excel

Bio::SeqIO::excel(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::excel(3pm)

NAME

       Bio::SeqIO::excel - sequence input/output stream from a
			   MSExcel-formatted table

SYNOPSIS

	 #It is probably best not to use this object directly, but
	 #rather go through the SeqIO handler system. Go:

	 $stream = Bio::SeqIO->new(-file => $filename, -format => 'excel');

	 while ( my $seq = $stream->next_seq() ) {
	       # do something with $seq
	 }

DESCRIPTION

       This class transforms records in a MS Excel workbook file into Bio::Seq objects. It is derived from the table format module and merely
       defines additional properties and overrides the way to get data from the file and advance to the next record.

       The module permits specifying which columns hold which type of annotation. The semantics of certain attributes, if present, are pre-
       defined, e.g., accession number and sequence. Additional attributes may be added to the annotation bundle. See Bio::SeqIO::table for a
       complete list of parameters and capabilities.

       You may also specify the worksheet from which to obtain the data, and after finishing one worksheet you may change the name to keep reading
       from another worksheet (in the same file).

       This module depends on Spreadsheet::ParseExcel to parse the underlying Excel file.

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 email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp
       Email hlapp at gmx.net

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::SeqIO->new(-file => $filename, -format => 'excel')
	Function: Returns a new seqstream
	Returns : A Bio::SeqIO stream for a MS Excel format

	Args	: Supports the same named parameters as Bio::SeqIO::table,
		  except -delim, which obviously does not apply to a binary
		  format. In addition, the following parameters are supported.

		    -worksheet the name of the worksheet holding the table;
			       if unspecified the first worksheet will be
			       used

   worksheet
	Title	: worksheet
	Usage	: $obj->worksheet($newval)
	Function: Get/set the name of the worksheet holding the table. The
		  worksheet name may also be a numeric index.

		  You may change the value during parsing at any time in
		  order to start reading from a different worksheet (in the
		  same file).

	Example :
	Returns : value of worksheet (a scalar)
	Args	: on set, new value (a scalar or undef, optional)

   close
	Title	: close
	Usage	:
	Function: Close and/or release the resources used by this parser instance.

		  We override this here in order to free up the worksheet and
		  other related objects.

	Example :
	Returns :
	Args	:

Internal methods
       All methods with a leading underscore are not meant to be part of the 'official' API. They are for use by this module only, consider them
       private unless you are a developer trying to modify this module.

   _worksheet
	Title	: _worksheet
	Usage	: $obj->_worksheet($newval)
	Function: Get/set the worksheet object to be used for accessing cells.
	Example :
	Returns : value of _worksheet (a Spreadsheet::ParseExcel::Worksheet object)
	Args	: on set, new value (a Spreadsheet::ParseExcel::Worksheet
		  object or undef, optional)

   _next_record
	Title	: _next_record
	Usage	:
	Function: Navigates the underlying file to the next record.

		  We override this here in order to adapt navigation to data
		  in an Excel worksheet.

	Example :
	Returns : TRUE if the navigation was successful and FALSE
		  otherwise. Unsuccessful navigation will usually be treated
		  as an end-of-file condition.
	Args	:

   _get_row_values
	Title	: _get_row_values
	Usage	:
	Function: Get the values for the current line (or row) as an array in
		  the order of columns.

		  We override this here in order to adapt access to column
		  values to data contained in an Excel worksheet.

	Example :
	Returns : An array of column values for the current row.
	Args	:

perl v5.14.2							    2012-03-02						    Bio::SeqIO::excel(3pm)