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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Variation::IO \- Handler for sequence variation IO Formats .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& use Bio::Variation::IO; \& \& $in = Bio::Variation::IO\->new(\-file => "inputfilename" , \& \-format => \*(Aqflat\*(Aq); \& $out = Bio::Variation::IO\->new(\-file => ">outputfilename" , \& \-format => \*(Aqxml\*(Aq); \& \& while ( my $seq = $in\->next() ) { \& $out\->write($seq); \& } \& \& # or \& \& use Bio::Variation::IO; \& \& #input file format can be read from the file extension (dat|xml) \& $in = Bio::Variation::IO\->newFh(\-file => "inputfilename"); \& $out = Bio::Variation::IO\->newFh(\-format => \*(Aqxml\*(Aq); \& \& # World\*(Aqs shortest flat<\->xml format converter: \& print $out $_ while <$in>; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Bio::Variation::IO is a handler module for the formats in the Variation \s-1IO\s0 set (eg, Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which most people should use. .PP The structure, conventions and most of the code is inherited from Bio::SeqIO module. The main difference is that instead of using methods next_seq and write_seq, you drop '_seq' from the method names. .PP 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 SeqIO object instance is configured for either input or output. A specific example of a stream object is the Bio::Variation::IO::flat object. .PP Each stream object has functions .PP .Vb 1 \& $stream\->next(); .Ve .PP and .PP .Vb 1 \& $stream\->write($seqDiff); .Ve .PP also .PP .Vb 1 \& $stream\->type() # returns \*(AqINPUT\*(Aq or \*(AqOUTPUT\*(Aq .Ve .PP As an added bonus, you can recover a filehandle that is tied to the SeqIO object, allowing you to use the standard <> and print operations to read and write sequence objects: .PP .Vb 1 \& use Bio::Variation::IO; \& \& $stream = Bio::Variation::IO\->newFh(\-format => \*(Aqflat\*(Aq); \& # read from standard input \& \& while ( $seq = <$stream> ) { \& # do something with $seq \& } .Ve .PP and .PP .Vb 1 \& print $stream $seq; # when stream is in output mode .Ve .PP This makes the simplest ever reformatter .PP .Vb 1 \& #!/usr/local/bin/perl \& \& $format1 = shift; \& $format2 = shift; \& \& use Bio::Variation::IO; \& \& $in = Bio::Variation::IO\->newFh(\-format => $format1 ); \& $out = Bio::Variation::IO\->newFh(\-format => $format2 ); \& \& print $out $_ while <$in>; .Ve .SH "CONSTRUCTORS" .IX Header "CONSTRUCTORS" .SS "Bio::Variation::IO\->\fInew()\fP" .IX Subsection "Bio::Variation::IO->new()" .Vb 3 \& $seqIO = Bio::Variation::IO\->new(\-file => \*(Aqfilename\*(Aq, \-format=>$format); \& $seqIO = Bio::Variation::IO\->new(\-fh => \e*FILEHANDLE, \-format=>$format); \& $seqIO = Bio::Variation::IO\->new(\-format => $format); .Ve .PP The \fInew()\fR class method constructs a new Bio::Variation::IO object. The returned object can be used to retrieve or print BioSeq objects. \fInew()\fR accepts the following parameters: .IP "\-file" 4 .IX Item "-file" A file path to be opened for reading or writing. The usual Perl conventions apply: .Sp .Vb 6 \& \*(Aqfile\*(Aq # open file for reading \& \*(Aq>file\*(Aq # open file for writing \& \*(Aq>>file\*(Aq # open file for appending \& \*(Aq+new(\-fh => \e*STDIN); .Ve .Sp Note that you must pass filehandles as references to globs. .Sp If neither a filehandle nor a filename is specified, then the module will read from the \f(CW@ARGV\fR array or \s-1STDIN,\s0 using the familiar <> semantics. .IP "\-format" 4 .IX Item "-format" Specify the format of the file. Supported formats include: .Sp .Vb 2 \& flat pseudo EMBL format \& xml seqvar xml format .Ve .Sp 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, Fasta format is assumed. .Sp The format name is case insensitive. '\s-1FLAT\s0', 'Flat' and 'flat' are all supported. .SS "Bio::Variation::IO\->\fInewFh()\fP" .IX Subsection "Bio::Variation::IO->newFh()" .Vb 3 \& $fh = Bio::Variation::IO\->newFh(\-fh => \e*FILEHANDLE, \-format=>$format); \& $fh = Bio::Variation::IO\->newFh(\-format => $format); \& # etc. \& \& #e.g. \& $out = Bio::Variation::IO\->newFh( \*(Aq\-FORMAT\*(Aq => \*(Aqflat\*(Aq); \& print $out $seqDiff; .Ve .PP This constructor behaves like \fInew()\fR, but returns a tied filehandle rather than a Bio::Variation::IO object. You can read sequences from this object using the familiar <> operator, and write to it using \fIprint()\fR. The usual array and \f(CW$_\fR semantics work. For example, you can read all sequence objects into an array like this: .PP .Vb 1 \& @mutations = <$fh>; .Ve .PP Other operations, such as \fIread()\fR, \fIsysread()\fR, \fIwrite()\fR, \fIclose()\fR, and \fIprintf()\fR are not supported. .SH "OBJECT METHODS" .IX Header "OBJECT METHODS" See below for more detailed summaries. The main methods are: .ie n .SS "$sequence = $seqIO\->\fInext()\fP" .el .SS "\f(CW$sequence\fP = \f(CW$seqIO\fP\->\fInext()\fP" .IX Subsection "$sequence = $seqIO->next()" Fetch the next sequence from the stream. .ie n .SS "$seqIO\->write($sequence [,$another_sequence,...])" .el .SS "\f(CW$seqIO\fP\->write($sequence [,$another_sequence,...])" .IX Subsection "$seqIO->write($sequence [,$another_sequence,...])" Write the specified sequence(s) to the stream. .SS "\s-1\fITIEHANDLE\s0()\fP, \s-1\fIREADLINE\s0()\fP, \s-1\fIPRINT\s0()\fP" .IX Subsection "TIEHANDLE(), READLINE(), PRINT()" These provide the tie interface. See perltie for more details. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "Mailing Lists" User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Heikki Lehvaslaiho" .IX Header "AUTHOR - Heikki Lehvaslaiho" Email: heikki-at-bioperl-dot-org .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 7 \& Title : new \& Usage : $stream = Bio::Variation::IO\->new(\-file => $filename, \-format => \*(AqFormat\*(Aq) \& Function: Returns a new seqstream \& Returns : A Bio::Variation::IO::Handler initialised with the appropriate format \& Args : \-file => $filename \& \-format => format \& \-fh => filehandle to attach to .Ve .SS "format" .IX Subsection "format" .Vb 5 \& Title : format \& Usage : $format = $stream\->format() \& Function: Get the variation format \& Returns : variation format \& Args : none .Ve .SS "next" .IX Subsection "next" .Vb 5 \& Title : next \& Usage : $seqDiff = $stream\->next \& Function: reads the next $seqDiff object from the stream \& Returns : a Bio::Variation::SeqDiff object \& Args : .Ve .SS "write" .IX Subsection "write" .Vb 5 \& Title : write \& Usage : $stream\->write($seq) \& Function: writes the $seq object into the stream \& Returns : 1 for success and 0 for error \& Args : Bio::Variation::SeqDiff object .Ve .SS "_guess_format" .IX Subsection "_guess_format" .Vb 6 \& Title : _guess_format \& Usage : $obj\->_guess_format($filename) \& Function: \& Example : \& Returns : guessed format of filename (lower case) \& Args : .Ve