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.\" ========================================================================
.\"
.IX Title "Bio::Assembly::IO 3pm"
.TH Bio::Assembly::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::Assembly::IO \- Handler for Assembly::IO Formats
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Bio::Assembly::IO;
\&
\&    $in  = Bio::Assembly::IO\->new(\-file=>"<inputfilename",
\&                                  \-format=>\*(Aqphrap\*(Aq);
\&    $out = Bio::Assembly::IO\->new(\-file=>">outputfilename",
\&                                  \-format=>\*(Aqphrap\*(Aq);
\&
\&    while ( my $scaffold = $in\->next_assembly() ) {
\&       # do something with Bio::Assembly::Scaffold instance
\&       # ...
\&       $out\->write_assembly(\-scaffold => $scaffold);
\&    }
\&
\&    $in\->close;
\&    $out\->close;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Bio::Assembly::IO is a handler module for formats in the Assembly::IO set
(e.g. Bio::Assembly::IO::phrap).
.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"
Robson Francisco de Souza
.PP
E\-mail: rfsouza@citri.iq.usp.br
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
#
.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 8
\& Title   : new
\& Usage   : $stream = Bio::Assembly::IO\->new( \-file   => $filename,
\&                                             \-format =>\*(Aqformat\*(Aq    )
\& Function: Returns a new assembly stream
\& Returns : A Bio::Assembly::IO::Handler initialised
\&           with the appropriate format
\& Args    : \-file   => $filename
\&           \-format => format
.Ve
.SS "format"
.IX Subsection "format"
.Vb 5
\& Title   : format
\& Usage   : $format = $stream\->format()
\& Function: Get the assembly format
\& Returns : assembly format
\& Args    : none
.Ve
.SS "next_assembly"
.IX Subsection "next_assembly"
.Vb 5
\& Title   : next_assembly
\& Usage   : $scaffold = $stream\->next_assembly()
\& Function: Reads the next assembly object from the stream and returns it.
\& Returns : a Bio::Assembly::ScaffoldI compliant object
\& Args    : none
.Ve
.SS "next_contig"
.IX Subsection "next_contig"
.Vb 5
\& Title   : next_contig
\& Usage   : $contig = $stream\->next_contig()
\& Function: Reads the next contig or singlet from the stream and returns it.
\& Returns : a Bio::Assembly::Contig or Bio::Contig::Assembly::Singlet
\& Args    : none
.Ve
.SS "write_assembly"
.IX Subsection "write_assembly"
.Vb 6
\&  Title   : write_assembly
\&  Usage   : $stream\->write_assembly($assembly)
\&  Function: Write the assembly object in desired format. This method calls
\&            write_header(), write_contigs() and write_footer() internally.
\&  Returns : 1 on success, 0 for error
\&  Args    : A Bio::Assembly::Scaffold object
.Ve
.SS "write_header"
.IX Subsection "write_header"
.Vb 7
\&  Title   : write_header
\&  Usage   : $stream\->write_header($assembly)
\&  Function: Write the start of the assembly file. It can be called at any time,
\&            not when starting to write the assembly file. 
\&  Returns : 1 on success, 0 for error
\&  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
\&            driver for more details)
.Ve
.SS "write_contig"
.IX Subsection "write_contig"
.Vb 5
\&  Title   : write_contig
\&  Usage   : $stream\->write_contig($contig)
\&  Function: Write a contig object in the desired format.
\&  Returns : 1 on success, 0 for error
\&  Args    : A Bio::Assembly::Contig object
.Ve
.SS "write_footer"
.IX Subsection "write_footer"
.Vb 6
\&  Title   : write_footer
\&  Usage   : $stream\->write_footer($assembly)
\&  Function: Write the start of the assembly file.
\&  Returns : 1 on success, 0 for error
\&  Args    : A Bio::Assembly::Scaffold object or ... (check the specific format
\&            driver for more details)
.Ve
.SS "_load_format_module"
.IX Subsection "_load_format_module"
.Vb 6
\& Title   : _load_format_module
\& Usage   : *INTERNAL Assembly::IO stuff*
\& Function: Loads up (like use) a module at run time on demand
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "_guess_format"
.IX Subsection "_guess_format"
.Vb 8
\& 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   : formats that _filehandle() will guess includes
\&           ace, phrap and tigr at the moment
.Ve
.SS "_sort"
.IX Subsection "_sort"
.Vb 6
\&    Title   : _sort
\&    Usage   : @sorted_values = $ass_io\->_sort(@values)
\&    Function: Sort a list of values naturally if Sort::Naturally is installed
\&              (nicer), lexically otherwise (not as nice, but safe)
\&    Returns : array of sorted values
\&    Args    : array of values to sort
.Ve