Provided by: libbio-perl-perl_1.7.2-3_all bug


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


         #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


       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

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


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       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        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

        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)

        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.

        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)

        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    :

        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    :