object Args : none =cut sub next_structure { my ($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(); ##} =head2 write_structure Title : write_structure Usage : $stream->write_structure($structure) Function: writes the $structure object into the stream Returns : 1 for success and 0 for error Args : Bio::Structure object =cut sub write_seq { my ($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 $self->{'alphabet'}; ##} =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL Structure::IO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($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; } =head2 _concatenate_lines Title : _concatenate_lines Usage : $s = _concatenate_lines($line, $continuation_line) Function: Private. Concatenates two strings assuming that the second stems from a continuation line of the first. Adds a space between both unless the first ends with a dash. Takes care of either arg being empty. Example : Returns : A string. Args : =cut sub _concatenate_lines { my ($self, $s1, $s2) = @_; $s1 .= " " if($s1 && ($s1 !~ /-$/) && $s2); return ($s1 ? $s1 : "") . ($s2 ? $s2 : ""); } =head2 _filehandle Title : _filehandle Usage : $obj->_filehandle($newval) Function: This method is deprecated. Call _fh() instead. Example : Returns : value of _filehandle Args : newvalue (optional) =cut sub _filehandle { my ($self,@args) = @_; return $self->_fh(@args); } =head2 _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : =cut 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; } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my ($class,$val) = @_; return bless {'structio' => $val}, $class; } 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; } sub PRINT { my $self = shift; $self->{'structio'}->write_seq(@_); } 1;