--- name: "Bio::FeatureIO" section: "3pm" platform: "linux" package: "libbio-featureio-perl" version: "1.6.905-2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::FeatureIO" --- # Bio::FeatureIO(3pm) Handler for FeatureIO ## NAME Bio::FeatureIO - Handler for FeatureIO ## SYNOPSIS ``` use Bio::FeatureIO; #read from a file $in = Bio::FeatureIO->new(-file => "my.gff" , -format => 'GFF'); #read from a filehandle $in = Bio::FeatureIO->new(-fh => \*GFF , -format => 'GFF'); #read features already attached to a sequence my $feat = Bio::FeatureIO->new(-seq => $seq , -format => 'features'); #read new features for existing sequence my $seq = Bio::FeatureIO->new(-seq => $seq , -format => 'Das'); #write out features $out = Bio::FeatureIO->new(-file => ">outputfilename" , -format => 'GFF' , -version => 3); while ( my $feature = $in->next_feature() ) { $out->write_feature($feature); } ``` ## DESCRIPTION An I/O iterator subsystem for genomic sequence features. Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI. 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 FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object. Each stream object has functions: ``` $stream->next_feature(); $stream->write_feature($feature); ``` ## SUPPORTED FORMATS ``` name module ----------------------------------- BED bed.pm GFF gff.pm GTF gtf.pm InterPro (IPRScan 4.0) interpro.pm PTT (NCBI protein table) ptt.pm ``` ## CONSTRUCTORS ### Bio::FeatureIO-\>new() ``` $featureIO = Bio::FeatureIO->new(-file => 'filename', -format=>$format); $featureIO = Bio::FeatureIO->new(-fh => \*FILEHANDLE, -format=>$format); $featureIO = Bio::FeatureIO->new(-seq => $seq, -format=>$format); ``` The **new()** class method constructs a new Bio::FeatureIO object. The returned object can be used to retrieve or print Seq 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 '+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. 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: ``` use Bio::FeatureIO; use IO::String; my $in = Bio::FeatureIO->new('-file' => "my.gff" , '-format' => 'EMBL'); while ( my $f = $in->next_feature() ) { # the output handle is reset for every file my $stringio = IO::String->new($string); my $out = Bio::FeatureIO->new('-fh' => $stringio, '-format' => 'gtf'); # output goes into $string $out->write_feature($f); # modify $string $string =~ s|(>)(\w+)|$1$2|g; # print into STDOUT print $string; } ``` - \-format Specify the format of the file. See above for list of supported formats - \-flush By default, all files (or filehandles) opened for writing sequences will be flushed after each **write\_seq()** (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 $f1 = Bio::FeatureIO->new -file => " "f1"; my $f2 = Bio::FeatureIO->new -file => ">a.f2", -format => "f2", -flush => 0; # go as fast as we can! while($feature = $f1->next_feature) { $f2->write_feature($feature) } ``` ### Bio::FeatureIO-\>newFh() ``` $fh = Bio::FeatureIO->newFh(-fh => \*FILEHANDLE, -format=>$format); $fh = Bio::FeatureIO->newFh(-format => $format); # etc. ``` This constructor behaves like **new()**, but returns a tied filehandle rather than a Bio::FeatureIO object. You can read sequences from this object using the familiar \<\> operator, and write to it using **print()**. The usual array and `$_` semantics work. For example, you can read all sequence objects into an array like this: ``` @features = <$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: - next\_feature Fetch the next feature from the stream. - write\_feature Write the specified feature(s) to the stream. - feature\_factory This gets/sets the specific Bio::Factory::FeatureFactoryI The following methods delegate to the inter - feature\_class Set the specific Bio::SeqFeatureI class to return - type\_features Boolean flag, ensures the returned features are typed - unflatten\_features Ensure the returned features are unflattened ### 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/ ``` ## AUTHOR - Allen Day Email allenday@ucla.edu ## 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::FeatureIO->new(-file => $filename, -format => 'Format') Function: Returns a new feature stream Returns : A Bio::FeatureIO stream initialised with the appropriate format Args : Named parameters: -file => $filename -fh => filehandle to attach to -format => format ``` ### newFh ``` Title : newFh Usage : $fh = Bio::FeatureIO->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::FeatureIO->newFh(-file=>$filename,-format=>'Format') $feature = <$fh>; # read a feature object print $fh $feature; # write a feature object Returns : filehandle tied to the Bio::FeatureIO::Fh class Args : ``` See Bio::FeatureIO::Fh ### fh ``` Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $feature = <$fh>; # read a feature object print $fh $feature; # write a feature object Returns : filehandle tied to Bio::FeatureIO class Args : none ``` ### next\_feature ``` Title : next_feature Usage : $feature = stream->next_feature Function: Reads the next feature 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). Returns : a Bio::SeqFeatureI feature object Args : none ``` See Bio::Root::RootI, Bio::SeqFeatureI ### write\_feature ``` Title : write_feature Usage : $stream->write_feature($feature) Function: writes the $feature object into the stream Returns : 1 for success and 0 for error Args : Bio::SeqFeature object ``` ### \_load\_format\_module ``` Title : _load_format_module Usage : *INTERNAL FeatureIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : ``` ### seq ``` Title : seq Usage : $obj->seq() OR $obj->seq($newSeq) Example : Returns : Bio::SeqI object Args : newSeq (optional) ``` ### \_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: guess format based on file suffix Example : Returns : guessed format of filename (lower case) Args : Notes : See "SUPPORTED FORMATS" ```