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.\" ========================================================================
.\"
.IX Title "Bio::Restriction::IO 3pm"
.TH Bio::Restriction::IO 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Restriction::IO \- Handler for sequence variation IO Formats
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::Restriction::IO;
\&
\&    $in  = Bio::Restriction::IO\->new(\-file => "inputfilename" ,
\&                                     \-format => \*(Aqwithrefm\*(Aq);
\&    my $res = $in\->read; # a Bio::Restriction::EnzymeCollection
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::Restriction::IO is a handler module for the formats in the
Restriction \s-1IO\s0 set, e.g. \f(CW\*(C`Bio::Restriction::IO::xxx\*(C'\fR. 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. The main difference is that instead of using methods
\&\f(CW\*(C`next_seq\*(C'\fR, you drop \f(CW\*(C`_seq\*(C'\fR from the method name.
.PP
Also, instead of dealing only with individual Bio::Restriction::Enzyme
objects, \f(CW\*(C`read()\*(C'\fR will slurp in all enzymes into a 
Bio::Restriction::EnzymeCollection object.
.PP
For more details, see documentation in Bio::SeqIO.
.SH "TO DO"
.IX Header "TO DO"
At the moment, these can be use mainly to get a custom set if enzymes in
\&\f(CW\*(C`withrefm\*(C'\fR or \f(CW\*(C`itype2\*(C'\fR formats into Bio::Restriction::Enzyme or
Bio::Restriction::EnzymeCollection objects.  Using \f(CW\*(C`bairoch\*(C'\fR format is
highly experimental and is not recommmended at this time.
.PP
This class inherits from Bio::SeqIO for convenience sake, though this should
inherit from Bio::Root::Root.  Get rid of Bio::SeqIO inheritance by
copying relevant methods in.
.PP
\&\f(CW\*(C`write()\*(C'\fR methods are currently not implemented for any format except \f(CW\*(C`base\*(C'\fR.
Using \f(CW\*(C`write()\*(C'\fR even with \f(CW\*(C`base\*(C'\fR format is not recommended as it does not
support multicut/multisite enzyme output.
.PP
Should additional formats be supported (such as \s-1XML\s0)?
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::SeqIO, 
Bio::Restriction::Enzyme, 
Bio::Restriction::EnzymeCollection
.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"
.IX Header "AUTHOR"
Rob Edwards, redwards@utmem.edu
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Heikki Lehvaslaiho, 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 9
\& Title   : new
\& Usage   : $stream = Bio::Restriction::IO\->new(\-file => $filename,
\&                                               \-format => \*(AqFormat\*(Aq)
\& Function: Returns a new seqstream
\& Returns : A Bio::Restriction::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 restriction format
\& Returns : restriction format
\& Args    : none
.Ve
.SS "read"
.IX Subsection "read"
.Vb 5
\& Title   : read
\& Usage   : $renzs = $stream\->read
\& Function: reads all the restrction enzymes from the stream
\& Returns : a Bio::Restriction::EnzymeCollection 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::Restriction::EnzymeCollection 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