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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)
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