Raw content of Bio::AlignIO # $Id: AlignIO.pm,v 1.28 2002/10/22 07:38:23 lapp Exp $ # # BioPerl module for Bio::AlignIO # # based on the Bio::SeqIO module # by Ewan Birney <birney@sanger.ac.uk> # and Lincoln Stein <lstein@cshl.org> # # Copyright Peter Schattner # # You may distribute this module under the same terms as perl itself # # _history # October 18, 1999 SeqIO largely rewritten by Lincoln Stein # September, 2000 AlignIO written by Peter Schattner # POD documentation - main docs before the code =head1 NAME Bio::AlignIO - Handler for AlignIO Formats =head1 SYNOPSIS use Bio::AlignIO; $inputfilename = "testaln.fasta"; $in = Bio::AlignIO->new(-file => $inputfilename , '-format' => 'fasta'); $out = Bio::AlignIO->new(-file => ">out.aln.pfam" , '-format' => 'pfam'); # note: we quote -format to keep older perl's from complaining. while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } or use Bio::AlignIO; $inputfilename = "testaln.fasta"; $in = Bio::AlignIO->newFh(-file => $inputfilename , '-format' => 'fasta'); $out = Bio::AlignIO->newFh('-format' => 'pfam'); # World's shortest Fasta<->pfam format converter: print $out $_ while <$in>; =head1 DESCRIPTION Bio::AlignIO is a handler module for the formats in the AlignIO set (eg, Bio::AlignIO::fasta). It is the officially sanctioned way of getting at the alignment objects, which most people should use. The resulting alignment is a Bio::Align::AlignI compliant object. See L<Bio::Align::AlignI> for more information. 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 AlignIO object instance is configured for either input or output. A specific example of a stream object is the Bio::AlignIO::fasta object. Each stream object has functions $stream->next_aln(); and $stream->write_aln($aln); also $stream->type() # returns 'INPUT' or 'OUTPUT' As an added bonus, you can recover a filehandle that is tied to the AlignIO object, allowing you to use the standard E<lt>E<gt> and print operations to read and write sequence objects: use Bio::AlignIO; # read from standard input $stream = Bio::AlignIO->newFh(-format => 'Fasta'); while ( $aln = <$stream> ) { # do something with $aln } and print $stream $aln; # when stream is in output mode This makes the simplest ever reformatter #!/usr/local/bin/perl $format1 = shift; $format2 = shift || die "Usage: reformat format1 format2 < input > output"; use Bio::AlignIO; $in = Bio::AlignIO->newFh(-format => $format1 ); $out = Bio::AlignIO->newFh(-format => $format2 ); # note: you might want to quote -format to keep # older perl's from complaining. print $out $_ while <$in>; AlignIO.pm is patterned on the module SeqIO.pm and shares most the SeqIO.pm features. One significant difference currently is that AlignIO.pm usually handles IO for only a single alignment at a time (SeqIO.pm handles IO for multiple sequences in a single stream.) The principal reason for this is that whereas simultaneously handling multiple sequences is a common requirement, simultaneous handling of multiple alignments is not. The only current exception is format "bl2seq" which parses results of the Blast bl2seq program and which may produce several alignment pairs. This set of alignment pairs can be read using multiple calls to next_aln. Capability for IO for more than one multiple alignment - other than for bl2seq format -(which may be of use for certain applications such as IO for Pfam libraries) may be included in the future. For this reason we keep the name "next_aln()" for the alignment input routine, even though in most cases only one alignment is read (or written) at a time and the name "read_aln()" might be more appropriate. =head1 CONSTRUCTORS =head2 Bio::AlignIO-E<gt>new() $seqIO = Bio::AlignIO->new(-file => 'filename', -format=>$format); $seqIO = Bio::AlignIO->new(-fh => \*FILEHANDLE, -format=>$format); $seqIO = Bio::AlignIO->new(-format => $format); The new() class method constructs a new Bio::AlignIO object. The returned object can be used to retrieve or print BioAlign 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: $seqIO = Bio::AlignIO->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. =item -format Specify the format of the file. Supported formats include: fasta FASTA format selex selex (hmmer) format stockholm stockholm format prodom prodom (protein domain) format clustalw clustalw (.aln) format msf msf (GCG) format mase mase (seaview) format bl2seq Bl2seq Blast output nexus Swofford et al NEXUS format pfam Pfam sequence alignment format phylip Felsenstein's PHYLIP format emboss EMBOSS water and needle format mega MEGA format meme MEME format psi PSI-BLAST format Currently only those formats which were implemented in L<Bio::SimpleAlign> have been incorporated in AlignIO.pm. Specifically, mase, stockholm and prodom have only been implemented for input. See the specific module (e.g. L<Bio::AlignIO::meme>) for notes on supported versions. If no format is specified and a filename is given, then the module will attempt to deduce it from the filename suffix. If this is unsuccessful, Fasta format is assumed. The format name is case insensitive. 'FASTA', 'Fasta' and 'fasta' are all supported. =back =head2 Bio::AlignIO-E<gt>newFh() $fh = Bio::AlignIO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::AlignIO->newFh(-format => $format); # etc. This constructor behaves like new(), but returns a tied filehandle rather than a Bio::AlignIO object. You can read sequences from this object using the familiar E<lt>E<gt> operator, and write to it using print(). The usual array and $_ semantics work. For example, you can read all sequence objects into an array like this: @sequences = <$fh>; Other operations, such as read(), sysread(), write(), close(), and printf() are not supported. =over 1 =item -flush By default, all files (or filehandles) opened for writing alignments will be flushed after each write_aln() (making the file immediately usable). If you don't need this facility and would like to marginally improve the efficiency of writing multiple sequences to the same file (or filehandle), pass the -flush option '0' or any other value that evaluates as defined but false: my $clustal = new Bio::AlignIO -file => "<prot.aln", -format => "clustalw"; my $msf = new Bio::AlignIO -file => ">prot.msf", -format => "msf", -flush => 0; # go as fast as we can! while($seq = $clustal->next_aln) { $msf->write_aln($seq) } =back =head1 OBJECT METHODS See below for more detailed summaries. The main methods are: =head2 $alignment = $AlignIO-E<gt>next_aln() Fetch an alignment from a formatted file. =head2 $AlignIO-E<gt>write_aln($aln) Write the specified alignment to a file.. =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://bio.perl.org/MailList.html - 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@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Peter Schattner Email: schattner@alum.mit.edu =head1 CONTRIBUTORS Jason Stajich, jason@bioperl.org =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::AlignIO; use strict; use vars qw(@ISA); use Bio::Root::Root; use Bio::Seq; use Bio::LocatableSeq; use Bio::SimpleAlign; use Bio::Root::IO; @ISA = qw(Bio::Root::Root Bio::Root::IO); =head2 new Title : new Usage : $stream = Bio::AlignIO->new(-file => $filename, '-format' => 'Format') Function: Returns a new seqstream Returns : A Bio::AlignIO::Handler initialised with the appropriate format Args : -file => $filename -format => format -fh => filehandle to attach to =cut sub new { my ($caller,@args) = @_; my $class = ref($caller) || $caller; # or do we want to call SUPER on an object if $caller is an # object? if( $class =~ /Bio::AlignIO::(\S+)/ ) { my ($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] ) || 'fasta'; $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization return undef unless( $class->_load_format_module($format) ); return "Bio::AlignIO::$format"->new(@args); } } =head2 newFh Title : newFh Usage : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::AlignIO->newFh(-file=>$filename,-format=>'Format') $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::AlignIO::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 $sequence = <$fh>; # read a sequence object print $fh $sequence; # write a sequence object Returns : filehandle tied to the Bio::AlignIO::Fh class Args : =cut sub fh { my $self = shift; my $class = ref($self) || $self; my $s = Symbol::gensym; tie $$s,$class,$self; return $s; } # _initialize is where the heavy stuff will happen when new is called sub _initialize { my($self,@args) = @_; $self->_initialize_io(@args); 1; } =head2 _load_format_module Title : _load_format_module Usage : *INTERNAL AlignIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : =cut sub _load_format_module { my ($self,$format) = @_; my $module = "Bio::AlignIO::" . $format; my $ok; eval { $ok = $self->_load_module($module); }; if ( $@ ) { print STDERR <<END; $self: $format cannot be found Exception $@ For more information about the AlignIO system please see the AlignIO docs. This includes ways of checking for formats at compile time, not run time END ; return; } return 1; } =head2 next_aln Title : next_aln Usage : $aln = stream->next_aln Function: reads the next $aln object from the stream Returns : a Bio::Align::AlignI compliant object Args : =cut sub next_aln { my ($self,$aln) = @_; $self->throw("Sorry, you cannot read from a generic Bio::AlignIO object."); } =head2 write_aln Title : write_aln Usage : $stream->write_aln($aln) Function: writes the $aln object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut sub write_aln { my ($self,$aln) = @_; $self->throw("Sorry, you cannot write to a generic Bio::AlignIO object."); } =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 'msf' if /\.(msf|pileup|gcg)$/i; return 'pfam' if /\.(pfam|pfm)$/i; return 'selex' if /\.(selex|slx|selx|slex|sx)$/i; return 'phylip' if /\.(phylip|phlp|phyl|phy|phy|ph)$/i; return 'nexus' if /\.(nexus|nex)$/i; return 'mega' if( /\.(meg|mega)$/i ); return 'clustalw' if( /\.aln$/i ); return 'meme' if( /\.meme$/i ); return 'emboss' if( /\.(water|needle)$/i ); return 'psi' if( /\.psi$/i ); } sub DESTROY { my $self = shift; $self->close(); } sub TIEHANDLE { my $class = shift; return bless {'alignio' => shift},$class; } sub READLINE { my $self = shift; return $self->{'alignio'}->next_aln() unless wantarray; my (@list,$obj); push @list,$obj while $obj = $self->{'alignio'}->next_aln(); return @list; } sub PRINT { my $self = shift; $self->{'alignio'}->write_aln(@_); } 1;