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

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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		  Bio::SeqIO::excel(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX | Internal methods

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