Christopher Fields > BioPerl > Bio::SeqIO::excel



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Module Version: 1.006924   Source  


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 file).

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


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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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:

AUTHOR - Hilmar Lapp ^

Email hlapp at


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    :
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